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Sample records for abundant organic molecules

  1. Organic Molecules in Meteorites

    NASA Astrophysics Data System (ADS)

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (<30%) consists of a rich organic inventory of soluble organic compounds, including key compounds important in terrestrial biochemistry [2-4]. Different carbonaceous meteorites contain soluble organic molecules with different abundances and distributions, which may reflect the extension of aqueous alteration or thermal metamorphism on the meteorite parent bodies. Extensive aqueous alteration on the meteorite parent body may result on 1) the decomposition of α-amino acids [5, 6]; 2) synthesis of β- and γ-amino acids [2, 6-9]; 3) higher relative abundances of alkylated polycyclic aromatic hydrocarbons (PAHs) [6, 10]; and 4) higher L-enantiomer excess (Lee) value of isovaline [6, 11, 12].The soluble organic content of carbonaceous meteorites may also have a contribution from Fischer-Tropsch/Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10

  2. A New Tool for NMR Crystallography: Complete (13)C/(15)N Assignment of Organic Molecules at Natural Isotopic Abundance Using DNP-Enhanced Solid-State NMR.

    PubMed

    Märker, Katharina; Pingret, Morgane; Mouesca, Jean-Marie; Gasparutto, Didier; Hediger, Sabine; De Paëpe, Gaël

    2015-11-01

    NMR crystallography of organic molecules at natural isotopic abundance (NA) strongly relies on the comparison of assigned experimental and computed NMR chemical shifts. However, a broad applicability of this approach is often hampered by the still limited (1)H resolution and/or difficulties in assigning (13)C and (15)N resonances without the use of structure-based chemical shift calculations. As shown here, such difficulties can be overcome by (13)C-(13)C and for the first time (15)N-(13)C correlation experiments, recorded with the help of dynamic nuclear polarization. We present the complete de novo (13)C and (15)N resonance assignment at NA of a self-assembled 2'-deoxyguanosine derivative presenting two different molecules in the asymmetric crystallographic unit cell. This de novo assignment method is exclusively based on aforementioned correlation spectra and is an important addition to the NMR crystallography approach, rendering firstly (1)H assignment straightforward, and being secondly a prerequisite for distance measurements with solid-state NMR. PMID:26485326

  3. Electrical Transport through Organic Molecules

    NASA Astrophysics Data System (ADS)

    Lau, C. N.; Chang, Shun-Chi; Williams, Stan

    2003-03-01

    We investigate electrical transport properties of single organic molecules using electromigration break junctions[1]. A self-assembled monolayer of various organic molecules such as 1,4-di(phenylethynyl-4'-methanethiol)benzene was grown on narrow metal wires, and single or a few molecules were incorporated into the junctions which were created by applying a large voltage and breaking the wires. The transport properties of these molecules were then measured at low temperatures. Latest experimental results will be discussed. [1] Park, J. et al, Nature, 417, 722 (2002); Liang W. et al, Nature, 417, 725 (2002).

  4. Abundances of Linear Carbon-Chain Molecules in Supernovae

    NASA Technical Reports Server (NTRS)

    Clayton, D. D.; Deneault, E.; Meyer, B. S.; The, L.-S.

    2001-01-01

    This paper evaluates the condensation of carbon solids in a gas of pure C and O atoms when these exist within the interior of an expanding young supernova. We calculate the abundances of large carbon molecules, which serve as nucleations for condensation of graphites. Additional information is contained in the original extended abstract.

  5. Organic heterocyclic molecules become superalkalis.

    PubMed

    Reddy, G Naaresh; Giri, Santanab

    2016-09-21

    An organic molecule which behaves like a superalkali has been designed from an aromatic heterocyclic molecule, pyrrole. Using first-principles calculation and a systematic two-step approach, we can have superalkali molecules with a low ionization energy, even lower than that of Cs. Couple cluster (CCSD) calculation reveals that a new heterocycle, C3N2(CH3)5 derived from a well-known aromatic heterocycle, pyrrole (C4H5N) has an ionization energy close to 3.0 eV. A molecular dynamics calculation on C3N2(CH3)5 reveals that the structure is dynamically stable. PMID:27530344

  6. Interstellar grain chemistry and organic molecules

    NASA Technical Reports Server (NTRS)

    Allamandola, L. J.; Sandford, S. A.

    1990-01-01

    The detection of prominant infrared absorption bands at 3250, 2170, 2138, 1670 and 1470 cm(-1) (3.08, 4.61, 4.677, 5.99 and 6.80 micron m) associated with molecular clouds show that mixed molecular (icy) grain mantles are an important component of the interstellar dust in the dense interstellar medium. These ices, which contain many organic molecules, may also be the production site of the more complex organic grain mantles detected in the diffuse interstellar medium. Theoretical calculations employing gas phase as well as grain surface reactions predict that the ices should be dominated only by the simple molecules H2O, H2CO, N2, CO, O2, NH3, CH4, possibly CH3OH, and their deuterated counterparts. However, spectroscopic observations in the 2500 to 1250 cm(-1)(4 to 8 micron m) range show substantial variation from source reactions alone. By comparing these astronomical spectra with the spectra of laboratory-produced analogs of interstellar ices, one can determine the composition and abundance of the materials frozen on the grains in dense clouds. Experiments are described in which the chemical evolution of an interstellar ice analog is determined during irradiation and subsequent warm-up. Particular attention is paid to the types of moderately complex organic materials produced during these experiments which are likely to be present in interstellar grains and cometary ices.

  7. Interstellar grain chemistry and organic molecules

    NASA Astrophysics Data System (ADS)

    Allamandola, L. J.; Sandford, S. A.

    1990-04-01

    The detection of prominant infrared absorption bands at 3250, 2170, 2138, 1670 and 1470 cm(-1) (3.08, 4.61, 4.677, 5.99 and 6.80 micron m) associated with molecular clouds show that mixed molecular (icy) grain mantles are an important component of the interstellar dust in the dense interstellar medium. These ices, which contain many organic molecules, may also be the production site of the more complex organic grain mantles detected in the diffuse interstellar medium. Theoretical calculations employing gas phase as well as grain surface reactions predict that the ices should be dominated only by the simple molecules H2O, H2CO, N2, CO, O2, NH3, CH4, possibly CH3OH, and their deuterated counterparts. However, spectroscopic observations in the 2500 to 1250 cm(-1)(4 to 8 micron m) range show substantial variation from source reactions alone. By comparing these astronomical spectra with the spectra of laboratory-produced analogs of interstellar ices, one can determine the composition and abundance of the materials frozen on the grains in dense clouds. Experiments are described in which the chemical evolution of an interstellar ice analog is determined during irradiation and subsequent warm-up. Particular attention is paid to the types of moderately complex organic materials produced during these experiments which are likely to be present in interstellar grains and cometary ices.

  8. Characterization of Interstellar Organic Molecules

    SciTech Connect

    Gencaga, Deniz; Knuth, Kevin H.; Carbon, Duane F.

    2008-11-06

    Understanding the origins of life has been one of the greatest dreams throughout history. It is now known that star-forming regions contain complex organic molecules, known as Polycyclic Aromatic Hydrocarbons (PAHs), each of which has particular infrared spectral characteristics. By understanding which PAH species are found in specific star-forming regions, we can better understand the biochemistry that takes place in interstellar clouds. Identifying and classifying PAHs is not an easy task: we can only observe a single superposition of PAH spectra at any given astrophysical site, with the PAH species perhaps numbering in the hundreds or even thousands. This is a challenging source separation problem since we have only one observation composed of numerous mixed sources. However, it is made easier with the help of a library of hundreds of PAH spectra. In order to separate PAH molecules from their mixture, we need to identify the specific species and their unique concentrations that would provide the given mixture. We develop a Bayesian approach for this problem where sources are separated from their mixture by Metropolis Hastings algorithm. Separated PAH concentrations are provided with their error bars, illustrating the uncertainties involved in the estimation process. The approach is demonstrated on synthetic spectral mixtures using spectral resolutions from the Infrared Space Observatory (ISO). Performance of the method is tested for different noise levels.

  9. Hydrophobic Porous Material Adsorbs Small Organic Molecules

    NASA Technical Reports Server (NTRS)

    Sharma, Pramod K.; Hickey, Gregory S.

    1994-01-01

    Composite molecular-sieve material has pore structure designed specifically for preferential adsorption of organic molecules for sizes ranging from 3 to 6 angstrom. Design based on principle that contaminant molecules become strongly bound to surface of adsorbent when size of contaminant molecules is nearly same as that of pores in adsorbent. Material used to remove small organic contaminant molecules from vacuum systems or from enclosed gaseous environments like closed-loop life-support systems.

  10. Triton - Stratospheric molecules and organic sediments

    NASA Technical Reports Server (NTRS)

    Thompson, W. Reid; Singh, Sushil K.; Khare, B. N.; Sagan, Carl

    1989-01-01

    Continuous-flow plasma discharge techniques show production rates of hydrocarbons and nitriles in N2 + CH4 atmospheres appropriate to the stratosphere of Titan, and indicate that a simple eddy diffusion model together with the observed electron flux quantitatively matches the Voyager IRIS observations for all the hydrocarbons, except for the simplest ones. Charged particle chemistry is very important in Triton's stratosphere. In the more CH4-rich case of Titan, many hydrocarbons and nitriles are produced in high yield. If N2 is present, the CH4 fraction is low, but hydrocarbons and nitriles are produced in fair yield, abundances of HCN and C2H2 in Triton's stratosphere exceed 10 to the 19th molecules/sq cm per sec, and NCCN, C3H4, and other species are predicted to be present. These molecules may be detected by IRIS if the stratosphere is as warm as expected. Both organic haze and condensed gases will provide a substantial UV and visible opacity in Triton's atmosphere.

  11. Relative Sizes of Organic Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  12. Circularly Polarized Luminescence from Simple Organic Molecules.

    PubMed

    Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

    2015-09-21

    This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. PMID:26136234

  13. New observations of interstellar organic molecules

    NASA Technical Reports Server (NTRS)

    Irvine, W. M.; Friberg, P.; Matthews, H. E.; Minh, Y. C.; Ziurys, L. M.

    1990-01-01

    Discussed here are new observations of 3-carbon-containing interstellar molecules which play an important role in the chemistry of dense molecular clouds: protonated carbon dioxide, formic acid, and propynal. In 1984 a new oxide of carbon, C3O, was discovered in the interstellar medium (Matthews et al. 1984; Brown et al. 1985). Theoretical models suggest that C3O is produced by dissociative electron recombination with the ion H3C3O+. Although no laboratory data for the branching ratios of such a recombination exist, it seemed to us likely that additional products would include H2C3O. This molecule has more than one isomeric form, but one stable species is propynal (HC2CHO), which had been suggested as a possible interstellar molecule by Winnewisser (1973). In observations at the National Radio Astronomy Observatory 43 m telescope in Green Bank earlier this year, researchers detected a line in the cold cloud TMC-1 which they assign to the 2(0,2)-1(0,1) transition of propynal. The observed line agrees with the laboratory frequency to well within the experimental uncertainty a few parts in 10 to the 7th power. Researchers sought and failed to detect the corresponding 2(1,1)-1(1,0) line, which is understandable given the presence of both a and b components of the electric dipole moment in propynal. The b type transitions will drain population from energy levels with K(sub p) does not equal 0 into the K(sub p) equal 0 stack. If the researchers' assignment is correct, this is the first interstellar detection of propynal. Assuming typical rotational temperatures for TMC-1 and that the line is optically thin, the column density determined is about 5 times 10 to the 12th power cm to the -2nd power, or about three times that for C3O. Formic acid (HCOOH) was the first organic acid to be observed in the interstellar medium, in the Galactic center source Sgr B2. The only other interstellar detection has been recently made in the giant molecular cloud in Orion. As part of the

  14. Search for complex organic molecules in space

    NASA Astrophysics Data System (ADS)

    Ohishi, Masatoshi

    2016-07-01

    It was 1969 when the first organic molecule in space, H2CO, was discovered. Since then many organic molecules were discovered by using the NRAO 11 m (upgraded later to 12 m), Nobeyama 45 m, IRAM 30 m, and other highly sensitive radio telescopes as a result of close collaboration between radio astronomers and microwave spectroscopists. It is noteworthy that many famous organic molecules such as CH3OH, C2H5OH, (CH3)2O and CH3NH2 were detected by 1975. Organic molecules were found in so-called hot cores where molecules were thought to form on cold dust surfaces and then to evaporate by the UV photons emitted from the central star. These days organic molecules are known to exist not only in hot cores but in hot corinos (a warm, compact molecular clump found in the inner envelope of a class 0 protostar) and even protoplanetary disks. As was described above, major organic molecules were known since 1970s. It was very natural that astronomers considered a relationship between organic molecules in space and the origin of life. Several astronomers challenged to detect glycine and other prebiotic molecules without success. ALMA is expected to detect such important materials to further consider the gexogenous deliveryh hypothesis. In this paper I summarize the history in searching for complex organic molecules together with difficulties in observing very weak signals from larger species. The awfully long list of references at the end of this article may be the most useful part for readers who want to feel the exciting discovery stories.

  15. Complex organic molecules in organic-poor massive young stellar objects

    NASA Astrophysics Data System (ADS)

    Fayolle, Edith C.; Öberg, Karin I.; Garrod, Robin T.; van Dishoeck, Ewine F.; Bisschop, Suzanne E.

    2015-04-01

    Context. Massive young stellar objects (MYSOs) with hot cores are classic sources of complex organic molecules. The origins of these molecules in such sources, as well as the small- and large-scale differentiation between nitrogen- and oxygen-bearing complex species, are poorly understood. Aims: We aim to use complex molecule abundances toward a chemically less explored class of MYSOs with weak hot organic emission lines to constrain the impact of hot molecular cores and initial ice conditions on the chemical composition toward MYSOs. Methods: We use the IRAM 30 m and the Submillimeter Array to search for complex organic molecules over 8-16 GHz in the 1 mm atmospheric window toward three MYSOs with known ice abundances, but without luminous molecular hot cores. Results: Complex molecules are detected toward all three sources at comparable abundances with respect to CH3OH to classical hot core sources. The relative importance of CH3CHO, CH3CCH, CH3OCH3, CH3CN, and HNCO differ between the organic-poor MYSOs and hot cores, however. Furthermore, the N-bearing molecules are generally concentrated toward the source centers, while most O- and C-bearing molecules are present both in the center and in the colder envelope. Gas-phase HNCO/CH3OH ratios are tentatively correlated with the ratios of NH3 ice over CH3OH ice in the same lines of sight, which is consistent with new gas-grain model predictions. Conclusions: Hot cores are not required to form complex organic molecules, and source temperature and initial ice composition both seem to affect complex organic distributions toward MYSOs. To quantify the relative impact of temperature and initial conditions requires, however, a larger spatially resolved survey of MYSOs with ice detections.

  16. The missing organic molecules on Mars

    PubMed Central

    Benner, Steven A.; Devine, Kevin G.; Matveeva, Lidia N.; Powell, David H.

    2000-01-01

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m2 of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life. PMID:10706606

  17. The missing organic molecules on Mars

    NASA Technical Reports Server (NTRS)

    Benner, S. A.; Devine, K. G.; Matveeva, L. N.; Powell, D. H.

    2000-01-01

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m(2) of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life.

  18. Complex organic molecules and star formation

    NASA Astrophysics Data System (ADS)

    Bacmann, A.; Faure, A.

    2014-12-01

    Star forming regions are characterised by the presence of a wealth of chemical species. For the past two to three decades, ever more complex organic species have been detected in the hot cores of protostars. The evolution of these molecules in the course of the star forming process is still uncertain, but it is likely that they are partially incorporated into protoplanetary disks and then into planetesimals and the small bodies of planetary systems. The complex organic molecules seen in star forming regions are particularly interesting since they probably make up building blocks for prebiotic chemistry. Recently we showed that these species were also present in the cold gas in prestellar cores, which represent the very first stages of star formation. These detections question the models which were until now accepted to account for the presence of complex organic molecules in star forming regions. In this article, we shortly review our current understanding of complex organic molecule formation in the early stages of star formation, in hot and cold cores alike and present new results on the formation of their likely precursor radicals.

  19. Organic chemistry: Precision pruning of molecules

    NASA Astrophysics Data System (ADS)

    Yang, Kin S.; Engle, Keary M.

    2016-05-01

    If organic molecules were trees, then the numerous carbon-hydrogen bonds within them would be leaves. A catalyst that targets one 'leaf' out of many similar other ones looks set to be a huge leap for synthetic chemistry. See Letter p.230

  20. Organic molecules in translucent interstellar clouds.

    PubMed

    Krełowski, Jacek

    2014-09-01

    Absorption spectra of translucent interstellar clouds contain many known molecular bands of CN, CH+, CH, OH, OH(+), NH, C2 and C3. Moreover, one can observe more than 400 unidentified absorption features, known as diffuse interstellar bands (DIBs), commonly believed to be carried by complex, carbon-bearing molecules. DIBs have been observed in extragalactic sources as well. High S/N spectra allow to determine precisely the corresponding column densities of the identified molecules, rotational temperatures which differ significantly from object to object in cases of centrosymmetric molecular species, and even the (12)C/(13)C abundance ratio. Despite many laboratory based studies of possible DIB carriers, it has not been possible to unambiguously link these bands to specific species. An identification of DIBs would substantially contribute to our understanding of chemical processes in the diffuse interstellar medium. The presence of substructures inside DIB profiles supports the idea that DIBs are very likely features of gas phase molecules. So far only three out of more than 400 DIBs have been linked to specific molecules but none of these links was confirmed beyond doubt. A DIB identification clearly requires a close cooperation between observers and experimentalists. The review presents the state-of-the-art of the investigations of the chemistry of interstellar translucent clouds i.e. how far our observations are sufficient to allow some hints concerning the chemistry of, the most common in the Galaxy, translucent interstellar clouds, likely situated quite far from the sources of radiation (stars). PMID:25467771

  1. Quaternary ammonium compounds can be abundant in some soils and are taken up as intact molecules by plants.

    PubMed

    Warren, Charles R

    2013-04-01

    Studies of organic nitrogen (N) cycling and uptake by plants have focused on protein amino acids, but the soil solution includes organic N compounds from many other compound classes. The two aims of this study were to characterize the 30-50 most abundant molecules of small (< 250 Da), nonpeptide organic N in the soil solution from six soils, and to determine if two ecologically disparate species (nonmycorrhizal Banksia oblongifolia and mycorrhizal Triticum aestivum) have the ability to take up intact molecules of three quaternary ammonium compounds (betaine, carnitine and acetyl-carnitine). Protein amino acids were dominant components of the pool of small nonpeptide organic N in all soils. The most abundant other compound classes were quaternary ammonium compounds (1-28% of nonpeptide small organic N) and nonprotein amino acids (3-19% of nonpeptide small organic N). B. oblongifolia and T. aestivum took up intact quaternary ammonium compounds from dilute hydroponic solution, while T. aestivum growing in field soil took up intact quaternary ammonium compounds injected into soil. Results of this study show that the pool of organic N in soil is more diverse and plants have an even broader palate than is suggested by most of the literature on organic N. PMID:23397895

  2. Distribution and abundance of organic thiols

    NASA Technical Reports Server (NTRS)

    Fahey, R.

    1985-01-01

    The role of glutathione (GSH) in protecting against the toxicity of oxygen and oxygen by products is well established for all eukaryotes studied except Entamoeba histolytica which lacks mitochrondria, chloroplasts, and microtubules. The GSH is not universal among prokaryotes. Entamoeba histolytica does not produce GSH or key enzymes of GSH metabolism. A general method of thiol analysis based upon fluorescent labeling with monobromobimane and HPLC separation of the resulting thiol derivatives was developed to determine the occurrence of GSH and other low molecular weight thiols in bacteria. Glutathione is the major thiol in cyanobacteria and in most bacteria closely related to the purple photosynthetic bacteria, but GSH was not found in archaebacteria, green bacteria, or GRAM positive bacteria. It suggested that glutathione metabolism was incorporated into eukaryotes at the time that mitochondria and chloroplasts were acquired by endosymbiosis. In Gram positive aerobes, coenzyme A occurs at millimolar levels and CoA disulfide reductases are identified. The CoA, rather than glutathione, may function in the oxygen detoxification processes of these organisms.

  3. Driving Organic Molecule Crystalliztion with Surface Reconstructions

    NASA Astrophysics Data System (ADS)

    Bickel, Jessica; Trovato, Gianfranco

    This work examines how surface reconstructions can drive crystallization of organic molecules via self-assembly. Organic electronic molecules have low conductivities compared to inorganic materials, but crystallizing these polymers increases their conductivity. This project uses surface reconstructions with periodically repeating topographies to drive the crystallization process. The samples are grown by placing a drop of a dilute PEDOT solution on the clean Si(001)-(2x1) or Si(111)-(7x7) surface reconstruction and heating the surface up to both evaporate the solvent and promote diffusion of the polymer to the thermodynamically defined lowest energy position. The resulting samples are characterized by scanning tunneling microscopy (STM) with respect to their crystallinity and electronic properties. Of particular interest is whether there is a preferential location for the PEDOT molecule to adsorb and whether there are any conformational changes upon adsorption that modify the HOMO-LUMO gap. This work is being done in a new pan-style RHK-STM enclosed in a glovebox at Cleveland State University. The glovebox has O2 and H2O levels of less than 1ppm. This allows for sample preparation and imaging in a controlled environment that is free from contamination.

  4. Formation of simple organic molecules in inner T Tauri disks

    NASA Astrophysics Data System (ADS)

    Agúndez, M.; Cernicharo, J.; Goicoechea, J. R.

    2008-06-01

    Aims: We present time dependent chemical models for a dense and warm O-rich gas exposed to a strong, far ultraviolet (FUV) field aimed at exploring the formation of simple organic molecules in the inner regions of protoplanetary disks around T Tauri stars. Methods: An up-to-date chemical network is used to compute the evolution of molecular abundances. Reactions of H2 with small organic radicals such as C2 and C2H, which are not included in current astrochemical databases, overcome their moderate activation energies at warm temperatures and become very important for the gas phase synthesis of C-bearing molecules. Results: The photodissociation of CO and release of C triggers the formation of simple organic species such as C2H2, HCN, and CH4. In timescales between 1 and 104 years, depending on the density and FUV field, a steady state is reached in the model in which molecules are continuously photodissociated, but also formed, mainly through gas phase chemical reactions involving H2. Conclusions: The application of the model to the upper layers of inner protoplanetary disks predicts large gas phase abundances of C2H2 and HCN. The implied vertical column densities are as large as several 1016 cm-2 in the very inner disk (<1 AU), in good agreement with the recent infrared observations of warm C2H2 and HCN in the inner regions of IRS 46 and GV Tau disks. We also compare our results with previous chemical models studying the photoprocessing in the outer disk regions, and find that the gas phase chemical composition in the upper layers of the inner terrestrial zone (a few AU) is predicted to be substantially different from that in the upper layers of the outer disk (>50 AU).

  5. Endogenous Synthesis of Prebiotic Organic Molecules

    NASA Technical Reports Server (NTRS)

    Miller, Stanley L.

    1996-01-01

    The necessary condition for the synthesis of organic compounds on the primitive earth is the presence of reducing conditions. This means an atmosphere of CH4, CO, or CO2 + H2. The atmospheric nitrogen can be N2 with a trace of NH3, but NH4(+) is needed in the ocean at least for amino acid synthesis. Many attempts have been made to use CO2 + H2O atmospheres for prebiotic synthesis, but these give at best extremely low yields of organic compounds, except in the presence of H2. Even strong reducing agents such as FeS + H2S or the mineral assemblages of the submarine vents fail to give significant yields of organic compounds with CO2. There appears to be a high kinetic barrier to the non-biological reduction of CO2 at low temperatures using geological reducing agents. The most abundant source of energy for prebiotic synthesis is ultraviolet light followed by electric discharges, with electric discharges being more efficient, although it is not clear which was the important energy source. Photochemical process would also make significant contributions. In an atmosphere Of CO2, N2, and H2O with no H2, the production rates of HCN and H2CO would be very low, 0.001 or less than that of a relatively reducing atmosphere. The concentration of organic compounds under these non-reducing conditions would be so low that there is doubt whether the concentration mechanism would be adequate for further steps toward the origin of life. A number of workers have calculated the influx of comets and meteorites on the primitive earth as a source of organic compounds. We conclude that while some organic material was added to the earth from comets and meteorites the amount available from these sources at a given time was at best only a few percent of that from earth bases syntheses under reducing conditions.

  6. Size selective hydrophobic adsorbent for organic molecules

    NASA Technical Reports Server (NTRS)

    Sharma, Pramod K. (Inventor); Hickey, Gregory S. (Inventor)

    1997-01-01

    The present invention relates to an adsorbent formed by the pyrolysis of a hydrophobic silica with a pore size greater than 5 .ANG., such as SILICALITE.TM., with a molecular sieving polymer precursor such as polyfurfuryl alcohol, polyacrylonitrile, polyvinylidene chloride, phenol-formaldehyde resin, polyvinylidene difluoride and mixtures thereof. Polyfurfuryl alcohol is the most preferred. The adsorbent produced by the pyrolysis has a silicon to carbon mole ratio of between about 10:1 and 1:3, and preferably about 2:1 to 1:2, most preferably 1:1. The pyrolysis is performed as a ramped temperature program between about 100.degree. and 800.degree. C., and preferably between about 100.degree. and 600.degree. C. The present invention also relates to a method for selectively adsorbing organic molecules having a molecular size (mean molecular diameter) of between about 3 and 6 .ANG. comprising contacting a vapor containing the small organic molecules to be adsorbed with the adsorbent composition of the present invention.

  7. The Distribution of Complex Organic Molecules in the Orion KL Molecular Core

    NASA Technical Reports Server (NTRS)

    Kuan, Yi-Jehng; Hsu, Yu-Sen; Charnley, Steven B.; Wang, Kuo-Song

    2011-01-01

    We conducted high angular-resolution observations toward the massive star-forming region Orion KL at 1.3 mm using the Submillimeter Array (SMA). Spectral emission from twelve complex organic molecules was simultaneously imaged. We discuss the distinct chemical characteristics among four sub- regions in Orion KL by comparing the spatial distributions and fractional abundances of these complex molecules. These observations will allow us to test and constrain chemical models of interstellar organic synthesis.

  8. Oligomer Molecules for Efficient Organic Photovoltaics.

    PubMed

    Lin, Yuze; Zhan, Xiaowei

    2016-02-16

    Solar cells, a renewable, clean energy technology that efficiently converts sunlight into electricity, are a promising long-term solution for energy and environmental problems caused by a mass of production and the use of fossil fuels. Solution-processed organic solar cells (OSCs) have attracted much attention in the past few years because of several advantages, including easy fabrication, low cost, lightweight, and flexibility. Now, OSCs exhibit power conversion efficiencies (PCEs) of over 10%. In the early stage of OSCs, vapor-deposited organic dye materials were first used in bilayer heterojunction devices in the 1980s, and then, solution-processed polymers were introduced in bulk heterojunction (BHJ) devices. Relative to polymers, vapor-deposited small molecules offer potential advantages, such as a defined molecular structure, definite molecular weight, easy purification, mass-scale production, and good batch-to-batch reproducibility. However, the limited solubility and high crystallinity of vapor-deposited small molecules are unfavorable for use in solution-processed BHJ OSCs. Conversely, polymers have good solution-processing and film-forming properties and are easily processed into flexible devices, whereas their polydispersity of molecular weights and difficulty in purification results in batch to batch variation, which may hamper performance reproducibility and commercialization. Oligomer molecules (OMs) are monodisperse big molecules with intermediate molecular weights (generally in the thousands), and their sizes are between those of small molecules (generally with molecular weights <1000) and polymers (generally with molecular weights >10000). OMs not only overcome shortcomings of both vapor-deposited small molecules and solution-processed polymers, but also combine their advantages, such as defined molecular structure, definite molecular weight, easy purification, mass-scale production, good batch-to-batch reproducibility, good solution processability

  9. Organic Optoelectronic Devices Employing Small Molecules

    NASA Astrophysics Data System (ADS)

    Fleetham, Tyler Blain

    Organic optoelectronic devices have remained a research topic of great interest over the past two decades, particularly in the development of efficient organic photovoltaics (OPV) and organic light emitting diodes (OLED). In order to improve the efficiency, stability, and materials variety for organic optoelectronic devices a number of emitting materials, absorbing materials, and charge transport materials were developed and employed in a device setting. Optical, electrical, and photophysical studies of the organic materials and their corresponding devices were thoroughly carried out. Two major approaches were taken to enhance the efficiency of small molecule based OPVs: developing material with higher open circuit voltages or improved device structures which increased short circuit current. To explore the factors affecting the open circuit voltage (VOC) in OPVs, molecular structures were modified to bring VOC closer to the effective bandgap, DeltaE DA, which allowed the achievement of 1V VOC for a heterojunction of a select Ir complex with estimated exciton energy of only 1.55eV. Furthermore, the development of anode interfacial layer for exciton blocking and molecular templating provide a general approach for enhancing the short circuit current. Ultimately, a 5.8% PCE was achieved in a single heterojunction of C60 and a ZnPc material prepared in a simple, one step, solvent free, synthesis. OLEDs employing newly developed deep blue emitters based on cyclometalated complexes were demonstrated. Ultimately, a peak EQE of 24.8% and nearly perfect blue emission of (0.148,0.079) was achieved from PtON7dtb, which approaches the maximum attainable performance from a blue OLED. Furthermore, utilizing the excimer formation properties of square-planar Pt complexes, highly efficient and stable white devices employing a single emissive material were demonstrated. A peak EQE of over 20% for pure white color (0.33,0.33) and 80 CRI was achieved with the tridentate Pt complex, Pt

  10. X-ray characterization of solid small molecule organic materials

    SciTech Connect

    Billinge, Simon; Shankland, Kenneth; Shankland, Norman; Florence, Alastair

    2014-06-10

    The present invention provides, inter alia, methods of characterizing a small molecule organic material, e.g., a drug or a drug product. This method includes subjecting the solid small molecule organic material to x-ray total scattering analysis at a short wavelength, collecting data generated thereby, and mathematically transforming the data to provide a refined set of data.

  11. CHEMICAL TRANSPORT FACILITATED BY COLLOIDAL-SIZED ORGANIC MOLECULES

    EPA Science Inventory

    The fluid passing through the pores of soils and geologic materials is not just water with dissolved inorganic chemicals, but a complex mixture of organic and inorganic molecules. Large organic molecules such as humic and fulvic materials may impact the movement of contaminants. ...

  12. Investigation of claims for interstellar organisms and complex organic molecules

    NASA Astrophysics Data System (ADS)

    Davies, Robert E.; Delluva, Adelaide M.; Koch, Robert H.

    1984-10-01

    For many years, Hoyle, Wickramasinghe and their associates have examined interstellar (IS) absorption features in the ultraviolet, visible and infrared and `identified' them with a variety of organic structures or organisms. Among these there have been generalized, pre-biotic molecules1, polyoxymethylene whiskers2, polysaccharides and hydrocarbons3,4, tryptophan (and inferentially proteins)5-all claimed to be coatings on IS grains. In other cases, the grains1,6 have been described as 10-100% alkanes, alkenes, alkynes or aromatics by mass. In extensions of these claims, the grains are supposed to be microorganisms (such as viruses and bacteria7, algae8, siliceous cells similar to diatoms9, yeasts10 or other eukaryotic cells11) in whole or in part. Finally, a case has been advanced for possible interstellar and interplanetary insects11. The `identifications' in these and many other publications call into question the intrinsic origin of Earth life itself12,13 and the uniqueness and validity of darwinian evolution11. We now report on ultraviolet spectra of specimens of the types cited by these workers and compare our results with infrared and ultraviolet data published previously. We conclude that the identifications claimed by Hoyle, Wickramasinghe and their colleagues are unwarranted.

  13. Method of monitoring photoactive organic molecules in-situ during gas-phase deposition of the photoactive organic molecules

    SciTech Connect

    Forrest, Stephen R.; Vartanian, Garen; Rolin, Cedric

    2015-06-23

    A method for in-situ monitoring of gas-phase photoactive organic molecules in real time while depositing a film of the photoactive organic molecules on a substrate in a processing chamber for depositing the film includes irradiating the gas-phase photoactive organic molecules in the processing chamber with a radiation from a radiation source in-situ while depositing the film of the one or more organic materials and measuring the intensity of the resulting photoluminescence emission from the organic material. One or more processing parameters associated with the deposition process can be determined from the photoluminescence intensity data in real time providing useful feedback on the deposition process.

  14. Organic molecules and water in the planet formation region of young circumstellar disks.

    PubMed

    Carr, John S; Najita, Joan R

    2008-03-14

    The chemical composition of protoplanetary disks is expected to hold clues to the physical and chemical processes that influence the formation of planetary systems. However, characterizing the gas composition in the planet formation region of disks has been a challenge to date. We report here that the protoplanetary disk within 3 astronomical units of AA Tauri possesses a rich molecular emission spectrum in the mid-infrared, indicating a high abundance of simple organic molecules (HCN, C2H2, and CO2), water vapor, and OH. These results suggest that water is abundant throughout the inner disk and that the disk supports an active organic chemistry. PMID:18339932

  15. Near-infrared spectroscopy of M dwarfs. I. CO molecule as an abundance indicator of carbon†

    NASA Astrophysics Data System (ADS)

    Tsuji, Takashi; Nakajima, Tadashi

    2014-10-01

    Based on the near-infrared spectra of 42 M dwarfs, carbon abundances are determined from the ro-vibrational lines of the CO (2-0) band. We apply Teff values based on the angular diameters if available or use the Teff values in a log Teff-M3.4 relation (M3.4 is the absolute magnitude at 3.4 μm based on the WISE W1 flux and the Hipparcos parallax) to estimate Teff values of objects for which angular diameters are unknown. Also, we discuss briefly the HR diagram of low-mass stars. On the observed spectrum of the M dwarf, the continuum is depressed by the numerous weak lines of H2O and only the depressed continuum or the pseudo-continuum can be seen. On the theoretical spectrum of the M dwarf, the true continuum can be evaluated easily but the pseudo-continuum can also be evaluated accurately thanks to the recent H2O line database. Then spectroscopic analysis of the M dwarf can be done by referring to the pseudo-continuum both on the observed and theoretical spectra. Since the basic principle of the spectroscopic analysis should be the same whether the true- or pseudo-continuum is referred to, the difficulty related to the continuum in cool stars can in principle be overcome. Then, the numerous CO lines can be excellent abundance indicators of carbon, since almost all the carbon atoms are in stable CO molecules which suffer little effect of the uncertainties in photospheric structure, and carbon abundances in late-type stars can best be determined in M dwarfs rather than in solar type stars. The resulting C/Fe ratios for most M dwarfs are nearly constant at about the solar value based on the classical high carbon abundance rather than on the recently revised lower value. This result implies that the solar carbon abundance is atypical for its metallicity among the stellar objects in the solar neighborhood if the downward revised carbon abundance is correct.

  16. Constraining the Abundances of Complex Organics in the Inner Regions of Solar-Type Protostars

    NASA Astrophysics Data System (ADS)

    López-Sepulcre, A.; Taquet, V.; Ceccarelli, C.; Neri, R.; Kahane, C.; Charnley, S. B.

    2015-12-01

    We present arcsecond-resolution observations, obtained with the IRAM Plateau de Bure interferometer, of multiple complex organic molecules in two hot corino protostars: IRAS 2A and IRAS 4A, in the NGC 1333 star-forming region. The distribution of the line emission is very compact, indicating the presence of COMs is mostly concentrated in the inner hot corino regions. A comparison of the COMs abundances with astrochemical models favours a gas-phase formation route for CH3OCH3, and a grain formation of C2H5OH, C2H5CN, and HCOCH2OH. The high abundances of methyl formate (HCOOCH3) remain underpredicted by an order of magnitude.

  17. Metal oxide charge transport material doped with organic molecules

    DOEpatents

    Forrest, Stephen R.; Lassiter, Brian E.

    2016-08-30

    Doping metal oxide charge transport material with an organic molecule lowers electrical resistance while maintaining transparency and thus is optimal for use as charge transport materials in various organic optoelectronic devices such as organic photovoltaic devices and organic light emitting devices.

  18. Molecular spectral line surveys and the organic molecules in the interstellar molecular clouds

    NASA Astrophysics Data System (ADS)

    Ohishi, Masatoshi

    2008-10-01

    It is known that more than 140 interstellar and circumstellar molecules have so far been detected, mainly by means of the radio astronomy observations. Many organic molecules are also detected, including alcohols, ketons, ethers, aldehydes, and others, that are distributed from dark clouds and hot cores in the giant molecular clouds. It is believed that most of the organic molecules in space are synthesized through the grain surface reactions, and are evaporated from the grain surface when they are heated up by the UV radiation from adjacent stars. On the other hand the recent claim on the detection of glycine have raised an important issue how difficult it is to confirm secure detection of weak spectra from less abundant organic molecules in the interstellar molecular cloud. I will review recent survey observations of organic molecules in the interstellar molecular clouds, including independent observations of glycine by the 45 m radio telescope in Japan, and will discuss the procedure to securely identify weak spectral lines from organic molecules and the importance of laboratory measurement of organic species.

  19. The Origin of Complex Organic Molecules in Prestellar Cores

    NASA Astrophysics Data System (ADS)

    Vastel, C.; Ceccarelli, C.; Lefloch, B.; Bachiller, R.

    2014-11-01

    Complex organic molecules (COMs) have been detected in a variety of environments including cold prestellar cores. Given the low temperatures of these objects, these detections challenge existing models. We report here new observations toward the prestellar core L1544. They are based on an unbiased spectral survey of the 3 mm band at the IRAM 30 m telescope as part of the Large Program ASAI. The observations allow us to provide a full census of the oxygen-bearing COMs in this source. We detected tricarbon monoxide, methanol, acetaldehyde, formic acid, ketene, and propyne with abundances varying from 5 × 10-11 to 6 × 10-9. The non-LTE analysis of the methanol lines shows that they are likely emitted at the border of the core at a radius of ~8000 AU, where T ~ 10 K and n H_2 ~2 × 104 cm-3. Previous works have shown that water vapor is enhanced in the same region because of the photodesorption of water ices. We propose that a non-thermal desorption mechanism is also responsible for the observed emission of methanol and COMs from the same layer. The desorbed oxygen and a small amount of desorbed methanol and ethene are enough to reproduce the abundances of tricarbon monoxide, methanol, acetaldehyde, and ketene measured in L1544. These new findings open the possibility that COMs in prestellar cores originate in a similar outer layer rather than in the dense inner cores, as previously assumed, and that their formation is driven by the non-thermally desorbed species.

  20. THE ORIGIN OF COMPLEX ORGANIC MOLECULES IN PRESTELLAR CORES

    SciTech Connect

    Vastel, C.; Ceccarelli, C.; Lefloch, B.; Bachiller, R.

    2014-11-01

    Complex organic molecules (COMs) have been detected in a variety of environments including cold prestellar cores. Given the low temperatures of these objects, these detections challenge existing models. We report here new observations toward the prestellar core L1544. They are based on an unbiased spectral survey of the 3 mm band at the IRAM 30 m telescope as part of the Large Program ASAI. The observations allow us to provide a full census of the oxygen-bearing COMs in this source. We detected tricarbon monoxide, methanol, acetaldehyde, formic acid, ketene, and propyne with abundances varying from 5 × 10{sup –11} to 6 × 10{sup –9}. The non-LTE analysis of the methanol lines shows that they are likely emitted at the border of the core at a radius of ∼8000 AU, where T ∼ 10 K and n {sub H{sub 2}} ∼2 × 10{sup 4} cm{sup –3}. Previous works have shown that water vapor is enhanced in the same region because of the photodesorption of water ices. We propose that a non-thermal desorption mechanism is also responsible for the observed emission of methanol and COMs from the same layer. The desorbed oxygen and a small amount of desorbed methanol and ethene are enough to reproduce the abundances of tricarbon monoxide, methanol, acetaldehyde, and ketene measured in L1544. These new findings open the possibility that COMs in prestellar cores originate in a similar outer layer rather than in the dense inner cores, as previously assumed, and that their formation is driven by the non-thermally desorbed species.

  1. Electrocatalytic recycling of CO2 and small organic molecules.

    PubMed

    Lee, Jaeyoung; Kwon, Youngkook; Machunda, Revocatus L; Lee, Hye Jin

    2009-10-01

    As global warming directly affects the ecosystems and humankind in the 21st century, attention and efforts are continuously being made to reduce the emission of greenhouse gases, especially carbon dioxide (CO2). In addition, there have been numerous efforts to electrochemically convert CO2 gas to small organic molecules (SOMs) and vice versa. Herein, we highlight recent advances made in the electrocatalytic recycling of CO2 and SOMs including (i) the overall trend of research activities made in this area, (ii) the relations between reduction conditions and products in the aqueous phase, (iii) the challenges in the use of gas diffusion electrodes for the continuous gas phase CO2 reduction, as well as (iv) the development of state of the art hybrid techniques for industrial applications. Perspectives geared to fully exploit the potential of zero-gap cells for CO2 reduction in the gaseous phase and the high applicability on a large scale are also presented. We envision that the hybrid system for CO2 reduction supported by sustainable solar, wind, and geothermal energies and waste heat will provide a long term reduction of greenhouse gas emissions and will allow for continued use of the abundant fossil fuels by industries and/or power plants but with zero emissions. PMID:19579251

  2. Sedimentary organic molecules: Origins and information content

    NASA Technical Reports Server (NTRS)

    Hayes, J. M.; Freeman, K. H.

    1991-01-01

    To progress in the study of organic geochemistry, we must dissect the processes controlling the composition of sedimentary organic matter. Structurally, this has proven difficult. Individual biomarkers can often be recognized, but their contribution to total organic materials is small, and their presence does not imply that their biochemical cell mates have survived. We are finding, however, that a combination of structural and isotopic lines of evidence provides new information. A starting point is provided by the isotopic compositions of primary products (degradation products of chlorophylls, alkenones derived from coccoliths). We find strong evidence that the isotopic difference between primary carbonate and algal organic material can be interpreted in terms of the concentration of dissolved CO2. Moreover, the isotopic difference between primary and total organic carbon can be interpreted in terms of characteristic isotopic shifts imposed by secondary processes (responsive, for example, to O2 levels in the depositional environment. In favorable cases, isotopic compositions of a variety of secondary products can be interpreted in terms of flows of carbon, and, therefore, in terms of specific processes and environmental conditions within the depositional environment.

  3. The IUPAC Rules for Naming Organic Molecules

    ERIC Educational Resources Information Center

    Skonieczny, Stanislaw

    2006-01-01

    A systematic approach to naming polyfunctional organic compounds is presented. Latest IUPAC rules are incorporated and the table of order of precedence for the major functional groups is assembled. The scope of nomenclature is limited to common functional groups that are covered by undergraduate courses in colleges and universities. (Contains 1…

  4. Formation of organic molecules on Titan

    NASA Technical Reports Server (NTRS)

    Capone, L. A.; Prasad, S. S.; Huntress, W. T.; Whitten, R. C.; Dubach, J.; Santhanam, K.

    1981-01-01

    A mechanism is proposed for the formation of complex organic nitrogen compounds in the dense lower atmosphere of Titan. The mechanism is based on three-body association reactions with HCNH(+) ions formed by the reaction of N(+) with CH4, which lead to the production of ethyl cyanide, vinyl cyanide and cyanoacetylene. Calculations for a model atmosphere consistent with the preliminary interpretation of Voyager 1 data for the region of maximum cosmic ray activated chemistry, corresponding to a temperature between 150 and 160 K and a pressure of 20 mbar, are presented which show substantial organic nitrile and hydrogen cyanide production rates. Based on these production rates, it is expected that significant equilibrium concentrations of these compounds will be found on Titan.

  5. Constraining the Abundances of Complex Organics in the Inner Regions of Solar-type Protostars

    NASA Astrophysics Data System (ADS)

    Taquet, Vianney; López-Sepulcre, Ana; Ceccarelli, Cecilia; Neri, Roberto; Kahane, Claudine; Charnley, Steven B.

    2015-05-01

    The high abundances of Complex Organic Molecules (COMs) with respect to methanol, the most abundant COM, detected toward low-mass protostars, tend to be underpredicted by astrochemical models. This discrepancy might come from the large beam of the single-dish telescopes, encompassing several components of the studied protostar, commonly used to detect COMs. To address this issue, we have carried out multi-line observations of methanol and several COMs toward the two low-mass protostars NGC 1333-IRAS 2A and -IRAS 4A with the Plateau de Bure interferometer at an angular resolution of 2″, resulting in the first multi-line detection of the O-bearing species glycolaldehyde and ethanol and of the N-bearing species ethyl cyanide toward low-mass protostars other than IRAS 16293. The high number of detected transitions from COMs (more than 40 methanol transitions for instance) allowed us to accurately derive the source size of their emission and the COM column densities. The COM abundances with respect to methanol derived toward IRAS 2A and IRAS 4A are slightly, but not substantitally, lower than those derived from previous single-dish observations. The COM abundance ratios do not vary significantly with the protostellar luminosity, over five orders of magnitude, implying that low-mass hot corinos are quite chemically rich as high-mass hot cores. Astrochemical models still underpredict the abundances of key COMs, such as methyl formate or di-methyl ether, suggesting that our understanding of their formation remains incomplete.

  6. Organic molecules in ices and their release into the gas phase

    NASA Astrophysics Data System (ADS)

    Fayolle, Edith; Oberg, Karin I.; Garrod, Robin; van Dishoeck, Ewine; Rajappan, Mahesh; Bertin, Mathieu; Romanzin, Claire; Michaut, Xavier; Fillion, Jean-Hugues

    2015-08-01

    Organic molecules in the early stages of star formation are mainly produced in icy mantles surrounding interstellar dust grains. Identifying these complex organics and quantifying their abundance during the evolution of young stellar objects is of importance to understand the emergence of life. Simple molecules in ices, up to methanol in size, have been identified in the interstellar medium through their mid-IR vibrations, but band confusion prevents detections of more complex and less abundant organic molecules in interstellar ices. The presence of complex organics on grains can instead be indirectly inferred from observations of their rotational lines in the gas phase following ice sublimation.Thermal sublimation of protostellar ices occurs when icy grains flow toward a central protostar, resulting in the formation of a hot-core or a hot-corinos. The high degree of chemical complexity observed in these dense and warm regions can be the results of i) direct synthesis on the grains followed by desorption, but also to ii) the desorption of precursors from the ice followed by gas-phase chemistry. I will show how spatially resolved millimetric observations of hot cores and cooler protostellar environments, coupled to ice observations can help us pinpoint the ice or gas-phase origin of these organic species.Organic molecules have also recently been observed in cold environments where thermal desorption can be neglected. The presence of these cold molecules in the gas phase is most likely due to non-thermal desorption processes induced by, for e.g., photon-, electron-, cosmic-ray-irradiation, shock, exothermic reactions... I will present laboratory and observational efforts that push our current understanding of these non-thermal desorption processes and how they could be use to quantify the amount of organics in ices.

  7. Single Molecule Study of DNA Organization and Recombination

    NASA Astrophysics Data System (ADS)

    Xiao, Botao

    We have studied five projects related to DNA organization and recombination using mainly single molecule force-spectroscopy and statistical tools. First, HU is one of the most abundant DNA-organizing proteins in bacterial chromosomes and participates in gene regulation. We report experiments that study the dependence of DNA condensation by HU on force, salt and HU concentration. A first important result is that at physiological salt levels, HU only bends DNA, resolving a previous paradox of why a chromosome-compacting protein should have a DNA-stiffening function. A second major result is quantitative demonstration of strong dependencies of HU-DNA dissociation on both salt concentration and force. Second, we have used a thermodynamic Maxwell relation to count proteins driven off large DNAs by tension, an effect important to understanding DNA organization. Our results compare well with estimates of numbers of proteins HU and Fis in previous studies. We have also shown that a semi-flexible polymer model describes our HU experimental data well. The force-dependent binding suggests mechano-chemical mechanisms for gene regulation. Third, the elusive role of protein H1 in chromatin has been clarified with purified H1 and Xenopus extracts. We find that H1 compacts DNA by both bending and looping. Addition of H1 enhances chromatin formation and maintains the plasticity of the chromatin. Fourth, the topology and mechanics of DNA twisting are critical to DNA organization and recombination. We have systematically measured DNA extension as a function of linking number density from 0.08 to -2 with holding forces from 0.2 to 2.4 pN. Unlike previous proposals, the DNA extension decreases with negative linking number. Finally, DNA recombination is a dynamic process starting from enzyme-DNA binding. We report that the Int-DBD domain of lambda integrase binds to DNA without compaction at low Int-DBD concentration. High concentration of Int-DBD loops DNA below a threshold force

  8. A Self-Perpetuating Catalyst for the Production of Complex Organic Molecules in Protostellar Nebulae

    NASA Technical Reports Server (NTRS)

    Nuth, Joseph A.; Johnson, N. M.

    2010-01-01

    The formation of abundant carbonaceous material in meteorites is a long standing problem and an important factor in the debate on the potential for the origin of life in other stellar systems. Many mechanisms may contribute to the total organic content in protostellar nebulae, ranging from organics formed via ion-molecule and atom-molecule reactions in the cold dark clouds from which such nebulae collapse, to similar ion-molecule and atom-molecule reactions in the dark regions of the nebula far from the proto star, to gas phase reactions in sub-nebulae around growing giant planets and in the nebulae themselves. The Fischer-Tropsch-type (FTT) catalytic reduction of CO by hydrogen was once the preferred model for production of organic materials in the primitive solar nebula. The Haber-Bosch catalytic reduction of N2 by hydrogen was thought to produce the reduced nitrogen found in meteorites. However, the clean iron metal surfaces that catalyze these reactions are easily poisoned via reaction with any number of molecules, including the very same complex organics that they produce and both reactions work more efficiently in the hot regions of the nebula. We have demonstrated that many grain surfaces can catalyze both FTT and HB-type reactions, including amorphous iron and magnesium silicates, pure silica smokes as well as several minerals. Although none work as well as pure iron grains, and all produce a wide range of organic products rather than just pure methane, these materials are not truly catalysts.

  9. Adsorption of organic molecules on silica surface.

    PubMed

    Parida, Sudam K; Dash, Sukalyan; Patel, Sabita; Mishra, B K

    2006-09-13

    The adsorption behaviour of various organic adsorbates on silica surface is reviewed. Most of the structural information on silica is obtained from IR spectral data and from the characteristics of water present at the silica surface. Silica surface is generally embedded with hydroxy groups and ethereal linkages, and hence considered to have a negative charged surface prone to adsorption of electron deficient species. Adsorption isotherms of the adsorbates delineate the nature of binding of the adsorbate with silica. Aromatic compounds are found to involve the pi-cloud in hydrogen bonding with silanol OH group during adsorption. Cationic and nonionic surfactants adsorb on silica surface involving hydrogen bonding. Sometimes, a polar part of the surfactants also contributes to the adsorption process. Styryl pyridinium dyes are found to anchor on silica surface in flat-on position. On modification of the silica by treating with alkali, the adsorption behaviour of cationic surfactant or polyethylene glycol changes due to change in the characteristics of silica or modified silica surface. In case of PEG-modified silica, adsolubilization of the adsorbate is observed. By using a modified adsorption equation, hemimicellization is proposed for these dyes. Adsorptions of some natural macromolecules like proteins and nucleic acids are investigated to study the hydrophobic and hydrophilic binding sites of silica. Artificial macromolecules like synthetic polymers are found to be adsorbed on silica surface due to the interaction of the multifunctional groups of the polymers with silanols. Preferential adsorption of polar adsorbates is observed in case of adsorbate mixtures. When surfactant mixtures are considered to study competitive adsorption on silica surface, critical micelle concentration of individual surfactant also contributes to the adsorption isotherm. The structural study of adsorbed surface and the thermodynamics of adsorption are given some importance in this review

  10. Electrospray deposition of organic molecules on bulk insulator surfaces

    PubMed Central

    Pawlak, Rémy; Glatzel, Thilo

    2015-01-01

    Summary Large organic molecules are of important interest for organic-based devices such as hybrid photovoltaics or molecular electronics. Knowing their adsorption geometries and electronic structures allows to design and predict macroscopic device properties. Fundamental investigations in ultra-high vacuum (UHV) are thus mandatory to analyze and engineer processes in this prospects. With increasing size, complexity or chemical reactivity, depositing molecules by thermal evaporation becomes challenging. A recent way to deposit molecules in clean conditions is Electrospray Ionization (ESI). ESI keeps the possibility to work with large molecules, to introduce them in vacuum, and to deposit them on a large variety of surfaces. Here, ESI has been successfully applied to deposit triply fused porphyrin molecules on an insulating KBr(001) surface in UHV environment. Different deposition coverages have been obtained and characterization of the surface by in-situ atomic force microscopy working in the non-contact mode shows details of the molecular structures adsorbed on the surface. We show that UHV-ESI, can be performed on insulating surfaces in the sub-monolayer regime and to single molecules which opens the possibility to study a variety of complex molecules. PMID:26665062

  11. Complex organic molecules during low-mass star formation: Pilot survey results

    SciTech Connect

    Öberg, Karin I.; Graninger, Dawn; Lauck, Trish

    2014-06-10

    Complex organic molecules (COMs) are known to be abundant toward some low-mass young stellar objects (YSOs), but how these detections relate to typical COM abundance are not yet understood. We aim to constrain the frequency distribution of COMs during low-mass star formation, beginning with this pilot survey of COM lines toward six embedded YSOs using the IRAM 30 m Telescope. The sample was selected from the Spitzer c2d ice sample and covers a range of ice abundances. We detect multiple COMs, including CH{sub 3}CN, toward two of the YSOs, and tentatively toward a third. Abundances with respect to CH{sub 3}OH vary between 0.7% and 10%. This sample is combined with previous COM observations and upper limits to obtain a frequency distributions of CH{sub 3}CN, HCOOCH{sub 3}, CH{sub 3}OCH{sub 3}, and CH{sub 3}CHO. We find that for all molecules more than 50% of the sample have detections or upper limits of 1%-10% with respect to CH{sub 3}OH. Moderate abundances of COMs thus appear common during the early stages of low-mass star formation. A larger sample is required, however, to quantify the COM distributions, as well as to constrain the origins of observed variations across the sample.

  12. The formation of oxygen-containing organic molecules in the Orion compact ridge

    NASA Technical Reports Server (NTRS)

    Millar, T. J.; Herbst, Eric; Charnley, S. B.

    1991-01-01

    Following a suggestion of Blake et al. (1987), an attempt was made to account for the unusually large abundances of selected oxygen-containing organic molecules in the so-called 'compact ridge' source directed toward Orion KL by a gas-phase chemical model in which large amounts of water are injected into the source from the IRc2 outflow. Although quantitative model results show that the calculated abundances of methanol, methyl formate, and dimethyl ether can be enhanced relative to their values in the absence of water injection, the enhancements fall far short of explaining the very large observed abundances of these species. Models in which methanol is injected rather than water are more successful, although the source of the methanol is unclear.

  13. Interstellar Organic Molecules: from Clouds to Solar Nebula

    NASA Astrophysics Data System (ADS)

    Kuan, Yi-Jehng; Huang, Hui-Chun; Charnley, Steven B.; Markwick, Andrew; Botta, Oliver; Ehrenfreund, Pascale; Kisiel, Zbigniew; Butner, Harold M.

    Although laboratory experiments involving energetic processing of simple molecules were able to reproduce many of the biomolecules that are the building blocks of living organisms impacts of comets and asteroids could have delivered large amounts of organic matter to the early Earth. Volatile cometary matter appears to retain a significant interstellar signature; observations of recent bright comets indicate that they have a molecular inventory consistent with their ices being largely unmodified interstellar material. Many simple organic molecules with biochemical significance observed in circumstellar envelopes and in molecular clouds similar to that from which the Solar System formed may have acted as the precursors of the more complex organics found in meteorites. Therefore there is potentially a strong link between interstellar organics and prebiotic chemical evolution. Radioastronomical observations particularly at millimeter wavelengths allow us to determine the chemical composition and characteristics of the molecular inventory in interstellar space. We have thus conducted an extensive astronomical search for complex organic molecules Quinoline Isoquinoline Pyridine and Pyrimidine. Some of our recent results for interstellar organics will be presented.

  14. Anisotropic behavior of organic molecules on prepatterned surfaces

    NASA Astrophysics Data System (ADS)

    Hopp, Stefan Frieder; Heuer, Andreas

    2012-04-01

    The nucleation of organic molecules on surfaces, prepatterned with stripes, is investigated with emphasis on anisotropy effects. Representing the molecules as ellipsoids, the related particle-particle interaction is modeled by means of a generalized Gay-Berne potential for similar biaxial particles. The orientation behavior of these ellipsoidal molecules induced by the stripe pattern is studied for the first monolayer by performing kinetic Monte Carlo simulations. It is shown how the properties of the particle alignment depend on energy scales, temperature, and flux. Based on the fact the particles strictly arrange in rows, it is furthermore instructive to analyze the orientation behavior within the different rows. Finally, the transfer of orientation from a preset row of molecules with fixed orientation to other nucleating particles is examined.

  15. Anisotropic behavior of organic molecules on prepatterned surfaces.

    PubMed

    Hopp, Stefan Frieder; Heuer, Andreas

    2012-04-21

    The nucleation of organic molecules on surfaces, prepatterned with stripes, is investigated with emphasis on anisotropy effects. Representing the molecules as ellipsoids, the related particle-particle interaction is modeled by means of a generalized Gay-Berne potential for similar biaxial particles. The orientation behavior of these ellipsoidal molecules induced by the stripe pattern is studied for the first monolayer by performing kinetic Monte Carlo simulations. It is shown how the properties of the particle alignment depend on energy scales, temperature, and flux. Based on the fact the particles strictly arrange in rows, it is furthermore instructive to analyze the orientation behavior within the different rows. Finally, the transfer of orientation from a preset row of molecules with fixed orientation to other nucleating particles is examined. PMID:22519314

  16. Coordinative alignment of molecules in chiral metal-organic frameworks.

    PubMed

    Lee, Seungkyu; Kapustin, Eugene A; Yaghi, Omar M

    2016-08-19

    A chiral metal-organic framework, MOF-520, was used to coordinatively bind and align molecules of varying size, complexity, and functionality. The reduced motional degrees of freedom obtained with this coordinative alignment method allowed the structures of molecules to be determined by single-crystal x-ray diffraction techniques. The chirality of the MOF backbone also served as a reference in the structure solution for an unambiguous assignment of the absolute configuration of bound molecules. Sixteen molecules representing four common functional groups (primary alcohol, phenol, vicinal diol, and carboxylic acid), ranging in complexity from methanol to plant hormones (gibberellins, containing eight stereocenters), were crystallized and had their precise structure determined. We distinguished single and double bonds in gibberellins, and we enantioselectively crystallized racemic jasmonic acid, whose absolute configuration had only been inferred from derivatives. PMID:27540171

  17. The birth and death of organic molecules in protoplanetary disks

    NASA Astrophysics Data System (ADS)

    Henning, Thomas; Semenov, Dmitry

    2008-10-01

    The most intriguing question related to the chemical evolution of protoplanetary disks is the genesis of pre-biotic organic molecules in the planet-forming zone. In this contribution we briefly review current observational knowledge of physical structure and chemical composition of disks and discuss whether organic molecules can be present in large amounts at the verge of planet formation. We predict that some molecules, including CO-bearing species such as H2CO, can be underabundant in inner regions of accreting protoplanetary disks around low-mass stars due to the high-energy stellar radiation and chemical processing on dust grain surfaces. These theoretical predictions are further compared with high-resolution observational data and the limitations of current models are discussed.

  18. Searching for Bio-Precursors and Complex Organic Molecules in Space using the GBT

    NASA Technical Reports Server (NTRS)

    Cordiner, M.; Charnley, S.; Kisiel, Z.

    2012-01-01

    Using the latest microwave receiver technology, large organic molecules with abundances as low as approx. 10(exp -11) times that of molecular hydrogen are detectable in cold interstellar clouds via their rotational emission line spectra. We report new observations to search for complex molecules, including molecules of possible pre-biotic importance, using the newly-commissioned Kband focal plane array (KFPA) of the NRAO Robert C. Byrd Green Bank Telescope. Spectra are presented of the dense molecular cloud TMC-1, showing strict upper limits on the level of emission from nitrogen-bearing rings pyrimidine, quinoline and iso-quinoline, carbon-chain oxides C60, C70, HC60 and HC70, and the carbon-chain anion C4H-. The typical RMS brightness temperature noise levels we achieved are approx. 1 mK at around 20 GHz.

  19. Meteors do not break exogenous organic molecules into high yields of diatomics

    NASA Technical Reports Server (NTRS)

    Jenniskens, Peter; Schaller, Emily L.; Laux, Christophe O.; Wilson, Michael A.; Schmidt, Greg; Rairden, Rick L.

    2004-01-01

    Meteoroids that dominate the Earth's extraterrestrial mass influx (50-300 microm size range) may have contributed a unique blend of exogenous organic molecules at the time of the origin of life. Such meteoroids are so large that most of their mass is ablated in the Earth's atmosphere. In the process, organic molecules are decomposed and chemically altered to molecules differently from those delivered to the Earth's surface by smaller (<50 microm) micrometeorites and larger (>10 cm) meteorites. The question addressed here is whether the organic matter in these meteoroids is fully decomposed into atoms or diatomic compounds during ablation. If not, then the ablation products made available for prebiotic organic chemistry, and perhaps early biology, might have retained some memory of their astrophysical nature. To test this hypothesis we searched for CN emission in meteor spectra in an airborne experiment during the 2001 Leonid meteor storm. We found that the meteor's light-emitting air plasma, which included products of meteor ablation, contained less than 1 CN molecule for every 30 meteoric iron atoms. This contrasts sharply with the nitrogen/iron ratio of 1:1.2 in the solid matter of comet 1P/Halley. Unless the nitrogen content or the abundance of complex organic matter in the Leonid parent body, comet 55P/Tempel-Tuttle, differs from that in comet 1P/Halley, it appears that very little of that organic nitrogen decomposes into CN molecules during meteor ablation in the rarefied flow conditions that characterize the atmospheric entry of meteoroids approximately 50 microm-10 cm in size. We propose that the organics of such meteoroids survive instead as larger compounds.

  20. Organic Molecules in Oxygen-Rich Circumstellar Envelopes: Methanol and Hydrocarbons

    NASA Technical Reports Server (NTRS)

    Charnley, S. B.; Tielens, A. G. G. M.; Kress, M. E.

    1995-01-01

    The existence of anomalously high abundances of gaseous CH4 has been invoked to explain the unexpectedly high abundances of the carbon-bearing molecules HCN and H2CO in the outflows from O-rich red giants. We have modelled the chemistry that proceeds in the outer envelope when CH4 is injected from the inner envelope. We find that photolysis by the interstellar radiation field drives an ion-neutral chemistry which produces several organic molecules. The calculated abundances of CH3OH, C2H and C2 can be comparable to those calculated for H2CO and HCN. Species such as C2H4, C2H2 and CH3CN can also be abundant. A search for CH3OH and C2H in several O-rich outflows known to exhibit strong HCN emission is needed. As it derives entirely from the CH4 photochain, is insensitive to the envelope temperature distribution, and has accessible transitions at millimetre wavelengths, the detection of the C2H radical would provide further indirect support for the presence of the hypothesized methane.

  1. Recent observations of organic molecules in nearby cold, dark interstellar clouds

    NASA Technical Reports Server (NTRS)

    Suzuki, H.; Ohishi, M.; Morimoto, M.; Kaifu, N.; Friberg, P.

    1985-01-01

    Recent investigations of the organic chemistry of relatively nearby cold, dark interstellar clouds are reported. Specifically, the presence of interstellar tricarbon monoxide (C3O) in Taurus Molecular Cloud 1 (TMC-1) is confirmed. The first detection in such regions of acetaldehyde (CH3CHO), the most complex oxygen-containing organic molecule yet found in dark clouds is reported, as well as the first astronomical detection of several molecular rotational transitions, including the J = 18-17 and 14-13 transitions of cyanodiacetylene (HC5N), the 1(01)-0(00) transition of acetaldehyde, and the J = 5-4 transition of C3O. A significant upper limit is set on the abundance of cyanocarbene (HCCN) as a result of the first reported interstellar search for this molecule.

  2. Unified Microscopic-Macroscopic Monte Carlo Simulations of Complex Organic Molecule Chemistry in Cold Cores

    NASA Astrophysics Data System (ADS)

    Chang, Qiang; Herbst, Eric

    2016-03-01

    The recent discovery of methyl formate and dimethyl ether in the gas phase of cold cores with temperatures as cold as 10 K challenges our previous astrochemical models concerning the formation of complex organic molecules (COMs). The strong correlation between the abundances and distributions of methyl formate and dimethyl ether further shows that current astrochemical models may be missing important chemical processes in cold astronomical sources. We investigate a scenario in which COMs and the methoxy radical can be formed on dust grains via a so-called chain reaction mechanism, in a similar manner to CO2. A unified gas-grain microscopic-macroscopic Monte Carlo approach with both normal and interstitial sites for icy grain mantles is used to perform the chemical simulations. Reactive desorption with varying degrees of efficiency is included to enhance the nonthermal desorption of species formed on cold dust grains. In addition, varying degrees of efficiency for the surface formation of methoxy are also included. The observed abundances of a variety of organic molecules in cold cores can be reproduced in our models. The strong correlation between the abundances of methyl formate and dimethyl ether in cold cores can also be explained. Nondiffusive chemical reactions on dust grain surfaces may play a key role in the formation of some COMs.

  3. Organic matter formed from hydrolysis of metal carbides of the iron peak of cosmic elemental abundance

    NASA Astrophysics Data System (ADS)

    Cataldo, Franco

    2003-01-01

    This work is a modern revisitation of an old idea of great chemists of the past such as Berthelot, Mendeleev, Cloez and Moissan: the formation of organic matter under pre-biotic conditions starting from the hydrolysis of metal carbides. This idea was originally proposed for the formation of petroleum in the Earth and was extended to other bodies of the solar system by Sokolov at the end of the 19th century. The reason for this revisitation lies in the fact that complex organic matter resembling a petroleum fraction may exist in certain protoplanetary nebulae. The present work starts with a survey of the theory of the inorganic origin of petroleum and reports on current evidence for its derivation from residues of formerly living matter, but also considers theories that admit both a biogenic and an abiogenic origin for petroleum. By considering the cosmic abundance of elements and the evidence concerning the presence of carbides in meteorites, we discuss the formation, structure and hydrolysis products derived from the metal carbides of the iron peak of cosmic elemental abundance. Chromium carbide (Cr3C2) has then been used as a model compound for all the key carbides of the iron peak of the cosmic abundance (Cr, Fe, Ni, V, Mn, Co) and it has been hydrolysed under different conditions and the hydrocarbons formed have been analysed using electronic spectroscopy, high-performance liquid chromatography with a diode-array detector (HPLC-DAD) and by Fourier-transform infrared (FT-IR) spectroscopy. Methane, a series of about 20 different alkenes with single and conjugated double bonds have been detected. Paraffins are formed simultaneously with the alkene series but no acetylenic hydrocarbons have been detected. This study confirms early works considering the easy hydrolysis of the carbides of Cr, Fe, Ni, Mn and Co with the formation of H2, a series of alkanes including methane and a series of alkenes including ethylene. The peculiar behaviour of copper carbide (copper is

  4. Ultra-Stable Organic Fluorophores for Single-Molecule Research

    PubMed Central

    Zheng, Qinsi; Juette, Manuel F.; Jockusch, Steffen; Wasserman, Michael R.; Zhou, Zhou; Altman, Roger B.; Blanchard, Scott C.

    2013-01-01

    Fluorescence provides a mechanism for achieving contrast in biological imaging that enables investigations of molecular structure, dynamics, and function at high spatial and temporal resolution. Small-molecule organic fluorophores have proven essential for such efforts and are widely used in advanced applications such as single-molecule and super-resolution microscopy. Yet, organic fluorophores, like all fluorescent species, exhibit instabilities in their emission characteristics, including blinking and photobleaching that limit their utility and performance. Here, we review the photophysics and photochemistry of organic fluorophores as they pertain to mitigating such instabilities, with a specific focus on the development of stabilized fluorophores through derivatization. Self-healing organic fluorophores, wherein the triplet state is intramolecularly quenched by a covalently attached protective agent, exhibit markedly improved photostabilities. We discuss the potential for further enhancements towards the goal of developing “ultra-stable” fluorophores spanning the visible spectrum and how such fluorophores are likely to impact the future of single-molecule research. PMID:24177677

  5. Observation of Organic Molecules at the Aerosol Surface.

    PubMed

    Wu, Yajing; Li, Wanyi; Xu, Bolei; Li, Xia; Wang, Han; McNeill, V Faye; Rao, Yi; Dai, Hai-Lung

    2016-06-16

    Organic molecules at the gas-particle interface of atmospheric aerosols influence the heterogeneous chemistry of the aerosol and impact climate properties. The ability to probe the molecules at the aerosol particle surface in situ therefore is important but has been proven challenging. We report the first successful observations of molecules at the surface of laboratory-generated aerosols suspended in air using the surface-sensitive technique second harmonic light scattering (SHS). As a demonstration, we detect trans-4-[4-(dibutylamino)styryl]-1-methylpyridinium iodide and determine its population and adsorption free energy at the surface of submicron aerosol particles. This work illustrates a new and versatile experimental approach for studying how aerosol composition may affect the atmospheric properties. PMID:27249662

  6. Footprint organization of chiral molecules on metallic surfaces

    NASA Astrophysics Data System (ADS)

    Uñac, R. O.; Rabaza, A. V. Gil; Vidales, A. M.; Zgrablich, G.

    2007-10-01

    We study the behavior of chiral molecules adsorbed on clean metallic surfaces using a lattice-gas model and Monte Carlo simulation. The aim is to model and simulate the structure (footprints and organization) formed by molecules on the surface as they adsorb. The model, which is applicable to chiral species like S- and R-alanine, or similar, discloses the conditions to generate different ordered phases that have been observed in experiments by other authors. In our model, each enantiomer may adsorb in two different configurations (species) and several effects are taken into account: inhibition, blockage of neighboring adsorptive sites (steric effects) and promotion of sites representing, in some sense, modifications in the surface properties due to molecule-surface interactions. These adsorption rules are inspired by the enantiomeric character of adsorbed species. We perform a systematic study of the different phases formed in order to qualitatively understand the mechanism for the formation of adsorbate structures experimentally found by other authors.

  7. Anatomy of a cluster IDP. Part 2: Noble gas abundances, trace element geochemistry, isotopic abundances, and trace organic chemistry of several fragments from L2008#5

    NASA Technical Reports Server (NTRS)

    Thomas, K. L.; Clemett, S. J.; Flynn, G. J.; Keller, L. P.; Mckay, David S.; Messenger, S.; Nier, A. O.; Schlutter, D. J.; Sutton, S. R.; Walker, R. M.

    1994-01-01

    The topics discussed include the following: noble gas content and release temperatures; trace element abundances; heating summary of cluster fragments; isotopic measurements; and trace organic chemistry.

  8. Carbon Dioxide Influence on the Thermal Formation of Complex Organic Molecules in Interstellar Ice Analogs

    NASA Astrophysics Data System (ADS)

    Vinogradoff, V.; Duvernay, F.; Fray, N.; Bouilloud, M.; Chiavassa, T.; Cottin, H.

    2015-08-01

    Interstellar ices are submitted to energetic processes (thermal, UV, and cosmic-ray radiations) producing complex organic molecules. Laboratory experiments aim to reproduce the evolution of interstellar ices to better understand the chemical changes leading to the reaction, formation, and desorption of molecules. In this context, the thermal evolution of an interstellar ice analogue composed of water, carbon dioxide, ammonia, and formaldehyde is investigated. The ice evolution during the warming has been monitored by IR spectroscopy. The formation of hexamethylenetetramine (HMT) and polymethylenimine (PMI) are observed in the organic refractory residue left after ice sublimation. A better understanding of this result is realized with the study of another ice mixture containing methylenimine (a precursor of HMT) with carbon dioxide and ammonia. It appears that carbamic acid, a reaction product of carbon dioxide and ammonia, plays the role of catalyst, allowing the reactions toward HMT and PMI formation. This is the first time that such complex organic molecules (HMT, PMI) are produced from the warming (without VUV photolysis or irradiation with energetic particles) of abundant molecules observed in interstellar ices (H2O, NH3, CO2, H2CO). This result strengthens the importance of thermal reactions in the ices’ evolution. HMT and PMI, likely components of interstellar ices, should be searched for in the pristine objects of our solar system, such as comets and carbonaceous chondrites.

  9. In Situ Detection of Organic Molecules on the Martian Surface With the Mars Organic Molecule Analyzer (MOMA) on Exomars 2018

    NASA Technical Reports Server (NTRS)

    Li, Xiang; Brinckerhoff, William B.; Pinnick, Veronica T; van Amerom, Friso H. W.; Danell, Ryan M.; Arevalo, Ricardo D., Jr.; Getty, Stephanie; Mahaffy, Paul R.

    2015-01-01

    The Mars Organic Molecule Analyzer (MOMA) investigation on the 2018 ExoMars rover will examine the chemical composition of samples acquired from depths of up to two meters below the martian surface, where organics may be protected from radiative and oxidative degradation. The MOMA instrument is centered around a miniaturized linear ion trap (LIT) that facilitates two modes of operation: i) pyrolysisgas chromatography mass spectrometry (pyrGC-MS); and, ii) laser desorptionionization mass spectrometry (LDI-MS) at ambient Mars pressures. The LIT also enables the structural characterization of complex molecules via complementary analytical capabilities, such as multi-frequency waveforms (i.e., SWIFT) and tandem mass spectrometry (MSMS). When combined with the complement of instruments in the rovers Pasteur Payload, MOMA has the potential to reveal the presence of a wide range of organics preserved in a variety of mineralogical environments, and to begin to understand the structural character and potential origin of those compounds.

  10. VizieR Online Data Catalog: Molecule and grain abundances (Marchand+, 2016)

    NASA Astrophysics Data System (ADS)

    Marchand, P.; Masson, J.; Chabrier, G.; Hennebelle, P.; Commercon, B.; Vaytet, N.

    2016-06-01

    chemistry.tar is the fortran code that was used to compute the following table. abundance.txt is a 3D table giving the abundances of several ionised species over a wide range of density, temperature and cosmic rays ionisation rate, useful in prestellar core collapse conditions. The table is organised as follow : density (cm-3), temperature (K), ionisation rate (s-1), abundance of electrons, abundances of ions (metal (Mg etc.), molecular ions (HCO+), H3+, H+, C+, He+, K+, Na+), abundances of grains (grains +, grain -, neutral grains) for bins 1 to 5 (see Sect. 2.4 of the paper), total abundances of grains, integration time. Format : '(31(e24.17,2X))' Reading : ------------------------------------------------------------------------- read(unit,format) nrho, nT, nX, nvar read(unit,format) read(unit,format) read(unit,format) read(unit,format) do i=1,nX do j=1,nT do k=1,nrho read(unit,format) rho(k), T(j), Xi(i), abundance(k,j,i,1:nvar) end do read(unit,format) read(unit,format) end do read(unit,format) read(unit,format) end do ---------------------------------------------------------------------- The description of each column can be found in the header of the file. You can compute the resistivities using read_table.f90, which creates a table of resistivities with the same parameters and adding the magnetic field dependance (see Sect. 2.1 of the paper for the formulae used). You can use it as a subroutine in your code. (4 data files).

  11. Ultrafast electron injection into photo-excited organic molecules.

    PubMed

    Cvetko, Dean; Fratesi, Guido; Kladnik, Gregor; Cossaro, Albano; Brivio, Gian Paolo; Venkataraman, Latha; Morgante, Alberto

    2016-08-10

    Charge transfer rates at metal/organic interfaces affect the efficiencies of devices for organic based electronics and photovoltaics. A quantitative study of electron transfer rates, which take place on the femtosecond timescale, is often difficult, especially since in most systems the molecular adsorption geometry is unknown. Here, we use X-ray resonant photoemission spectroscopy to measure ultrafast charge transfer rates across pyridine/Au(111) interfaces while also controlling the molecular orientation on the metal. We demonstrate that a bi-directional charge transfer across the molecule/metal interface is enabled upon creation of a core-exciton on the molecule with a rate that has a strong dependence on the molecular adsorption angle. Through density functional theory calculations, we show that the alignment of molecular levels relative to the metal Fermi level is dramatically altered when a core-hole is created on the molecule, allowing the lowest unoccupied molecular orbital to fall partially below the metal Fermi level. We also calculate charge transfer rates as a function of molecular adsorption geometry and find a trend that agrees with the experiment. These findings thus give insight into the charge transfer dynamics of a photo-excited molecule on a metal surface. PMID:27444572

  12. Design and engineering of organic molecules for customizable Terahertz tags

    NASA Astrophysics Data System (ADS)

    Ray, Shaumik; Dash, Jyotirmayee; Nallappan, Kathirvel; Kaware, Vaibhav; Basutkar, Nitin; Ambade, Ashootosh; Joshi, Kavita; Pesala, Bala

    2014-03-01

    Terahertz (THz) frequency band lies between the microwave and infrared region of the electromagnetic spectrum. Molecules having strong resonances in this frequency range are ideal for realizing "Terahertz tags" which can be easily incorporated into various materials. THz spectroscopy of molecules, especially at frequencies below 10 THz, provides valuable information on the low frequency vibrational modes, viz. intermolecular vibrational modes, hydrogen bond stretching, torsional vibrations in several chemical and biological compounds. So far there have been very few attempts to engineer molecules which can demonstrate customizable resonances in the THz frequency region. In this paper, Diamidopyridine (DAP) based molecules are used as a model system to demonstrate engineering of THz resonances (< 10 THz) by fine-tuning the molecular mass and bond strengths. Density Functional Theory (DFT) simulations have been carried out to explain the origin of THz resonances and factors contributing to the shift in resonances due to the addition of various functional groups. The design approach presented here can be easily extended to engineer various organic molecules suitable for THz tags application.

  13. Surface functionalization of aluminosilicate nanotubes with organic molecules

    PubMed Central

    Ma, Wei; Yah, Weng On; Otsuka, Hideyuki

    2012-01-01

    Summary The surface functionalization of inorganic nanostructures is an effective approach for enriching the potential applications of existing nanomaterials. Inorganic nanotubes attract great research interest due to their one-dimensional structure and reactive surfaces. In this review paper, recent developments in surface functionalization of an aluminosilicate nanotube, “imogolite”, are introduced. The functionalization processes are based on the robust affinity between phosphate groups of organic molecules and the aluminol (AlOH) surface of imogolite nanotubes. An aqueous modification process employing a water soluble ammonium salt of alkyl phosphate led to chemisorption of molecules on imogolite at the nanotube level. Polymer-chain-grafted imogolite nanotubes were prepared through surface-initiated polymerization. In addition, the assembly of conjugated molecules, 2-(5’’-hexyl-2,2’:5’,2’’-terthiophen-5-yl)ethylphosphonic acid (HT3P) and 2-(5’’-hexyl-2,2’:5’,2’’-terthiophen-5-yl)ethylphosphonic acid 1,1-dioxide (HT3OP), on the imogolite nanotube surface was achieved by introducing a phosphonic acid group to the corresponding molecules. The optical and photophysical properties of these conjugated-molecule-decorated imogolite nanotubes were characterized. Moreover, poly(3-hexylthiophene) (P3HT) chains were further hybridized with HT3P modified imogolite to form a nanofiber hybrid. PMID:22428100

  14. Luminescence stability of porous Si terminated by hydrophilic organic molecules

    NASA Astrophysics Data System (ADS)

    Matsumoto, Kimihisa; Kamiguchi, Masao; Kamiya, Kazuhide; Nomura, Takashi; Suzuki, Shinya

    2016-02-01

    The effects of the surface termination of a porous Si surface by propionic acid and by undecylenic acid on their hydrophilicity and luminescence stability were studied. In the measurements of the contact angle of water droplets on porous Si films, the hydrophilicity of porous Si is improved by the surface termination each types of organic molecule. The PL intensity of as-prepared porous Si decreased with increasing aging time in ambient air. As PL quenching involves PL blue shift and increasing Si-O bonds density, nonradiative recombination centers are formed in the surface oxide. After the hydrosilylation process of propionic acid and undecylenic acid, PL intensity decreased and became 30% that of as-prepared porous Si film. However, the PL intensity was stable and exceeded that of the as-prepared film after 1000 min of aging in the ambient air. The PL stabilities are contributed to the termination by organic molecules that inhibits surface oxidation.

  15. Molecule-displacive ferroelectricity in organic supramolecular solids

    PubMed Central

    Ye, Heng-Yun; Zhang, Yi; Noro, Shin-ichiro; Kubo, Kazuya; Yoshitake, Masashi; Liu, Zun-Qi; Cai, Hong-Ling; Fu, Da-Wei; Yoshikawa, Hirofumi; Awaga, Kunio; Xiong, Ren-Gen; Nakamura, Takayoshi

    2013-01-01

    Ferroelectricity is essential to many forms of current technology, ranging from sensors and actuators to optical or memory devices. In this circumstance, organic ferroelectrics are of particular importance because of their potential application in tomorrow's organic devices, and several pure organic ferroelectrics have been recently developed. However, some problems, such as current leakage and/or low working frequencies, make their application prospects especially for ferroelectric memory (FeRAM) not clear. Here, we describe the molecule-displacive ferroelectricity of supramolecular adducts of tartaric acid and 1,4-diazabicyclo[2.2.2]octane N,N′-dioxide. The adducts show large spontaneous polarization, high rectangularity of the ferroelectric hysteresis loops even at high operation frequency (10 kHz), and high performance in polarization switching up to 1 × 106 times without showing fatigue. It opens great perspectives in terms of applications, especially in organic FeRAM. PMID:23873392

  16. Molecule-displacive ferroelectricity in organic supramolecular solids

    NASA Astrophysics Data System (ADS)

    Ye, Heng-Yun; Zhang, Yi; Noro, Shin-Ichiro; Kubo, Kazuya; Yoshitake, Masashi; Liu, Zun-Qi; Cai, Hong-Ling; Fu, Da-Wei; Yoshikawa, Hirofumi; Awaga, Kunio; Xiong, Ren-Gen; Nakamura, Takayoshi

    2013-07-01

    Ferroelectricity is essential to many forms of current technology, ranging from sensors and actuators to optical or memory devices. In this circumstance, organic ferroelectrics are of particular importance because of their potential application in tomorrow's organic devices, and several pure organic ferroelectrics have been recently developed. However, some problems, such as current leakage and/or low working frequencies, make their application prospects especially for ferroelectric memory (FeRAM) not clear. Here, we describe the molecule-displacive ferroelectricity of supramolecular adducts of tartaric acid and 1,4-diazabicyclo[2.2.2]octane N,N'-dioxide. The adducts show large spontaneous polarization, high rectangularity of the ferroelectric hysteresis loops even at high operation frequency (10 kHz), and high performance in polarization switching up to 1 × 106 times without showing fatigue. It opens great perspectives in terms of applications, especially in organic FeRAM.

  17. 13 ENDOR studies of organic radicals in natural isotopic abundance

    NASA Astrophysics Data System (ADS)

    Kirste, Burkhard

    13C ENDOR studies of phenoxyls, galvinoxyls, triphenylmethyl radicals, nitroxides, and cyclosilane and semiquinone radical anions with natural isotopic distribution are reported. The method is described, and it is shown that 13C coupling constants can be measured precisely; in favorable cases even the determination of signs is possible by general TRIPLE resonance. Studies of the relaxation behavior of 13C ENDOR signals or measurements of hyperfine shifts in liquid-crystalline solutions yield information about dipolar hyperfine interactions and hence π spin populations which is of aid in assignments to molecular positions. Complete sets of 13C coupling constants have been determined for 2,4,6-tri- tert-butylphenoxyl and Coppinger's radical. For the central carbon atoms of tert-butyl groups, a Q parameter of Qτ-Bu C = -34 MHz is proposed, and for a 29Si atom in trimethylsilyl groups, QTMSSi = +49 MHz. Favorable conditions for natural-abundance 13C ENDOR experiments, e.g., small hyperfine anisotropies and use of deuterated compounds, and limitations of the method are discussed.

  18. Ocean metabolism and dissolved organic matter: How do small dissolved molecules persist in the ocean?

    NASA Astrophysics Data System (ADS)

    Benner, Ronald

    2010-05-01

    The ocean reservoir of dissolved organic matter (DOM) is among the largest global reservoirs (~700 Pg C) of reactive organic carbon. Marine primary production (~50 Pg C/yr) by photosynthetic microalgae and cyanobacteria is the major source of organic matter to the ocean and the principal substrate supporting marine food webs. The direct release of DOM from phytoplankton and other organisms as well as a variety of other processes, such as predation and viral lysis, contribute to the ocean DOM reservoir. Continental runoff and atmospheric deposition are relatively minor sources of DOM to the ocean, but some components of this material appear to be resistant to decomposition and to have a long residence time in the ocean. Concentrations of DOM are highest in surface waters and decrease with depth, a pattern that reflects the sources and diagenesis of DOM in the upper ocean. Most (70-80%) marine DOM exists as small molecules of low molecular weight (<1 kDalton). Surprisingly, high-molecular-weight (>1 kDalton) DOM is relatively enriched in major biochemicals, such as combined neutral sugars and amino acids, and is more bioavailable than low-molecular-weight DOM. The observed relationships among the size, composition, and reactivity of DOM have led to the size-reactivity continuum model, which postulates that diagenetic processes lead to the production of smaller molecules that are structurally altered and resistant to microbial degradation. The radiocarbon content of these small dissolved molecules also indicates these are the most highly aged components of DOM. Chemical signatures of bacteria are abundant in DOM and increase during diagenesis, indicating bacteria are an important source of slowly cycling biochemicals. Recent analyses of DOM isolates by ultrahigh-resolution mass spectrometry have revealed an incredibly diverse mixture of molecules. Carboxyl-rich alicyclic molecules are abundant in DOM, and they appear to be derived from diagenetically

  19. The gas phase origin of complex organic molecules precursors in prestellar cores

    NASA Astrophysics Data System (ADS)

    Bacmann, A.; Faure, A.

    2016-05-01

    Complex organic molecules (COMs) have long been observed in the warm regions surrounding nascent protostars. The recent discovery of oxygen-bearing COMs like methyl formate or dimethyl ether in prestellar cores (Bacmann et al. [2]), where gas and dust temperatures rarely exceed 10-15 K, has challenged the previously accepted models according to which COM formation relied on the diffusion of heavy radicals on warm (˜30 K) grains. Following these detections, new questions have arisen: do non-thermal processes play a role in increasing radical mobility or should new gas-phase routes be explored? The radicals involved in the formation of the aforementioned COMs, HCO and CH3O represent intermediate species in the grain-surface synthesis of methanol which proceeds via successive hydrogenations of CO molecules in the ice. We present here observations of methanol and its grain-surface precursors HCO, H2CO, CH3O in a sample of prestellar cores and derive their relative abundances. We find that the relative abundances HCO:H2CO:CH3O:CH3OH are constant across the core sample, close to 10:100:1:100. Our results also show that the amounts of HCO and CH3O are consistent with a gas-phase synthesis of these species from H2CO and CH3OH via radical-neutral or ion-molecule reactions followed by dissociative recombinations. Thus, while grain chemistry is necessary to explain the abundances of the parent volatile CH3OH, and possibly H2CO, the reactive species HCO and CH3O might be daughter molecules directly produced in the gas-phase.

  20. Preservation of organic molecules at Mars' near-surface

    NASA Astrophysics Data System (ADS)

    Freissinet, Caroline

    2016-07-01

    One of the biggest concerns for the in situ detection of organics on extraterrestrial environment is the preservation potential of the molecules at the surface and subsurface given the harsh radiation conditions and oxidants they are exposed to. The Mars Science Laboratory (MSL) search for hydrocarbons is designed to understand taphonomic windows of organic preservation in the Mars' near-surface. The Sample Analysis at Mars (SAM) instrument on the MSL Curiosity rover discovered chlorohydrocarbon indigenous to a mudstone drilled sample, Cumberland (CB). The discovery of chlorohydrocarbons in the martian surface means that reduced material with covalent bonds has survived despite the severe degrading conditions. However, the precursors of the chlorohydrocarbons detected by pyrolysis at CB remain unknown. Organic compounds in this ancient sedimentary rock on Mars could include polycyclic aromatic hydrocarbons and refractory organic material, either formed on Mars from igneous, hydrothermal, atmospheric, or biological processes or, alternatively, delivered directly to Mars via meteorites, comets, or interplanetary dust particles. It has been postulated that organic compounds in near-surface rocks may undergo successive oxidation reactions that eventually form metastable benzenecarboxylates, including phthalic and mellitic acids. These benzenecarboxylates are good candidates as the precursors of the chlorohydrocarbons detected in SAM pyrolysis at CB. Indeed, recently, SAM performed a derivatization experiments on a CB sample, using the residual vapor of N-methyl-N-tertbutylsilyltrifluoroacetamide (MTBSTFA) leaking into the system. The preliminary interpretations are compatible with the presence of benzocarboxylates, coincidently with long chain carboxylic acids and alcohols. The analysis of this interesting data set to identify these derivatization products, as well as future SAM measurements on Mt Sharp, should shed additional light on the chemical nature and the

  1. Modeling adsorption and reactions of organic molecules at metal surfaces.

    PubMed

    Liu, Wei; Tkatchenko, Alexandre; Scheffler, Matthias

    2014-11-18

    CONSPECTUS: The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdW(surf) method that accurately accounts for the collective electronic

  2. The census of complex organic molecules in the solar-type protostar IRAS16293-2422

    SciTech Connect

    Jaber, Ali A.; Ceccarelli, C.; Kahane, C.; Caux, E.

    2014-08-10

    Complex organic molecules (COMs) are considered to be crucial molecules, since they are connected with organic chemistry, at the basis of terrestrial life. More pragmatically, they are molecules which in principle are difficult to synthesize in harsh interstellar environments and, therefore, are a crucial test for astrochemical models. Current models assume that several COMs are synthesized on lukewarm grain surfaces (≳30-40 K) and released in the gas phase at dust temperatures of ≳100 K. However, recent detections of COMs in ≲20 K gas demonstrate that we still need important pieces to complete the puzzle of COMs formation. Here, we present a complete census of the oxygen- and nitrogen-bearing COMs, previously detected in different Interstellar Medium (ISM) regions, toward the solar-type protostar IRAS16293-2422. The census was obtained from the millimeter-submillimeter unbiased spectral survey TIMASSS. Of the 29 COMs searched for, 6 were detected: methyl cyanide, ketene, acetaldehyde, formamide, dimethyl ether, and methyl formate. Multifrequency analysis of the last five COMs provides clear evidence that they are present in the cold (≲30 K) envelope of IRAS16293-2422, with abundances of 0.03-2 × 10{sup –10}. Our data do not allow us to support the hypothesis that the COMs abundance increases with increasing dust temperature in the cold envelope, as expected if COMs were predominately formed on lukewarm grain surfaces. Finally, when also considering other ISM sources, we find a strong correlation over five orders of magnitude between methyl formate and dimethyl ether, and methyl formate and formamide abundances, which may point to a link between these two couples of species in cold and warm gas.

  3. The Census of Complex Organic Molecules in the Solar-type Protostar IRAS16293-2422

    NASA Astrophysics Data System (ADS)

    Jaber, Ali A.; Ceccarelli, C.; Kahane, C.; Caux, E.

    2014-08-01

    Complex organic molecules (COMs) are considered to be crucial molecules, since they are connected with organic chemistry, at the basis of terrestrial life. More pragmatically, they are molecules which in principle are difficult to synthesize in harsh interstellar environments and, therefore, are a crucial test for astrochemical models. Current models assume that several COMs are synthesized on lukewarm grain surfaces (gsim30-40 K) and released in the gas phase at dust temperatures of gsim100 K. However, recent detections of COMs in lsim20 K gas demonstrate that we still need important pieces to complete the puzzle of COMs formation. Here, we present a complete census of the oxygen- and nitrogen-bearing COMs, previously detected in different Interstellar Medium (ISM) regions, toward the solar-type protostar IRAS16293-2422. The census was obtained from the millimeter-submillimeter unbiased spectral survey TIMASSS. Of the 29 COMs searched for, 6 were detected: methyl cyanide, ketene, acetaldehyde, formamide, dimethyl ether, and methyl formate. Multifrequency analysis of the last five COMs provides clear evidence that they are present in the cold (lsim30 K) envelope of IRAS16293-2422, with abundances of 0.03-2 × 10-10. Our data do not allow us to support the hypothesis that the COMs abundance increases with increasing dust temperature in the cold envelope, as expected if COMs were predominately formed on lukewarm grain surfaces. Finally, when also considering other ISM sources, we find a strong correlation over five orders of magnitude between methyl formate and dimethyl ether, and methyl formate and formamide abundances, which may point to a link between these two couples of species in cold and warm gas.

  4. Effects of Perchlorate on Organic Molecules under Simulated Mars Conditions

    NASA Astrophysics Data System (ADS)

    Carrier, B. L.; Kounaves, S. P.

    2014-12-01

    Perchlorate (ClO4-) was discovered in the northern polar region of Mars by the Mars Phoenix Lander in 2008 and has also been recently detected by the Curiosity Rover in Gale Crater [1,2]. Perchlorate has also been shown to be formed under current Mars conditions via the oxidation of mineral chlorides, further supporting the theory that perchlorate is present globally on Mars [3]. The discovery of perchlorate on Mars has raised important questions about the effects of perchlorate on the survival and detection of organic molecules. Although it has been shown that pyrolysis in the presence of perchlorate results in the alteration or destruction of organic molecules [4], few studies have been conducted on the potential effects of perchlorate on organic molecules under martian surface conditions. Although perchlorate is typically inert under Mars-typical temperatures [5], perchlorate does absorb high energy UV radiation, and has been shown to decompose to form reactive oxychlorine species such as chlorite (ClO2-) when exposed to martian conditions including UV or ionizing radiation [6,7]. Here we investigate the effects of perchlorate on the organic molecules tryptophan, benzoic acid and mellitic acid in order to determine how perchlorate may alter these compounds under Mars conditions. Experiments are performed in a Mars Simulation Chamber (MSC) capable of reproducing the temperature, pressure, atmospheric composition and UV flux found on Mars. Soil simulants are prepared consisting of SiO2 and each organic, as well as varying concentrations of perchlorate salts, and exposed in the MSC. Subsequent to exposure in the MSC samples are leached and the leachate analyzed by HPLC and LC-MS to determine the degree of degradation of the original organic and the identity of any potential decomposition products formed by oxidation or chlorination. References: [1] Kounaves et al., J. Geophys. Res. Planets, Vol. 115, p. E00E10, 2010 [2] Glavin et al., J. Geophys. Res. Planets, Vol

  5. Electrophoretic assembly of organic molecules and composites for electrochemical supercapacitors.

    PubMed

    Su, Y; Zhitomirsky, I

    2013-02-15

    Electrophoretic deposition (EPD) method has been developed for the fabrication of 1-pyrenebutyric acid (PBH) films from aqueous solutions. The films can be deposited at constant voltage or potentiodynamic conditions. The method allowed the formation of 0.1-2 μm thick films, containing needle-shape PBH particles. The deposition mechanism involved the electrophoresis, pH decrease at the anode surface, charge neutralization and formation of insoluble PBH films. The film morphology and shape of the PBH particles are controlled by the π-π stacking mechanism of the polyaromatic PBH molecules. The important finding was the possibility of controlled EPD of multiwalled carbon nanotubes (MWCNTs) using PBH as a charging, dispersing and film forming agent. It was found that at low voltages or low PBH concentrations the deposits contained mainly MWCNT. The increase in the deposition voltage or/and PBH concentration resulted in co-deposition of MWCNT and needle-shape PBH particles. The new approach to the deposition of MWCNT was used for the fabrication of composite MnO(2)-MWCNT films for electrodes of electrochemical supercapacitors, which showed a specific capacitance of 250 F g(-1). The EPD method developed in this investigation paves the way for the deposition of other small organic molecules and composites and their applications in new materials and devices, utilizing functional properties of the organic molecules, CNT, and other advanced materials. PMID:23141761

  6. INTERSTELLAR ICES AS WITNESSES OF STAR FORMATION: SELECTIVE DEUTERATION OF WATER AND ORGANIC MOLECULES UNVEILED

    SciTech Connect

    Cazaux, S.; Spaans, M.; Caselli, P.

    2011-11-10

    Observations of star-forming environments revealed that the abundances of some deuterated interstellar molecules are markedly larger than the cosmic D/H ratio of 10{sup -5}. Possible reasons for this pointed to grain surface chemistry. However, organic molecules and water, which are both ice constituents, do not enjoy the same deuteration. For example, deuterated formaldehyde is very abundant in comets and star-forming regions, while deuterated water rarely is. In this paper, we explain this selective deuteration by following the formation of ices (using the rate equation method) in translucent clouds, as well as their evolution as the cloud collapses to form a star. Ices start with the deposition of gas-phase CO and O onto dust grains. While reaction of oxygen with atoms (H or D) or molecules (H{sub 2}) yields H{sub 2}O (HDO), CO only reacts with atoms (H and D) to form H{sub 2}CO (HDCO, D{sub 2}CO). As a result, the deuteration of formaldehyde is sensitive to the gas D/H ratio as the cloud undergoes gravitational collapse, while the deuteration of water strongly depends on the dust temperature at the time of ice formation. These results reproduce well the deuterium fractionation of formaldehyde observed in comets and star-forming regions and can explain the wide spread of deuterium fractionation of water observed in these environments.

  7. Organic molecules in the gas phase of dense interstellar clouds.

    PubMed

    Irvine, W M

    1995-03-01

    Since a previous COSPAR review on this subject, the number of molecular species identified by astronomers in dense interstellar clouds or in the envelopes expelled by evolved stars has grown from about eighty to approximately one hundred. Recent detections in stellar envelopes include the radical CP, the second phosphorus-containing astronomical molecule; SiN, the first astronomical molecule with a Si-N bond; and the HCCN radical. In the dense interstellar clouds recent detections or verifications of previous possible identifications include the H3O+ ion, which is a critical intermediary in the production of H2O and O2; the CCO radical, which is isoelectronic with HCCN; the SO+ ion, which appears to be diagnostic of shock chemistry; two new isomers of cyanoacetylene, HCCNC and CCCNH; and the two cumulenes H2C3 and H2C4. Some recent work is also described on the mapping of interstellar clouds in multiple molecular transitions in order to separate variations in chemical abundance from gradients in physical parameters. PMID:11539249

  8. Analysis of the Spatial Organization of Molecules with Robust Statistics

    PubMed Central

    Lagache, Thibault; Lang, Gabriel; Sauvonnet, Nathalie; Olivo-Marin, Jean-Christophe

    2013-01-01

    One major question in molecular biology is whether the spatial distribution of observed molecules is random or organized in clusters. Indeed, this analysis gives information about molecules’ interactions and physical interplay with their environment. The standard tool for analyzing molecules’ distribution statistically is the Ripley’s K function, which tests spatial randomness through the computation of its critical quantiles. However, quantiles’ computation is very cumbersome, hindering its use. Here, we present an analytical expression of these quantiles, leading to a fast and robust statistical test, and we derive the characteristic clusters’ size from the maxima of the Ripley’s K function. Subsequently, we analyze the spatial organization of endocytic spots at the cell membrane and we report that clathrin spots are randomly distributed while clathrin-independent spots are organized in clusters with a radius of , which suggests distinct physical mechanisms and cellular functions for each pathway. PMID:24349021

  9. On the Teneurin track: a new synaptic organization molecule emerges

    PubMed Central

    Mosca, Timothy J.

    2015-01-01

    To achieve proper synaptic development and function, coordinated signals must pass between the pre- and postsynaptic membranes. Such transsynaptic signals can be comprised of receptors and secreted ligands, membrane associated receptors, and also pairs of synaptic cell adhesion molecules. A critical open question bridging neuroscience, developmental biology, and cell biology involves identifying those signals and elucidating how they function. Recent work in Drosophila and vertebrate systems has implicated a family of proteins, the Teneurins, as a new transsynaptic signal in both the peripheral and central nervous systems. The Teneurins have established roles in neuronal wiring, but studies now show their involvement in regulating synaptic connections between neurons and bridging the synaptic membrane and the cytoskeleton. This review will examine the Teneurins as synaptic cell adhesion molecules, explore how they regulate synaptic organization, and consider how some consequences of human Teneurin mutations may have synaptopathic origins. PMID:26074772

  10. Small-molecule organic solar cells with improved stability

    NASA Astrophysics Data System (ADS)

    Song, Q. L.; Li, F. Y.; Yang, H.; Wu, H. R.; Wang, X. Z.; Zhou, W.; Zhao, J. M.; Ding, X. M.; Huang, C. H.; Hou, X. Y.

    2005-11-01

    A stable small-molecule organic photovoltaic device with structure of ITO⧹donor⧹acceptor⧹buffer⧹cathode is presented. A thin layer (˜60 Å) of tris-8-hydroxy-quinolinato aluminum (Alq 3) instead of bathocuproine (BCP) is adopted as the buffer of the device, resulting in 150 times longer lifetime. The power conversion efficiency of the device is 2.11% under 75 mW/cm 2 AM1.5G simulated illumination, and no perceptible efficiency degradation is observed for long-term storage of the device in vacuum or nitrogen-filled glove box. More effective blocking of Alq 3 than BCP against diffusion of cathode atoms and permeation of oxygen and/or water molecules is considered as the main reason for the improved performance of the new device.

  11. The abundance and organization of polypeptides associated with antigens of the Rh blood group system.

    PubMed

    Gardner, B; Anstee, D J; Mawby, W J; Tanner, M J; von dem Borne, A E

    1991-06-01

    Twelve murine monoclonal antibodies, which react with human red cells of common Rh phenotype but give weak or negative reactions with Rh null erythrocytes, were used in quantitative binding assays and competitive binding assays to investigate the abundance and organization of polypeptides involved in the expression of antigens of the Rh blood group system. Antibodies of the R6A-type (R6A, BRIC-69, BRIC-207) and the 2D10-type (MB-2D10, LA18.18, LA23.40) recognize related structures and 100,000-200,000 molecules of each antibody bind maximally to erythrocytes of common Rh phenotype. Antibodies of the BRIC-125 type (BRICs 32, 122, 125, 126, 168, 211) recognize structures that are unrelated to those recognized by R6A-type and 2D10-type antibodies and between 10,000 and 50,000 antibody molecules bind maximally to erythrocytes of the common Rh phenotype. The binding of antibodies of the R6A-type and the 2D10-type, but not of antibodies of the BRIC-125-type could be partially inhibited by human anti-D antibodies (polyclonal and monoclonal) and a murine anti-e-like antibody. These results are consistent with evidence (Moore & Green 1987; Avent et al., 1988b) that the Rh blood group antigens are associated with a complex that comprises two groups of related polypeptides of M(r) 30,000 and M(r) 35,000-100,000, respectively, and suggest that there are 1-2 x 10(5) copies of this complex per erythrocyte. The polypeptide recognized by antibodies of the BRIC-125 type is likely to be associated with this complex. PMID:9259831

  12. Lateral organization of cholesterol molecules in lipid-cholesterol assemblies.

    SciTech Connect

    Singh, Rajiv R. P.; Slepoy, Alexander; Sengupta, Pinaki; Cox, Daniel L.

    2005-05-01

    We present results of an off-lattice simulation of a two-component planar system, as a model for lateral organization of cholesterol molecules in lipid-cholesterol assemblies. We explore the existence of 'superlattice' structures even in fluid systems, in the absence of an underlying translational long-range order, and study their coupling to hexatic or bond-orientational order. We discuss our results in context of geometric superlattice theories and 'condensation complexes' in understanding a variety of experiments in artificial lipid-cholesterol assemblies.

  13. Transient magnetization of core excited organic molecules adsorbed on graphene

    NASA Astrophysics Data System (ADS)

    Ravikumar, Abhilash; Baby, Anu; Lin, He; Brivio, Gian Paolo; Fratesi, Guido

    This work presents a density functional theory based computational investigation of electronic and magnetic properties of physisorbed and chemisorbed organic molecules on graphene in the ground state and core excited one at low molecular coverage. For physisorbed molecules, where the interaction with graphene is dominated by van der Waals forces and the system is non-magnetic in the ground state, it is found that the valence electrons relax towards a spin polarized configuration upon excitation of a core-level electron. The magnetism depends on efficient electron transfer from graphene on the femtosecond time scale. On the contrary, when graphene is covalently functionalized, the system is magnetic in the ground state presenting two spin dependent mid gap states localized around the adsorption site. At variance with the physisorbed case upon core-level excitation, the LUMO of the molecule and the mid gap states of graphene hybridize and the relaxed valence shell is not magnetic anymore. This project has received funding from the European Union Seventh Framework Programme under grant agreement n∘ 607232 [THINFACE].

  14. Self-organized lattice of ordered quantum dot molecules

    SciTech Connect

    Lippen, T. von; Noetzel, R.; Hamhuis, G.J.; Wolter, J.H.

    2004-07-05

    Ordered groups of InAs quantum dots (QDs), lateral QD molecules, are created by self-organized anisotropic strain engineering of a (In,Ga)As/GaAs superlattice (SL) template on GaAs (311)B in molecular-beam epitaxy. During stacking, the SL template self-organizes into a two-dimensionally ordered strain modulated network on a mesoscopic length scale. InAs QDs preferentially grow on top of the nodes of the network due to local strain recognition. The QDs form a lattice of separated groups of closely spaced ordered QDs whose number can be controlled by the GaAs separation layer thickness on top of the SL template. The QD groups exhibit excellent optical properties up to room temperature.

  15. Stereochemically constrained complex organic molecules extracted from olivine crystal matrix

    NASA Astrophysics Data System (ADS)

    Gerasimenko, I.; Freund, F. T.; Imanaka, H.; Rodgers, R.

    2011-12-01

    Paradoxically, the dense solid state of magmatic minerals is a medium, in which organic synthesis can take place. The reason is that gas-fluid components such as H2O, CO/CO2/N2 and H2S are omnipresent in terrestrial magmatic environments. Any silicate mineral that crystallizes from such magmas will incorporate small quantities of the fluid-phase components in the form of structurally incompatible low-z impurities. During cooling the solute species undergo a redox conversion, resulting in chemically reduced low-z elements. To the extent that these low-z impurities are diffusively mobile, they will exsolve to the surface and/or to major structural defects inside the crystal matrix such as dislocations. Dislocations provide a 3-D structured environment, where the low-z impurities will tend to form stereochemically constrained polyatomic Cn-H-O-N-S entities, which we call organic protomolecules. In Nature, during weathering, such protomolecules will be released into the environment in the form of complex organic molecules. In our study we crush samples under clean conditions as a way to expose Cn-H-O-N-S entities at the fracture surfaces. We conduct identical experiments with selected large olivine single crystals, mm-sized olivine from peridiotite nodules from the San Carlos Volcanic Field, Arizona, and the vesiculated basalt that had carried the nodules upward in the volcanic conduit. We Soxhlet-extract the crushed powders with water, THF and ethyl acetate. The extracts are analyzed at the FTICR-MS facility at Florida State University using ultrahigh resolution Mass Spectrometry techniques capable of determining the chemical composition of the organic molecules up to 600 amu and more. So far we have found several analog sequences of oxygen-rich aliphatic hydrocarbons, families with up to 34 carbon atoms, probably poly-carboxylic acids, and some families containing sulfur.

  16. The activated sludge ecosystem contains a core community of abundant organisms

    PubMed Central

    Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

    2016-01-01

    Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal. PMID:26262816

  17. Simple Organic Molecules as Catalysts for Enantioselective Synthesis of Amines and Alcohols

    PubMed Central

    Silverio, Daniel L.; Torker, Sebastian; Pilyugina, Tatiana; Vieira, Erika M.; Snapper, Marc L.; Haeffner, Fredrik; Hoveyda, Amir H.

    2012-01-01

    The discovery of new catalysts that can generate complex organic compounds via enantioselective transformations is central to advances in the life sciences;i for this reason, many chemists try to discover catalysts that can be used to produce chiral molecules with a strong preference for one mirror image isomer.ii The ideal catalyst should be devoid of precious elementsiii and should bring reactions to completion in a few hours using operationally simple procedures. In this manuscript, we introduce a set of small organic molecules that can catalyze reactions of unsaturated organoboron reagents with imines and carbonyls; the products of the reactions are enantiomerically pure amines and alcohols, which can be used to synthesize more complex, biologically active molecules. A distinguishing feature of this new catalyst class is the presence of a 'key' proton embedded within their structure. The catalyst is derived from the abundant amino acid valine and was prepared in large quantities in four steps using inexpensive reagents. Reactions are scalable, do not demand stringent conditions, and can be performed with as little as 0.25 mol % catalyst in less than six hours at room temperature to generate products in >85% yield and ≥97:3 enantiomeric ratio. The efficiency, selectivity and operational simplicity of the transformations and the range of boron-based reagents render this advance vital to future progress in chemistry, biology and medicine. PMID:23407537

  18. Cometary delivery of organic molecules to the early earth

    NASA Technical Reports Server (NTRS)

    Chyba, Christopher F.; Thomas, Paul J.; Sagan, Carl; Brookshaw, Leigh

    1990-01-01

    It has long been speculated that earth accreted prebiotic organic molecules important for the origins of life from impacts of carbonaceous asteroids and comets during the period of heavy bombardment 4.5 x 10 to the 9th to 3.8 x 10 to the 9th years ago. A comprehensive treatment of comet-asteroid interaction with the atmosphere, surface impact, and resulting organic pyrolysis demonstrates that organics will not survive impacts at velocities greater than about 10 kilometers per second and that even comets and asteroids as small as 100 meters in radius cannot be aerobraked to below this velocity in 1-bar atmospheres. However, for plausible dense (10-bar carbon dioxide) early atmospheres, it is found that 4.5 x 10 to the 9th years ago earth was accreting intact cometary organics at a rate of at least about 10 to the 6th to 10 to the 7th kilograms per year, a flux that thereafter declined with a half-life of about 10 to the 8th years. These results may be put in context by comparison with terrestrial oceanic and total biomasses, about 3 x 10 to the 12th kilograms and about 6 x 10 to the 14th kilograms, respectively.

  19. Optical and Transport Properties of Organic Molecules: Methods and Applications

    NASA Astrophysics Data System (ADS)

    Strubbe, David Alan

    Organic molecules are versatile and tunable building blocks for technology, in nanoscale and bulk devices. In this dissertation, I will consider some important applications for organic molecules involving optical and transport properties, and develop methods and software appropriate for theoretical calculations of these properties. Specifically, we will consider second-harmonic generation, a nonlinear optical process; photoisomerization, in which absorption of light leads to mechanical motion; charge transport in junctions formed of single molecules; and optical excitations in pentacene, an organic semiconductor with applications in photovoltaics, optoelectronics, and flexible electronics. In the Introduction (Chapter 1), I will give an overview of some phenomenology about organic molecules and these application areas, and discuss the basics of the theoretical methodology I will use: density-functional theory (DFT), time-dependent density-functional theory (TDDFT), and many-body perturbation theory based on the GW approximation. In the subsequent chapters, I will further discuss, develop, and apply this methodology. 2. I will give a pedagogical derivation of the methods for calculating response properties in TDDFT, with particular focus on the Sternheimer equation, as will be used in subsequent chapters. I will review the many different response properties that can be calculated (dynamic and static) and the appropriate perturbations used to calculate them. 3. Standard techniques for calculating response use either integer occupations (as appropriate for a system with an energy gap) or fractional occupations due to a smearing function, used to improve convergence for metallic systems. I will present a generalization which can be used to compute response for a system with arbitrary fractional occupations. 4. Chloroform (CHCl3) is a small molecule commonly used as a solvent in measurements of nonlinear optics. I computed its hyperpolarizability for second

  20. Inferring the abundances of ClO and HO sub 2 from Spacelab 3 atmospheric trace molecule spectroscopy observations

    SciTech Connect

    Allen, M.; Delitsky, M.L. )

    1991-02-20

    The vertical distributions of the important highly reactive stratospheric species, ClO and HO{sub 2}, have been inferred from Spacelab 3 (May 1985) Atmospheric Trace Molecule Spectroscopy (ATMOS) measurements of more detectable radical and reservoir species. A simple steady state algebraic expression for ClO, utilizing the observed ClONO{sub 2}/NO{sub 2} abundance ratio, approximates the ClO results of a time-dependent photochemical model at sunset (30{degree}N). Balloon measurements of ClO and comparisons of time-dependent photochemical model calculations of ClONO{sub 2} and HCl with the corresponding ATMOS profiles suggest that the actual ClO values are less than the time-dependent model profiles for ClO at sunset and sunrise (47{degree}S). Errors in the current model simulation of the partitioning among the principal free chlorine species (HCl, ClONO{sub 2}, and ClO) are indicated. However, a comparison of model results with observations of HOCl suggests that the calculated ClO abundance is not a significant overestimate of actual values. A similar methodology is applied to inferring the HO{sub 2} distribution, either algebraically using the ATMOS-measured HO{sub 2}NO{sub 2}/NO{sub 2} abundance ratio or numerically utilizing the time-dependent model. The algebraic results agree with the time-dependent model values to better than a factor of 2 at sunrise. The accuracy of the time-dependent model calculations of HO{sub 2} is suggested by the agreement between model results and ATMOS observations for HO{sub 2}NO{sub 2} and balloon measurements of HO{sub 2}. This confirms for the first time the procedure suggested previously by a number of authors of deriving HO{sub x} abundances from observed fields of O{sub 3} and H{sub 2}O.

  1. Chemical solver to compute molecule and grain abundances and non-ideal MHD resistivities in prestellar core-collapse calculations

    NASA Astrophysics Data System (ADS)

    Marchand, P.; Masson, J.; Chabrier, G.; Hennebelle, P.; Commerçon, B.; Vaytet, N.

    2016-07-01

    We develop a detailed chemical network relevant to calculate the conditions that are characteristic of prestellar core collapse. We solve the system of time-dependent differential equations to calculate the equilibrium abundances of molecules and dust grains, with a size distribution given by size-bins for these latter. These abundances are used to compute the different non-ideal magneto-hydrodynamics resistivities (ambipolar, Ohmic and Hall), needed to carry out simulations of protostellar collapse. For the first time in this context, we take into account the evaporation of the grains, the thermal ionisation of potassium, sodium, and hydrogen at high temperature, and the thermionic emission of grains in the chemical network, and we explore the impact of various cosmic ray ionisation rates. All these processes significantly affect the non-ideal magneto-hydrodynamics resistivities, which will modify the dynamics of the collapse. Ambipolar diffusion and Hall effect dominate at low densities, up to nH = 1012 cm-3, after which Ohmic diffusion takes over. We find that the time-scale needed to reach chemical equilibrium is always shorter than the typical dynamical (free fall) one. This allows us to build a large, multi-dimensional multi-species equilibrium abundance table over a large temperature, density and ionisation rate ranges. This table, which we make accessible to the community, is used during first and second prestellar core collapse calculations to compute the non-ideal magneto-hydrodynamics resistivities, yielding a consistent dynamical-chemical description of this process. The multi-dimensional multi-species equilibrium abundance table and a copy of the code are only 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/592/A18

  2. High performance small-molecule organic thin film transistors

    NASA Astrophysics Data System (ADS)

    Kuo, Chung-Chen

    The roadmap of developing microelectronics has a new branch: organic electronics. Organic electronics, which utilizes the electrical properties of organic materials in the active or passive layers, is an emerging technology that has received much attention. In conjunction with today's demands for new materials and devices, many technologies have emerged for developing organic electronics and consolidating applications and markets. An organic thin-film transistor is the essential device in this paradigm in addition to organic photodiodes and organic light emitting diodes. This thesis presents advances made in design and fabrication of organic thin-film transistors (OTFTs) using small-molecule organic semiconductors (pentacene, anthradithiophene, and their derivatives) as the active layer with record device performance. In this work OTFT test structures fabricated on oxidized silicon substrates were utilized to provide a convenient substrate, gate contact, and gate insulator for the processing and characterization of vapor-deposited organic materials and their transistors. By developing a gate dielectric treatment using silane coupling agents the performance and yield of pentacene OTFTs was improved and a field-effect mobility of larger than 2 cm2/V-s was achieved. Such device performance is comparable to a-Si:H TFTs and have the potential for electronic applications. In addition, the first direct photolithographic process for top contacts to pentacene OTFTs on oxidized silicon with an acceptable performance (a field-effect mobility of 0.3 cm2/V-s, an on/off current ratio of 10 7, and a subthreshold slope of 1 V/decade) was developed. The multiple layer photoresist process demonstrated the feasibility of creating source and drain metallic electrodes on vapor-deposited pentacene thin films with a resolution less than 10 mum. Subsequently, solution-processed OTFTs were then investigated and high performance transistors, with field-effect mobilities > 1 cm2/V-s and an

  3. Consequences of organic farming and landscape heterogeneity for species richness and abundance of farmland birds.

    PubMed

    Smith, Henrik G; Dänhardt, Juliana; Lindström, Ake; Rundlöf, Maj

    2010-04-01

    It has been suggested that organic farming may benefit farmland biodiversity more in landscapes that have lost a significant part of its former landscape heterogeneity. We tested this hypothesis by comparing bird species richness and abundance during the breeding season in organic and conventional farms, matched to eliminate all differences not directly linked to the farming practice, situated in either homogeneous plains with only a little semi-natural habitat or in heterogeneous farmland landscapes with abundant field borders and semi-natural grasslands. The effect of farm management on species richness interacted with landscape structure, such that there was a positive relationship between organic farming and diversity only in homogeneous landscapes. This pattern was mainly dependent on the species richness of passerine birds, in particular those that were invertebrate feeders. Species richness of non-passerines was positively related to organic farming independent of the landscape context. Bird abundance was positively related to landscape heterogeneity but not to farm management. This was mainly because the abundance of passerines, particularly invertebrate feeders, was positively related to landscape heterogeneity. We suggest that invertebrate feeders particularly benefit from organic farming because of improved foraging conditions through increased invertebrate abundances in otherwise depauperate homogeneous landscapes. Although many seed-eaters also benefit from increased insect abundance, they may also utilize crop seed resources in homogeneous landscapes and conventional farms. The occurrence of an interactive effect of organic farming and landscape heterogeneity on bird diversity will have consequences for the optimal allocation of resources to restore the diversity of farmland birds. PMID:20213151

  4. Detection of low abundant mutations in DNA using single-molecule FRET and ligase detection reactions

    NASA Astrophysics Data System (ADS)

    Wabuyele, Musundi B.; Farquar, Hannah; Stryjewski, Wieslaw J.; Hammer, Robert P.; Soper, Steven A.; Cheng, Yu-Wei; Barany, Francis

    2003-06-01

    New strategies for analyzing molecular signatures of disease states in real time using single pair fluorescence resonance energy transfer (spFRET) were developed to rapidly detect point mutations in unamplified genomic DNA (DNA diagnostics). The assay was carried out using allele-specific primers, which flanked the point mutation in the target gene fragment and were ligated using a thremostable ligase enzyme only when the genomic DNA carried this mutation (ligase detection reaction, LDR). We coupled LDR with spFRET to identify a single base mutation in codon 12 of a K-ras oncogene that has high diagnostic value for colorectal cancers. A simple diode laser-based fluorescence system capable of interrogating single fluorescent molecules undergoing FRET was used to detect photon bursts generated from the MB probes formed upon ligation. We demonstrated the ability to rapidly discriminate single base differences in heterogeneous populations having as little as 600 copies of human genomic DNA without PCR amplification. Single base difference in the K-ras gene was discriminated in less than 5 min at a frequency of 1 mutant DNA per 10 normals using only a single LDR thermal cycle of genomic DNA. Real time analyses of point mutations were also performed in PMMA microfluidic device.

  5. ORGANIC MOLECULES AND WATER IN THE INNER DISKS OF T TAURI STARS

    SciTech Connect

    Carr, John S.; Najita, Joan R. E-mail: najita@noao.edu

    2011-06-01

    We report high signal-to-noise Spitzer Infrared Spectrograph spectra of a sample of 11 classical T Tauri stars. Molecular emission from rotational transitions of H{sub 2}O and OH and rovibrational bands of simple organic molecules (CO{sub 2}, HCN, C{sub 2}H{sub 2}) is common among the sources in the sample. The emission shows a range in both flux and line-to-continuum ratio for each molecule and in the flux ratios of different molecular species. The gas temperatures (200-800 K) and emitting areas we derive are consistent with the emission originating in a warm disk atmosphere in the inner planet formation region at radii <2 AU. The H{sub 2}O emission appears to form under a limited range of excitation conditions, as demonstrated by the similarity in relative strengths of H{sub 2}O features from star to star and the narrow range in derived temperature and column density. Emission from highly excited rotational levels of OH is present in all stars; the OH emission flux increases with the stellar accretion rate, and the OH/H{sub 2}O flux ratio shows a relatively small scatter. We interpret these results as evidence for OH production via FUV photodissociation of H{sub 2}O in the disk surface layers. No obvious explanation is found for the observed range in the relative emission strengths of different organic molecules or in their strength with respect to water. We put forward the possibility that these variations reflect a diversity in organic abundances due to star-to-star differences in the C/O ratio of the inner disk gas. Stars with the largest HCN/H{sub 2}O flux ratios in our sample have the largest disk masses. While larger samples are required to confirm this, we speculate that such a trend could result if higher mass disks are more efficient at planetesimal formation and sequestration of water in the outer disk, leading to enhanced C/O ratios and abundances of organic molecules in the inner disk. A comparison of our derived HCN-to-H{sub 2}O column density ratio

  6. Organic molecules in the Sheepbed Mudstone, Gale Crater, Mars

    PubMed Central

    Freissinet, C; Glavin, D P; Mahaffy, P R; Miller, K E; Eigenbrode, J L; Summons, R E; Brunner, A E; Buch, A; Szopa, C; Archer, P D; Franz, H B; Atreya, S K; Brinckerhoff, W B; Cabane, M; Coll, P; Conrad, P G; Des Marais, D J; Dworkin, J P; Fairén, A G; François, P; Grotzinger, J P; Kashyap, S; ten Kate, I L; Leshin, L A; Malespin, C A; Martin, M G; Martin-Torres, F J; McAdam, A C; Ming, D W; Navarro-González, R; Pavlov, A A; Prats, B D; Squyres, S W; Steele, A; Stern, J C; Sumner, D Y; Sutter, B; Zorzano, M-P

    2015-01-01

    The Sample Analysis at Mars (SAM) instrument on board the Mars Science Laboratory Curiosity rover is designed to conduct inorganic and organic chemical analyses of the atmosphere and the surface regolith and rocks to help evaluate the past and present habitability potential of Mars at Gale Crater. Central to this task is the development of an inventory of any organic molecules present to elucidate processes associated with their origin, diagenesis, concentration, and long-term preservation. This will guide the future search for biosignatures. Here we report the definitive identification of chlorobenzene (150–300 parts per billion by weight (ppbw)) and C2 to C4 dichloroalkanes (up to 70 ppbw) with the SAM gas chromatograph mass spectrometer (GCMS) and detection of chlorobenzene in the direct evolved gas analysis (EGA) mode, in multiple portions of the fines from the Cumberland drill hole in the Sheepbed mudstone at Yellowknife Bay. When combined with GCMS and EGA data from multiple scooped and drilled samples, blank runs, and supporting laboratory analog studies, the elevated levels of chlorobenzene and the dichloroalkanes cannot be solely explained by instrument background sources known to be present in SAM. We conclude that these chlorinated hydrocarbons are the reaction products of Martian chlorine and organic carbon derived from Martian sources (e.g., igneous, hydrothermal, atmospheric, or biological) or exogenous sources such as meteorites, comets, or interplanetary dust particles. Key Points First in situ evidence of nonterrestrial organics in Martian surface sediments Chlorinated hydrocarbons identified in the Sheepbed mudstone by SAM Organics preserved in sample exposed to ionizing radiation and oxidative condition PMID:26690960

  7. Organic molecules in the Sheepbed Mudstone, Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Freissinet, C.; Glavin, D. P.; Mahaffy, P. R.; Miller, K. E.; Eigenbrode, J. L.; Summons, R. E.; Brunner, A. E.; Buch, A.; Szopa, C.; Archer, P. D., Jr.; Franz, H. B.; Atreya, S. K.; Brinckerhoff, W. B.; Cabane, M.; Coll, P.; Conrad, P. G.; Des Marais, D. J.; Dworkin, J. P.; Fairén, A. G.; François, P.; Grotzinger, J. P.; Kashyap, S.; ten Kate, I. L.; Leshin, L. A.; Malespin, C. A.; Martin, M. G.; Martin-Torres, J. F.; McAdam, A. C.; Ming, D. W.; Navarro-González, R.; Pavlov, A. A.; Prats, B. D.; Squyres, S. W.; Steele, A.; Stern, J. C.; Sumner, D. Y.; Sutter, B.; Zorzano, M.-P.; MSL Science Team

    2015-03-01

    The Sample Analysis at Mars (SAM) instrument on board the Mars Science Laboratory Curiosity rover is designed to conduct inorganic and organic chemical analyses of the atmosphere and the surface regolith and rocks to help evaluate the past and present habitability potential of Mars at Gale Crater. Central to this task is the development of an inventory of any organic molecules present to elucidate processes associated with their origin, diagenesis, concentration, and long-term preservation. This will guide the future search for biosignatures. Here we report the definitive identification of chlorobenzene (150-300 parts per billion by weight (ppbw)) and C2 to C4 dichloroalkanes (up to 70 ppbw) with the SAM gas chromatograph mass spectrometer (GCMS) and detection of chlorobenzene in the direct evolved gas analysis (EGA) mode, in multiple portions of the fines from the Cumberland drill hole in the Sheepbed mudstone at Yellowknife Bay. When combined with GCMS and EGA data from multiple scooped and drilled samples, blank runs, and supporting laboratory analog studies, the elevated levels of chlorobenzene and the dichloroalkanes cannot be solely explained by instrument background sources known to be present in SAM. We conclude that these chlorinated hydrocarbons are the reaction products of Martian chlorine and organic carbon derived from Martian sources (e.g., igneous, hydrothermal, atmospheric, or biological) or exogenous sources such as meteorites, comets, or interplanetary dust particles.

  8. Proton Transfer Rate Coefficient Measurements of Selected Volatile Organic Molecules

    NASA Astrophysics Data System (ADS)

    Brooke, G.; Popović, S.; Vušković, L.

    2002-05-01

    We have developed an apparatus based on the selected ion flow tube (SIFT)footnote D. Smith and N.G. Adams, Ads. At. Mol. Phys. 24, 1 (1987). that allows the study of proton transfer between various positive ions and volatile organic molecules. Reactions in the flow tube occur at pressures of approximately 300 mTorr, eliminating the requirement of thermal beam production. The proton donor molecule H_3O^+ has been produced using several types of electrical discharges in water vapor, such as a capacitively coupled RF discharge and a DC hollow cathode discharge. Presently we are developing an Asmussen-type microwave cavity discharge using the components of a standard microwave oven that has the advantages of simple design and operation, as well as low cost. We will be presenting the results of the microwave cavity ion source to produce H_3O^+, and compare it to the other studied sources. In addition, we will be presenting a preliminary measurement of the proton transfer rate coefficient in the reaction of H_3O^+ with acetone and methanol.

  9. Spectromicroscopy Study of the Organic Molecules Utilizing Polarized Radiation

    SciTech Connect

    Hsu, Y.J.; Wei, D.H.; Yin, G.C.; Chung, S.C.; Hu, W.S.; Tao, Y.T.

    2004-05-12

    Spectromicroscopy combined with polarized synchrotron radiation is a powerful tool for imaging and characterizing the molecular properties on surface. In this work we utilized the photoemission electron microscopy (PEEM) with linear polarized radiation provided by an elliptically polarized undulator to investigate the molecular orientations of pentacene on self-assembled monolayer (SAMs) modified gold surface and to observe the cluster domain of mixed monolayers after reorganization on silver. Varying the electric vector parallel or perpendicular to the surface, the relative intensity of {pi}* and {sigma}* transition in carbon K-edge can be used to determine the orientation of the planar-shaped pentacene molecule or long carbon chain of carboxylic acids which are important for organic semiconductor.

  10. Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules.

    PubMed

    Bereau, Tristan; Andrienko, Denis; von Lilienfeld, O Anatole

    2015-07-14

    Accurate representation of the molecular electrostatic potential, which is often expanded in distributed multipole moments, is crucial for an efficient evaluation of intermolecular interactions. Here we introduce a machine learning model for multipole coefficients of atom types H, C, O, N, S, F, and Cl in any molecular conformation. The model is trained on quantum-chemical results for atoms in varying chemical environments drawn from thousands of organic molecules. Multipoles in systems with neutral, cationic, and anionic molecular charge states are treated with individual models. The models' predictive accuracy and applicability are illustrated by evaluating intermolecular interaction energies of nearly 1,000 dimers and the cohesive energy of the benzene crystal. PMID:26575759

  11. Near-infrared spectroscopy of M dwarfs. II. H2O molecule as an abundance indicator of oxygen†

    NASA Astrophysics Data System (ADS)

    Tsuji, Takashi; Nakajima, Tadashi; Takeda, Yoichi

    2015-04-01

    Based on the near-infrared spectra (R ≈ 20000) of M dwarfs, oxygen abundances are determined from the rovibrational lines of H2O. Although H2O lines in M dwarfs are badly blended with each other and the continuum levels are depressed appreciably by the collective effect of the numerous H2O lines themselves, quantitative analysis of H2O lines has been carried out by referring to the pseudo-continua, consistently defined on the observed and theoretical spectra. For this purpose, the pseudo-continuum on the theoretical spectrum has been evaluated accurately by the use of the recent high-precision H2O line-list. Then, we propose a simple and flexible method of analyzing the equivalent widths (EWs) of blended features (i.e., not necessarily limited to single lines) by the use of a mini-curve-of-growth (CG), which is a small portion of the usual CG around the observed EW. The mini-CG is generated by using the theoretical EWs evaluated from the synthetic spectrum in exactly the same way as the EWs are measured from the observed spectrum. The observed EW is converted to the abundance by the use of the mini-CG, and the process is repeated for all the observed EWs line-by-line or blend-by-blend. In cool M dwarfs, almost all the oxygen atoms left after CO formation are in stable H2O molecules, which suffer little change for the uncertainties due to imperfect modelling of the photospheres. Thus the numerous H2O lines are excellent abundance indicators of oxygen. The oxygen abundances are determined to be log AO (AO = NO/NH) between -3.5 and -3.0 in 38 M dwarfs, but cannot be determined in four early M dwarfs in which H2O lines are detected only marginally. The resulting log AO/AC values plotted against log AC appear to be systematically smaller in the carbon-rich M dwarfs, showing the different formation histories of oxygen and carbon in the chemical evolution of the Galactic disk. Also, AO/AFe ratios in most M dwarfs are closer to the solar AO/AFe ratio, based on the

  12. Linear Ion Trap for the Mars Organic Molecule Analyzer

    NASA Astrophysics Data System (ADS)

    Brinckerhoff, William; Arevalo, Ricardo; Danell, Ryan; van Amerom, Friso; Pinnick, Veronica; Li, Xiang; Hovmand, Lars; Getty, Stephanie; Mahaffy, Paul; Goesmann, Fred; Steininger, Harald

    2014-05-01

    The 2018 ExoMars rover mission includes the Mars Organic Molecule Analyzer (MOMA) investigation. MOMA will examine the chemical composition of samples acquired from depths of up to two meters below the martian surface, where organics may be protected from radiative and oxidative degradation. When combined with the complement of instruments in the rover's Pasteur Payload, MOMA has the potential to reveal the presence of a wide range of organics preserved in a variety of mineralogical environments, and to begin to understand the structural character and potential origin of those compounds. MOMA includes a linear, or 2D, ion trap mass spectrometer (ITMS) that is designed to analyze molecular composition of (i) gas evolved from pyrolyzed powder samples and separated on a gas chromatograph and (ii) ions directly desorbed from solid samples at Mars ambient pressure using a pulsed laser and a fast-valve capillary ion inlet system. This "dual source" approach gives MOMA unprecedented breadth of detection over a wide range of molecular weights and volatilities. Analysis of nonvolatile, higher-molecular weight organics such as carboxylic acids and peptides even in the presence of significant perchlorate concentrations is enabled by the extremely short (~1 ns) pulses of the desorption laser. Use of the ion trap's tandem mass spectrometry mode permits selective focus on key species for isolation and controlled fragmentation, providing structural analysis capabilities. The flight-like engineering test unit (ETU) of the ITMS, now under construction, will be used to verify breadboard performance with high fidelity, while simultaneously supporting the development of analytical scripts and spectral libraries using synthetic and natural Mars analog samples guided by current results from MSL. ETU campaign data will strongly advise the specifics of the calibration applied to the MOMA flight model as well as the science operational procedures during the mission.

  13. Equilibrium 2H/ 1H fractionations in organic molecules: I. Experimental calibration of ab initio calculations

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Sessions, Alex L.; Nielsen, Robert J.; Goddard, William A., III

    2009-12-01

    Carbon-bound hydrogen in sedimentary organic matter can undergo exchange over geologic timescales, altering its isotopic composition. Studies investigating the natural abundance distribution of 1H and 2H in such molecules must account for this exchange, which in turn requires quantitative knowledge regarding the endpoint of exchange, i.e., the equilibrium isotopic fractionation factor ( α eq). To date, relevant data have been lacking for molecules larger than methane. Here we describe an experimental method to measure α eq for C-bound H positions adjacent to carbonyl group (H α) in ketones. H at these positions equilibrates on a timescale of days as a result of keto-enol tautomerism, allowing equilibrium 2H/ 1H distributions to be indirectly measured. Molecular vibrations for the same ketone molecules are then computed using Density Functional Theory at the B3LYP/6-311G∗∗ level and used to calculate α eq values for H α. Comparison of experimental and computational results for six different straight and branched ketones yields a temperature-dependent linear calibration curve with slope = 1.081-0.00376 T and intercept = 8.404-0.387 T, where T is temperature in degrees Celsius. Since the dominant systematic error in the calculation (omission of anharmonicity) is of the same size for ketones and C-bound H in most other linear compounds, we propose that this calibration can be applied to analogous calculations for a wide variety of organic molecules with linear carbon skeletons for temperatures below 100 °C. In a companion paper ( Wang et al., 2009) we use this new calibration dataset to calculate the temperature-dependent equilibrium isotopic fractionation factors for a range of linear hydrocarbons, alcohols, ethers, ketones, esters and acids.

  14. SEASONAL ABUNDANCE OF ORGANIC MOLECULAR MARKERS IN URBAN PARTICULATE MATTER FROM PHILADELPHIA, PA

    EPA Science Inventory

    Organic molecular markers were measured in airborne particulate matter (PM10) from the City of Philadelphia North Broad Street air quality monitoring site to identify the seasonal abundances of key tracer compounds together with their dominant sources. Daily PM10...

  15. Detection, Identification and Correlation of Complex Organic Molecules in 32 Interstellar Clouds Using Submm Observations

    NASA Astrophysics Data System (ADS)

    Wehres, Nadine; Wang, Shiya; Rad, Mary Lynn; Sanders, James; Kroll, Jay A.; Laas, Jacob; Hays, Brian; Cross, Trevor; Lis, D. C.; Herbst, Eric; Widicus Weaver, Susanna L.

    2014-06-01

    We present spectral line surveys of 32 galactic sources using the Caltech Submillimeter Observatory (CSO) and the HIFI instrument on the Herschel Space Observatory. This study covers the 220 -- 265 GHz frequency range using the CSO, as well as higher frequencies, 645 -- 676 GHz and 1.14 THz -- 1.19 THz using the HIFI instrument. Deconvolution of the double sideband spectra was performed using the CLASS program and the Herschel/HIFI pipeline. Analysis of the data sets was performed using Global Optimization and Broadband Analysis Software for Interstellar Chemistry (GOBASIC), a new software program developed by our group for the evaluation and study of large astronomical spectroscopic data sets. Initial analysis has focused on 12 complex organic molecules that can be used to trace grain-surface and gas-phase chemical processing in the interstellar medium. GOBASIC was used to determine molecular column densities and rotational temperatures. This information is being used to study correlations between molecular abundances within a given source, and source-to-source correlations for a given molecule, with the ultimate goal of determining which molecules can be used as clocks of the star-formation process. The spectra and the results of this initial analysis will be presented.

  16. Determining carbon-carbon connectivities in natural abundance organic powders using dipolar couplings.

    PubMed

    Dekhil, Myriam; Mollica, Giulia; Bonniot, Tristan Texier; Ziarelli, Fabio; Thureau, Pierre; Viel, Stéphane

    2016-06-30

    We present a solid-state NMR methodology capable of investigating the carbon skeleton of natural abundance organic powders. The methodology is based on the (13)C-(13)C dipolar coupling interaction and allows carbon-carbon connectivities to be unambiguously established for a wide range of organic solids. This methodology is particularly suitable for disordered solids, such as natural or synthetic macromolecules, which cannot be studied using conventional diffraction or NMR techniques. PMID:27319808

  17. Spectrophotometric and electrical properties of imperatorin: an organic molecule

    NASA Astrophysics Data System (ADS)

    Mir, Feroz A.

    2015-09-01

    Imperatorin (molecular formula = C16H14O4, molecular mass = 270) an organic molecule was isolated from ethyl acetate extract of the root parts of the plant Prangos pabularia. The optical study was carried out by ultraviolet-visible spectroscopy, and this compound showed an indirect allowed transition. The optical band gap ( E g ) was found around 3.75 eV. Photoluminescence shows various good emission bands. The frequency-dependent real part of the complex ac conductivity was found to follow the universal dielectric response: σ ac ( ω) α ω s [where σ ac ( ω) is the frequency-dependent total conductivity, ω is the frequency, and s is the frequency exponent]. From ac conductivity data analysis, correlated barrier hopping charge-transport mechanism is the dominant electrical transport process shown by this compound. The good emission, less absorption, wide band gap and good electrical properties shown by this compound project them as a bright choice for organic electronic devices.

  18. Water and complex organic molecules in the warm inner regions of solar-type protostars

    NASA Astrophysics Data System (ADS)

    Coutens, A.; Jørgensen, J. K.; Persson, M. V.; Lykke, J. M.; Taquet, V.; van Dishoeck, E. F.; Vastel, C.; Wampfler, S. F.

    2015-12-01

    Water and complex organic molecules play an important role in the emergence of Life. They have been detected in different types of astrophysical environments (protostars, prestellar cores, outflows, protoplanetary disks, comets, etc). In particular, they show high abundances towards the warm inner regions of protostars, where the icy grain mantles thermally desorb. Can a part of the molecular content observed in these regions be preserved during the star formation process and incorporated into asteroids and comets, that can deliver it to planetary embryos through impacts? By comparison with cometary studies, interferometric observations of solar-type protostars can help to address this important question. We present recent results obtained with the Plateau de Bure interferometer about water deuteration, glycolaldehyde and ethylene glycol towards the low-mass protostar NGC 1333 IRAS2A.

  19. The formation of glycine and other complex organic molecules in exploding ice mantles.

    PubMed

    Rawlings, J M C; Williams, D A; Viti, S; Cecchi-Pestellini, C; Duley, W W

    2014-01-01

    Complex Organic Molecules (COMs), such as propylene (CH3CHCH2) and the isomers of C2H4O2 are detected in cold molecular clouds (such as TMC-1) with high fractional abundances (Marcelino et al., Astrophys. J., 2007, 665, L127). The formation mechanism for these species is the subject of intense speculation, as is the possibility of the formation of simple amino acids such as glycine (NH2CH2COOH). At typical dark cloud densities, normal interstellar gas-phase chemistries are inefficient, whilst surface chemistry is at best ill defined and does not easily reproduce the abundance ratios observed in the gas phase. Whatever mechanism(s) is/are operating, it/they must be both efficient at converting a significant fraction of the available carbon budget into COMs, and capable of efficiently returning the COMs to the gas phase. In our previous studies we proposed a complementary, alternative mechanism, in which medium- and large-sized molecules are formed by three-body gas kinetic reactions in the warm high density gas phase. This environment exists, for a very short period of time, after the total sublimation of grain ice mantles in transient co-desorption events. In order to drive the process, rapid and efficient mantle sublimation is required and we have proposed that ice mantle 'explosions' can be driven by the catastrophic recombination of trapped hydrogen atoms, and other radicals, in the ice. Repeated cycles of freeze-out and explosion can thus lead to a cumulative molecular enrichment of the interstellar medium. Using existing studies we based our chemical network on simple radical addition, subject to enthalpy and valency restrictions. In this work we have extended the chemistry to include the formation pathways of glycine and other large molecular species that are detected in molecular clouds. We find that the mechanism is capable of explaining the observed molecular abundances and complexity in these sources. We find that the proposed mechanism is easily capable

  20. Searching for Improved Photoreleasing Abilities of Organic Molecules.

    PubMed

    Šolomek, Tomáš; Wirz, Jakob; Klán, Petr

    2015-12-15

    Photoremovable protecting groups (PPGs) are chemical auxiliaries that provide spatial and temporal control over the release of various molecules: bioagents (neurotransmitters and cell-signaling molecules, Ca(2+) ions), acids, bases, oxidants, insecticides, pheromones, fragrances, etc. A major challenge for the improvement of PPGs lies in the development of organic chromophores that release the desired bioagents upon continuous irradiation at wavelengths above 650 nm, that is, in the tissue-transparent window. Understanding of the photorelease reaction mechanisms, investigated by laser flash photolysis and rationalized with the aid of quantum chemical calculations, allows for achieving this goal. In particular, simple Hückel calculations provide useful guidelines for designing new PPGs, because both the lowest excited singlet and triplet states of conjugated systems can be reasonably well described by a single electronic configuration formed by promotion of a single electron from the highest occupied molecular orbital (HOMO) to the lowest unoccupied MO (LUMO) of the ground state configuration. Here we show that Hückel calculations permit rapid identification of common features in the nodal properties of the frontier orbitals of various chromophores that can be classified into distinct chromophore families. If the electronic excitation involves a substantial electron density transfer to an sp(2) carbon atom at which HOMO and LUMO are nearly disjoint, for example, by virtue of symmetry, favorable photoheterolysis can be expected when the corresponding atom carries a leaving group at the α-position. We show examples of photoheterolytic reactions that indicate that the efficiency of photoheterolysis diminishes for chromophores absorbing in the NIR region. We provide a rationale for more efficient photoheterolytic reactions occurring via the triplet state, and we demonstrate the advantages of this mechanistic pathway. Analogies in the structure

  1. The cell adhesion molecule Fasciclin2 regulates brush border length and organization in Drosophila renal tubules.

    PubMed

    Halberg, Kenneth A; Rainey, Stephanie M; Veland, Iben R; Neuert, Helen; Dornan, Anthony J; Klämbt, Christian; Davies, Shireen-Anne; Dow, Julian A T

    2016-01-01

    Multicellular organisms rely on cell adhesion molecules to coordinate cell-cell interactions, and to provide navigational cues during tissue formation. In Drosophila, Fasciclin 2 (Fas2) has been intensively studied due to its role in nervous system development and maintenance; yet, Fas2 is most abundantly expressed in the adult renal (Malpighian) tubule rather than in neuronal tissues. The role Fas2 serves in this epithelium is unknown. Here we show that Fas2 is essential to brush border maintenance in renal tubules of Drosophila. Fas2 is dynamically expressed during tubule morphogenesis, localizing to the brush border whenever the tissue is transport competent. Genetic manipulations of Fas2 expression levels impact on both microvilli length and organization, which in turn dramatically affect stimulated rates of fluid secretion by the tissue. Consequently, we demonstrate a radically different role for this well-known cell adhesion molecule, and propose that Fas2-mediated intermicrovillar homophilic adhesion complexes help stabilize the brush border. PMID:27072072

  2. The cell adhesion molecule Fasciclin2 regulates brush border length and organization in Drosophila renal tubules

    PubMed Central

    Halberg, Kenneth A.; Rainey, Stephanie M.; Veland, Iben R.; Neuert, Helen; Dornan, Anthony J.; Klämbt, Christian; Davies, Shireen-Anne; Dow, Julian A. T.

    2016-01-01

    Multicellular organisms rely on cell adhesion molecules to coordinate cell–cell interactions, and to provide navigational cues during tissue formation. In Drosophila, Fasciclin 2 (Fas2) has been intensively studied due to its role in nervous system development and maintenance; yet, Fas2 is most abundantly expressed in the adult renal (Malpighian) tubule rather than in neuronal tissues. The role Fas2 serves in this epithelium is unknown. Here we show that Fas2 is essential to brush border maintenance in renal tubules of Drosophila. Fas2 is dynamically expressed during tubule morphogenesis, localizing to the brush border whenever the tissue is transport competent. Genetic manipulations of Fas2 expression levels impact on both microvilli length and organization, which in turn dramatically affect stimulated rates of fluid secretion by the tissue. Consequently, we demonstrate a radically different role for this well-known cell adhesion molecule, and propose that Fas2-mediated intermicrovillar homophilic adhesion complexes help stabilize the brush border. PMID:27072072

  3. Exploring Molecular Complexity with ALMA: Deuterated complex organic molecules in Sgr B2

    NASA Astrophysics Data System (ADS)

    Belloche, A.; Müller, H. S. P.; Garrod, R. T.; Menten, K. M.

    2016-05-01

    Apart from the case of methanol, little is known about deuterium fractionation of complex organic molecules in the interstellar medium, especially in high mass star forming regions. We take advantage of the EMoCA spectral line survey to search for deuterated complex organic molecules toward the hot molecular core Sgr B2(N2). We report the secure detection of CH2DCN with a deuteration level of 0.4% and tentative detections of CH2DOH, CH2DCH2CN, CH3CHDCN, and DC3N with levels in the range 0.05-0.12%. Except for methyl cyanide, the measured deuteration levels lie at least a factor of four below the predictions of current astrochemical models. They are also lower than in Orion KL by a factor of a few up to a factor ten. These discrepancies and differences may be due to the higher temperatures that prevail in the Galactic Center region compared to nearby clouds, or they may result from a lower overall abundance of deuterium itself in the Galactic Center region by up to a factor ten.

  4. Ro-vibrational excitation of an organic molecule (HCN) in protoplanetary disks

    NASA Astrophysics Data System (ADS)

    Bruderer, Simon; Harsono, Daniel; van Dishoeck, Ewine F.

    2015-03-01

    Context. Organic molecules are important constituents of protoplanetary disks. Their ro-vibrational lines observed in the near- and mid-infrared are commonly detected toward T Tauri disks. These lines are the only way to probe the chemistry in the inner few au where terrestrial planets form. To understand this chemistry, accurate molecular abundances have to be determined. This is complicated by excitation effects that include radiative pumping. Most analyses so far have made the assumption of local thermal equilibrium (LTE), which may not be fulfilled because of the high gas densities required to collisionally thermalize the vibrational levels of the molecules. Aims: The non-LTE excitation effects of hydrogen cyanide (HCN) are studied to evaluate (i) how the abundance determination is affected by the LTE assumption; (ii) whether the ro-vibrational excitation is dominated by collisions or radiative pumping; and (iii) which regions of protoplanetary disks are traced by certain vibrational bands. Methods: Starting from estimates for the collisional rate coefficients of HCN, non-LTE slab models of the HCN emission were calculated to study the importance of different excitation mechanisms. Using a new radiative transfer model, the HCN emission from a full two-dimensional disk was then modeled to study the effect of the non-LTE excitation, together with the line formation. We ran models tailored to the T Tauri disk AS 205 (N) where HCN lines in both the 3 μm and 14 μm bands have been observed by VLT-CRIRES and the Spitzer Space Telescope. Results: Reproducing the observed 3 μm/14 μm flux ratios requires very high densities and kinetic temperatures (n> 1014 cm-3 and T> 750 K), if only collisional excitation is accounted for. Radiative pumping can, however, excite the lines easily out to considerable radii ~10 au. Consequently, abundances derived from LTE and non-LTE models do not differ by more than a factor of about 3. Models with both a strongly enhanced abundance

  5. Formation and Recondensation of Complex Organic Molecules during Protostellar Luminosity Outbursts

    NASA Astrophysics Data System (ADS)

    Taquet, Vianney; Wirström, Eva S.; Charnley, Steven B.

    2016-04-01

    During the formation of stars, the accretion of surrounding material toward the central object is thought to undergo strong luminosity outbursts followed by long periods of relative quiescence, even at the early stages of star formation when the protostar is still embedded in a large envelope. We investigated the gas-phase formation and recondensation of the complex organic molecules (COMs) di-methyl ether and methyl formate, induced by sudden ice evaporation processes occurring during luminosity outbursts of different amplitudes in protostellar envelopes. For this purpose, we updated a gas-phase chemical network forming COMs in which ammonia plays a key role. The model calculations presented here demonstrate that ion–molecule reactions alone could account for the observed presence of di-methyl ether and methyl formate in a large fraction of protostellar cores without recourse to grain-surface chemistry, although they depend on uncertain ice abundances and gas-phase reaction branching ratios. In spite of the short outburst timescales of about 100 years, abundance ratios of the considered species higher than 10% with respect to methanol are predicted during outbursts due to their low binding energies relative to water and methanol which delay their recondensation during cooling. Although the current luminosity of most embedded protostars would be too low to produce complex organics in the hot-core regions that are observable with current sub-millimetric interferometers, previous luminosity outburst events would induce the formation of COMs in extended regions of protostellar envelopes with sizes increasing by up to one order of magnitude.

  6. Organic and inorganic molecules as probes of mineral surfaces (Invited)

    NASA Astrophysics Data System (ADS)

    Sverjensky, D. A.

    2010-12-01

    Although the multi-site nature of mineral surfaces is to be expected based on the underlying crystal structure, definitive evidence of the need to use more than one site in modelling proton surface charge or adsorption of a single adsorbate at the mineral-water interface is lacking. Instead, a single-site approach affords a practical way of averaging over all possible crystal planes and sites in a powdered mineral sample. Extensive analysis of published proton surface charge and adsorption of metals on oxide mineral surfaces can be undertaken with a single site density for each mineral based on tritium exchange or estimation from averages of the site densities of likely exposed surfaces. Even in systems with competing metals (e.g. Cu and Pb on hematite), the same site density as used for proton surface charge can be employed depending on the reaction stoichiometry. All of this indicates that protons and metals can bind to a great variety of sites with the same overall site density. However, simple oxyanions such as carbonate, sulfate, selenate, arsenate and arsenite require a much lower site density for a given mineral. For example, on goethite these oxyanions utilize a site density that correlates with the BET surface area of the goethite. In this way, the oxyanions can be thought of as selectively probing the available sites on the mineral. The correlation probably arises because goethites with different BET surface areas have different proportions of singly and multiply-bonded oxygens, and only the singly-bonded oxygens are useful for inner-sphere surface complexation by the ligand exchange mechanism. Small organic molecules behave in a remarkably similar way. For example, adsorption of oxalate on goethite, and aspartate, glutamate, dihydroxyphenylalanine, lysine and arginine on rutile are all consistent with a much smaller site density than those required for metals such as calcium or neodymium. Overall, these results suggest that both inorganic oxyanions and

  7. Targeting organic molecules in hydrothermal environments on Mars

    NASA Astrophysics Data System (ADS)

    Parnell, J.; Bowden, S. A.; Lindgren, P.; Wilson, R.; Cooper, J. M.

    2008-09-01

    Hydrothermal deposits on Mars Hydrothermal systems are proposed as environments that could support organic synthesis, the evolution of life or the maintenance of life [1,2,3]. They have therefore been suggested as primary targets for exploration on Mars [1,2,4,].There is now confidence that hydrothermal deposits occur at the martian surface. This is based on a range of criteria that could point towards hydrothermal activity, including volcanic activity, magmatic-driven tectonism, impact cratering in icy terrains, hydrous alteration of minerals and typical hydrothermal mineralogies [4]. The proposals to search for evidence of life at martian hydrothermal sites have been focussed on seeking morphological evidence of microbial activity [5]. Here we discuss the potential to seek a chemical signature of organic matter in hydrothermal systems. Organics in terrestrial hydrothermal systems Terrestrial hydrothermal systems can have large quantities of organic matter because they intersect organic-rich sedimentary rocks or oil reservoirs. Thus the signatures that they contain reflect some preexisting concentration of fossil organic compounds, rather than life which was active in the hydrothermal system. If any extant life was incorporated in these hydrothermal systems, it is swamped by the fossil molecules. Examples of environments where organic materials may become entrained include subsurface hydrothermal mineral deposits, generation of hydrothermal systems by igneous intrusions, and hot fluid venting at the seafloor. Nevertheless, there is value in studying the interactions of hydrothermal systems with fossil organic matter, for information about the survivability of organic compounds, phase relationships between carbonaceous and noncarbonaceous materials, and where in hydrothermal deposits to find evidence of organic matter. Microbial colonization of hot spring systems is feasible at depth within the systems and at the surface where the hydrothermal waters discharge

  8. Small molecules as tracers in atmospheric secondary organic aerosol

    NASA Astrophysics Data System (ADS)

    Yu, Ge

    Secondary organic aerosol (SOA), formed from in-air oxidation of volatile organic compounds, greatly affects human health and climate. Although substantial research has been devoted to SOA formation and evolution, the modeled and lab-generated SOA are still low in mass and degree of oxidation compared to ambient measurements. In order to compensate for these discrepancies, the aqueous processing pathway has been brought to attention. The atmospheric waters serve as aqueous reaction media for dissolved organics to undergo further oxidation, oligomerization, or other functionalization reactions, which decreases the vapor pressure while increasing the oxidation state of carbon atoms. Field evidence for aqueous processing requires the identification of tracer products such as organosulfates. We synthesized the standards for two organosulfates, glycolic acid sulfate and lactic acid sulfate, in order to measure their aerosol-state concentration from five distinct locations via filter samples. The water-extracted filter samples were analyzed by LC-MS. Lactic acid sulfate and glycolic acid sulfate were detected in urban locations in the United States, Mexico City, and Pakistan with varied concentrations, indicating their potential as tracers. We studied the aqueous processing reaction between glyoxal and nitrogen-containing species such as ammonium and amines exclusively by NMR spectrometry. The reaction products formic acid and several imidazoles along with the quantified kinetics were reported. The brown carbon generated from these reactions were quantified optically by UV-Vis spectroscopy. The organic-phase reaction between oxygen molecule and alkenes photosensitized by alpha-dicarbonyls were studied in the same manner. We observed the fast kinetics transferring alkenes to epoxides under simulated sunlight. Statistical estimations indicate a very effective conversion of aerosol-phase alkenes to epoxides, potentially forming organosulfates in a deliquescence event and

  9. Aperture Valve for the Mars Organic Molecule Analyzer (MOMA)

    NASA Technical Reports Server (NTRS)

    Engler, Charles D.; Canham, John S.

    2014-01-01

    NASA's participation in the multi-nation ExoMars 2018 Rover mission includes a critical astrobiology Mass Spectrometer Instrument on the Rover called the Mars Organic Molecule Analyzer (MOMA). The Aperture Valve is a critical electromechanical valve used by the Mass Spectrometer to facilitate the transfer of ions from Martian soil to the Mass Spectrometer for analysis. The MOMA Aperture Valve development program will be discussed in terms of the Initial valve design and subsequent improvements that resulted from prototype testing. The Initial Aperture Valve concept seemed promising, based on calculations and perceived merits. However, performance results of this design were disappointing, due to delamination of TiN and DLC coatings applied to the Titanium base metals, causing debris from the coatings to seize the valve. While peer reviews and design trade studies are important forums to vet a concept design, results from testing should not be underestimated. Despite the lack of development progress to meet requirements, valuable information from weakness discovered in the Initial Valve design was used to develop a second, more robust Aperture valve. Based on a check-ball design, the ETU /flight valve design resulted in significantly less surface area to create the seal. Moreover, PVD coatings were eliminated in favor of hardened, nonmagnetic corrosion resistant alloys. Test results were impressive, with the valve achieving five orders of magnitude better sealing leak rate over end of life requirements. Cycle life was equally impressive, achieving 280,000 cycles without failure.

  10. Aperture Valve for the Mars Organic Molecule Analyzer (MOMA)

    NASA Technical Reports Server (NTRS)

    Engler, Charles; Canham, John

    2014-01-01

    NASA's participation in the multi-nation ExoMars 2018 Rover mission includes a critical astrobiology Mass Spectrometer Instrument on the Rover called the Mars Organic Molecule Analyzer (MOMA). The Aperture Valve is a critical electromechanical valve used by the Mass Spectrometer to facilitate the transfer of ions from Martian soil to the Mass Spectrometer for analysis. The MOMA Aperture Valve development program will be discussed in terms of the initial valve design and subsequent improvements that resulted from prototype testing. The initial Aperture Valve concept seemed promising, based on calculations and perceived merits. However, performance results of this design were disappointing, due to delamination of TiN and DLC coatings applied to the titanium base metals, causing debris from the coatings to seize the valve. While peer reviews and design trade studies are important forums to vet a concept design, results from testing should not be underestimated. Despite the lack of development progress to meet requirements, valuable information from weakness discovered in the initial Valve design was used to develop a second, more robust Aperture Valve. Based on a check-ball design, the ETU / flight valve design resulted in significantly less surface area to create the seal. Moreover, PVD coatings were eliminated in favor of hardened, non-magnetic corrosion resistant alloys. Test results were impressive, with the valve achieving five orders of magnitude better sealing leak rate over end of life requirements. Cycle life was equally impressive, achieving 280,000 cycles without failure.

  11. Aperture Valve for the Mars Organic Molecule Analyzer (MOMA)

    NASA Technical Reports Server (NTRS)

    Hakun, Claef F.; Engler, Charles D.; Barber, Willie E.; Canham, John S.

    2014-01-01

    NASA's participation in the multi-nation ExoMars 2018 Rover mission includes a critical astrobiology Mass Spectrometer Instrument on the Rover called the Mars Organic Molecule Analyzer (MOMA). The Aperture Valve is a critical electromechanical valve used by the Mass Spectrometer to facilitate the transfer of ions from Martian soil to the Mass Spectrometer for analysis. The MOMA Aperture Valve development program will be discussed in terms of the Initial valve design and subsequent improvements that resulted from prototype testing. The Initial Aperture Valve concept seemed promising, based on calculations and perceived merits. However, performance results of this design were disappointing, due to delamination of TiN and DLC coatings applied to the Titanium base metals, causing debris from the coatings to seize the valve. While peer reviews and design trade studies are important forums to vet a concept design, results from testing should not be underestimated.Despite the lack of development progress to meet requirements, valuable information from weakness discovered in the Initial Valve design was used to develop a second, more robust Aperture valve. Based on a check-ball design, the ETU flight valve design resulted in significantly less surface area to create the seal. Moreover, PVD coatings were eliminated in favor of hardened, nonmagnetic corrosion resistant alloys. Test results were impressive, with the valve achieving five orders of magnitude better sealing leak rate over end of life requirements. Cycle life was equally impressive, achieving 280,000 cycles without failure.

  12. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

    PubMed Central

    Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W.

    2011-01-01

    An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems. PMID:22022236

  13. Organic Matter Degradation Drives Benthic Cyanobacterial Mat Abundance on Caribbean Coral Reefs

    PubMed Central

    Brocke, Hannah J.; Polerecky, Lubos; de Beer, Dirk; Weber, Miriam; Claudet, Joachim; Nugues, Maggy M.

    2015-01-01

    Benthic cyanobacterial mats (BCMs) are impacting coral reefs worldwide. However, the factors and mechanisms driving their proliferation are unclear. We conducted a multi-year survey around the Caribbean island of Curaçao, which revealed highest BCM abundance on sheltered reefs close to urbanised areas. Reefs with high BCM abundance were also characterised by high benthic cover of macroalgae and low cover of corals. Nutrient concentrations in the water-column were consistently low, but markedly increased just above substrata (both sandy and hard) covered with BCMs. This was true for sites with both high and low BCM coverage, suggesting that BCM growth is stimulated by a localised, substrate-linked release of nutrients from the microbial degradation of organic matter. This hypothesis was supported by a higher organic content in sediments on reefs with high BCM coverage, and by an in situ experiment which showed that BCMs grew within days on sediments enriched with organic matter (Spirulina). We propose that nutrient runoff from urbanised areas stimulates phototrophic blooms and enhances organic matter concentrations on the reef. This organic matter is transported by currents and settles on the seabed at sites with low hydrodynamics. Subsequently, nutrients released from the organic matter degradation fuel the growth of BCMs. Improved management of nutrients generated on land should lower organic loading of sediments and other benthos (e.g. turf and macroalgae) to reduce BCM proliferation on coral reefs. PMID:25941812

  14. Organic matter degradation drives benthic cyanobacterial mat abundance on Caribbean coral reefs.

    PubMed

    Brocke, Hannah J; Polerecky, Lubos; de Beer, Dirk; Weber, Miriam; Claudet, Joachim; Nugues, Maggy M

    2015-01-01

    Benthic cyanobacterial mats (BCMs) are impacting coral reefs worldwide. However, the factors and mechanisms driving their proliferation are unclear. We conducted a multi-year survey around the Caribbean island of Curaçao, which revealed highest BCM abundance on sheltered reefs close to urbanised areas. Reefs with high BCM abundance were also characterised by high benthic cover of macroalgae and low cover of corals. Nutrient concentrations in the water-column were consistently low, but markedly increased just above substrata (both sandy and hard) covered with BCMs. This was true for sites with both high and low BCM coverage, suggesting that BCM growth is stimulated by a localised, substrate-linked release of nutrients from the microbial degradation of organic matter. This hypothesis was supported by a higher organic content in sediments on reefs with high BCM coverage, and by an in situ experiment which showed that BCMs grew within days on sediments enriched with organic matter (Spirulina). We propose that nutrient runoff from urbanised areas stimulates phototrophic blooms and enhances organic matter concentrations on the reef. This organic matter is transported by currents and settles on the seabed at sites with low hydrodynamics. Subsequently, nutrients released from the organic matter degradation fuel the growth of BCMs. Improved management of nutrients generated on land should lower organic loading of sediments and other benthos (e.g. turf and macroalgae) to reduce BCM proliferation on coral reefs. PMID:25941812

  15. A new weapon for the interstellar complex organic molecule hunt: the minimum energy principle

    NASA Astrophysics Data System (ADS)

    Lattelais, M.; Pauzat, F.; Ellinger, Y.; Ceccarelli, C.

    2010-09-01

    Context. The hunt for the interstellar complex organic molecules (COMs) supposed to be the building blocks of the molecules at the origin of life is a challenging but very expensive task. It starts with laboratory experiments, associated with theoretical calculations, that give the line frequencies and strengths of the relevant molecules to be identified and finishes with observations at the telescopes. Aims: The present study aims to suggest possible guidelines to optimize this hunt. Levering on the minimum energy principle (MEP) presented in a previous study, we discuss the link between thermodynamic stability and detectability of a number of structures in the important families of amides, sugars and aminonitriles. Methods: The question of the relative stability of these different species is addressed by means of quantum density functional theory simulations. The hybrid B3LYP formalism was used throughout. All 72 molecules part of this survey were treated on an equal footing. Each structure, fully optimized, was verified to be a stationary point by vibrational analysis. Results: A comprehensive screening of 72 isomers of CH3NO, C2H5NO, C3H7NO, C2H4O2, C3H6O3 and C2H4N2 chemical formula has been carried out. We found that formamide, acetamide and propanamide (the first two identified in the Inter-Stellar Medium) are the most stable compounds in their families demonstrating at the same time that the peptide bond >N-C=O at the origin of life is the most stable bond that can be formed. Dihydroxyacetone, whose detection awaits for confirmation, is far from being the most stable isomer of its family while aminoacetonitrile, that has been recently identified, is effectively the most stable species. Conclusions: The MEP appears to be a useful tool for optimizing the hunt for new species by identifying the potentially more abundant isomers of a given chemical formula.

  16. Organic amendments enhance microbial diversity and abundance of functional genes in Australian Soils

    NASA Astrophysics Data System (ADS)

    Aldorri, Sind; McMillan, Mary; Pereg, Lily

    2016-04-01

    Food and cash crops play important roles in Australia's economy with black, grey and red clay soil, widely use for growing cotton, wheat, corn and other crops in rotation. While the majority of cotton growers use nitrogen and phosphate fertilizers only in the form of agrochemicals, a few experiment with the addition of manure or composted plant material before planting. We hypothesized that the use of such organic amendments would enhance the soil microbial function through increased microbial diversity and abundance, thus contribute to improved soil sustainability. To test the hypothesis we collected soil samples from two cotton-growing farms in close geographical proximity and with mostly similar production practices other than one grower has been using composted plants as organic amendment and the second farmer uses only agrochemicals. We applied the Biolog Ecoplate system to study the metabolic signature of microbial communities and used qPCR to estimate the abundance of functional genes in the soil. The soil treated with organic amendments clearly showed higher metabolic activity of a more diverse range of carbon sources as well as higher abundance of genes involved in the nitrogen and phosphorous cycles. Since microbes undertake a large number of soil functions, the use of organic amendments can contribute to the sustainability of agricultural soils.

  17. ON THE RELATIVE ABUNDANCE OF LiH AND LiH{sup +} MOLECULES IN THE EARLY UNIVERSE: NEW RESULTS FROM QUANTUM REACTIONS

    SciTech Connect

    Bovino, Stefano; Tacconi, Mario; Gianturco, Franco A.; Galli, Daniele; Palla, Francesco

    2011-04-20

    The relative efficiencies of the chemical pathways that can lead to the destruction of LiH and LiH{sup +} molecules, conjectured to be present in the primordial gas and to control molecular cooling processes in the gravitational collapse of the post-recombination era, are revisited by using accurate quantum calculations for the several reactions involved. The new rates are employed to survey the behavior of the relative abundance of these molecules at redshifts of interest for early universe conditions. We find significant differences with respect to previous calculations, the present ones yielding LiH abundances higher than LiH{sup +} at all redshifts.

  18. Observing Organic Molecules in Interstellar Gases: Non Equilibrium Excitation.

    NASA Astrophysics Data System (ADS)

    Wiesenfeld, Laurent; Faure, Alexandre; Remijan, Anthony; Szalewicz, Krzysztof

    2014-06-01

    In order to observe quantitatively organic molecules in interstellar gas, it is necessary to understand the relative importance of photonic and collisional excitations. In order to do so, collisional excitation transfer rates have to be computed. We undertook several such studies, in particular for H_2CO and HCOOCH_3. Both species are observed in many astrochemical environments, including star-forming regions. We found that those two molecules behave in their low-lying rotational levels in an opposite way. For cis methyl-formate, a non-equilibrium radiative transfer treatment of rotational lines is performed, using a new set of theoretical collisional rate coefficients. These coefficients have been computed in the temperature range 5 to 30 K by combining coupled-channel scattering calculations with a high accuracy potential energy surface for HCOOCH_3 -- He. The results are compared to observations toward the Sagittarius B2(N) molecular cloud. A total of 2080 low-lying transitions of methyl formate, with upper levels below 25 K, were treated. These lines are found to probe a cold (30 K), moderately dense (n ˜ 104 cm-3) interstellar gas. In addition, our calculations indicate that all detected emission lines with a frequency below 30 GHz are collisionally pumped weak masers amplifying the background of Sgr B2(N). This result demonstrates the generality of the inversion mechanism for the low-lying transitions of methyl formate. For formaldehyde, we performed a similar non-equilibrium treatment, with H_2 as the collisional partner, thanks to the accurate H_2CO - H_2 potential energy surface . We found very different energy transfer rates for collisions with para-H_2 (J=0) and ortho-H_2 (J=1). The well-known absorption against the cosmological background of the 111→ 101 line is shown to depend critically on the difference of behaviour between para and ortho-H_2, for a wide range of H_2 density. We thank the CNRS-PCMI French national program for continuous support

  19. Implantation of Organic Molecules into Biotissue by Pulsed Laser Irradiation

    NASA Astrophysics Data System (ADS)

    Goto, Masahiro; Ichinose, Nobuyuki; Kawanishi, Shunichi; Fukumura, Hiroshi

    1999-01-01

    Zinc tetraphenyl porphyrin (ZnTPP) molecules were implanted into a piece of chicken skin by irradiation with KrF laser pulses. The study of the implanted ZnTPP at the skin surface using a fluorescence microscope indicated that the molecules are space-selectively introduced at the irradiated area.

  20. Studies of minute quantities of natural abundance molecules using 2D heteronuclear correlation spectroscopy under 100kHz MAS

    SciTech Connect

    Nishiyama, Y.; Kobayashi, T.; Malon, M.; Singappuli-Arachchige, D.; Slowing, I. I.; Pruski, M.

    2015-02-16

    Two-dimensional 1H{13C} heteronuclear correlation solid-state NMR spectra of naturally abundant solid materials are presented, acquired using the 0.75-mm magic angle spinning (MAS) probe at spinning rates up to 100 kHz. In spite of the miniscule sample volume (290 nL), high-quality HSQC-type spectra of bulk samples as well as surface-bound molecules can be obtained within hours of experimental time. The experiments are compared with those carried out at 40 kHz MAS using a 1.6-mm probe, which offered higher overall sensitivity due to a larger rotor volume. The benefits of ultrafast MAS in such experiments include superior resolution in 1H dimension without resorting to 1H–1H homonuclear RF decoupling, easy optimization, and applicability to mass-limited samples. As a result, the HMQC spectra of surface-bound species can be also acquired under 100 kHz MAS, although the dephasing of transverse magnetization has significant effect on the efficiency transfer under MAS alone.

  1. Studies of minute quantities of natural abundance molecules using 2D heteronuclear correlation spectroscopy under 100kHz MAS

    DOE PAGESBeta

    Nishiyama, Y.; Kobayashi, T.; Malon, M.; Singappuli-Arachchige, D.; Slowing, I. I.; Pruski, M.

    2015-02-16

    Two-dimensional 1H{13C} heteronuclear correlation solid-state NMR spectra of naturally abundant solid materials are presented, acquired using the 0.75-mm magic angle spinning (MAS) probe at spinning rates up to 100 kHz. In spite of the miniscule sample volume (290 nL), high-quality HSQC-type spectra of bulk samples as well as surface-bound molecules can be obtained within hours of experimental time. The experiments are compared with those carried out at 40 kHz MAS using a 1.6-mm probe, which offered higher overall sensitivity due to a larger rotor volume. The benefits of ultrafast MAS in such experiments include superior resolution in 1H dimensionmore » without resorting to 1H–1H homonuclear RF decoupling, easy optimization, and applicability to mass-limited samples. As a result, the HMQC spectra of surface-bound species can be also acquired under 100 kHz MAS, although the dephasing of transverse magnetization has significant effect on the efficiency transfer under MAS alone.« less

  2. Observations of some oxygen-containing and sulfur-containing organic molecules in cold dark clouds.

    PubMed

    Irvine, W M; Friberg, P; Kaifu, N; Kawaguchi, K; Kitamura, Y; Matthews, H E; Minh, Y; Saito, S; Ukita, N; Yamamoto, S

    1989-07-15

    Observations of nine oxygen- and sulfur-containing organic molecules have been made toward the cold dark clouds TMC-1 and L134N. We have confirmed the presence of para-ketene (H2C2O) in TMC-1, have for the first time observed ortho-ketene, and find a total ketene column density approximately 1 x 10(13) cm-2. Thioformaldehyde (H2CS) is easily detectable in both TMC-1 and L134N, with a column density about 5 times larger in the former source (approximately 3 x 10(13) cm-2). The fractional abundance of ketene is comparable to the predictions of ion-molecule chemistry, while that of thioformaldehyde in TMC-1 is one to two orders of magnitude greater than that expected from such models at steady state. Interstellar sulfur chemistry thus continues to be poorly understood. We set upper limits for the column densities of formic acid (HCOOH), vinyl alcohol (CH2CHOH), methyl formate (HCO2CH3), formamide (NH2CHO), methyl mercaptan (CH3SH), isothiocyanic acid (HNCS), and thioketene (H2C2S) in both sources. PMID:11538350

  3. Observations of some oxygen-containing and sulfur-containing organic molecules in cold dark clouds

    NASA Technical Reports Server (NTRS)

    Irvine, W. M.; Friberg, P.; Kaifu, N.; Kitamura, Y.; Kawaguchi, K.

    1989-01-01

    Observations of nine oxygen- and sulfur-containing organic molecules have been made toward the cold dark clouds TMC-1 and L134N. The presence of paraketene (H2C2O) in TMC-1 is confirmed for orthoketene, and has been observed for the first time and a total ketene column density of about 10 to the 13th/sq cm is found. Thioformaldehyde (H2CS) is easily detectable in both TMC-1 and L134N, with a column density about five times larger in the former source. The fractional abundance of ketene is comparable to the predictions of ion-molecule chemistry, while that of thioformaldehyde in TMC-1 is one to two orders of magnitude greater than that expected from such models at steady state. Interstellar sulfur chemistry thus continues to be poorly understood. Upper limits are set for the column densities of formic acid (HCOOH), vinyl alcohol (CH2CHOH), methyl formate (HCO2CH3), formamide (NH2CHO), methyl mercaptan (CH3SH), isothiocyanic acid (HNCS), and thioketene (H2C2S) in both sources.

  4. Site-selective patterning of organic luminescent molecules via gas phase deposition.

    PubMed

    Hao, Juanyuan; Lu, Nan; Wu, Qiong; Hu, Wei; Chen, Xiaodong; Zhang, Hongyu; Wu, Ying; Wang, Yue; Chi, Lifeng

    2008-05-20

    In this paper, we present a bottom-up approach to pattern organic luminescent molecules with a feature size down to sub-100 nm over wafer-sized areas. This method is based on the selective gas deposition of organic molecules on self-organized patterned structures, which consist of an organic monolayer with two different phases rather than different materials. The site selectivity is controllable by deposition rate and the pattern features. The reason for the site selectivity may be due to the nucleation and diffusion behaviors of the deposited organic molecules on different monolayer phases. PMID:18370416

  5. Inhomogeneous distribution of organic molecules adsorbed in sol gel glasses

    NASA Astrophysics Data System (ADS)

    Meneses-Nava, M. A.; Chávez-Cerda, S.; Sánchez-Villicaña, V.; Sánchez-Mondragón, J. J.; King, T. A.

    1999-09-01

    The effects of the porous matrix upon the radiative characteristics of quinine sulphate doped sol-gel glasses are investigated. The broadenings of the absorption and fluorescence spectra are explained by the attachment of the molecules on distorted sites or in a non-planar fashion, creating an inhomogeneous distribution of adsorbed molecules. For this reason, each emitting center relaxes with its own characteristics. This inhomogeneous distribution is also supported by the non-exponential and the wavelength dependence of the fluorescence decay.

  6. Molecules with multiple switching units on a Au(111) surface: self-organization and single-molecule manipulation

    NASA Astrophysics Data System (ADS)

    Mielke, Johannes; Selvanathan, Sofia; Peters, Maike; Schwarz, Jutta; Hecht, Stefan; Grill, Leonhard

    2012-10-01

    Three different molecules, each containing two azobenzene switching units, were synthesized, successfully deposited onto a Au(111) surface by sublimation and studied by scanning tunneling microscopy at low temperatures. To investigate the influence of electronic coupling between the switching units as well as to the surface, the two azo moieties were connected either via π-conjugated para-phenylene or decoupling meta-phenylene bridges, and the number of tert-butyl groups was varied in the meta-phenylene-linked derivatives. Single molecules were found to be intact after deposition as identified by their characteristic appearance in STM images. Due to their mobility on the Au(111) surface at room temperature, the molecules spontaneously formed self-organized molecular arrangements that reflected their chemical structure. While lateral displacement of the molecules was accomplished by manipulation, trans-cis isomerization processes, typical for azobenzene switches, could not be induced.

  7. Molecular characterization of dissolved organic matter in glacial ice: coupling natural abundance 1H NMR and fluorescence spectroscopy.

    PubMed

    Pautler, Brent G; Woods, Gwen C; Dubnick, Ashley; Simpson, André J; Sharp, Martin J; Fitzsimons, Sean J; Simpson, Myrna J

    2012-04-01

    Glaciers and ice sheets are the second largest freshwater reservoir in the global hydrologic cycle, and the onset of global climate warming has necessitated an assessment of their contributions to sea-level rise and the potential release of nutrients to nearby aquatic environments. In particular, the release of dissolved organic matter (DOM) from glacier melt could stimulate microbial activity in both glacial ecosystems and adjacent watersheds, but this would largely depend on the composition of the material released. Using fluorescence and (1)H NMR spectroscopy, we characterize DOM at its natural abundance in unaltered samples from a number of glaciers that differ in geographic location, thermal regime, and sample depth. Parallel factor analysis (PARAFAC) modeling of DOM fluorophores identifies components in the ice that are predominantly proteinaceous in character, while (1)H NMR spectroscopy reveals a mixture of small molecules that likely originate from native microbes. Spectrofluorescence also reveals a terrestrial contribution that was below the detection limits of NMR; however, (1)H nuclei from levoglucosan was identified in Arctic glacier ice samples. This study suggests that the bulk of the DOM from these glaciers is a mixture of biologically labile molecules derived from microbes. PMID:22385100

  8. Organic Nitrogen-Driven Stimulation of Arbuscular Mycorrhizal Fungal Hyphae Correlates with Abundance of Ammonia Oxidizers.

    PubMed

    Bukovská, Petra; Gryndler, Milan; Gryndlerová, Hana; Püschel, David; Jansa, Jan

    2016-01-01

    Large fraction of mineral nutrients in natural soil environments is recycled from complex and heterogeneously distributed organic sources. These sources are explored by both roots and associated mycorrhizal fungi. However, the mechanisms behind the responses of arbuscular mycorrhizal (AM) hyphal networks to soil organic patches of different qualities remain little understood. Therefore, we conducted a multiple-choice experiment examining hyphal responses to different soil patches within the root-free zone by two AM fungal species (Rhizophagus irregularis and Claroideoglomus claroideum) associated with Medicago truncatula, a legume forming nitrogen-fixing root nodules. Hyphal colonization of the patches was assessed microscopically and by quantitative real-time PCR (qPCR) using AM taxon-specific markers, and the prokaryotic and fungal communities in the patches (pooled per organic amendment treatment) were profiled by 454-amplicon sequencing. Specific qPCR markers were then designed and used to quantify the abundance of prokaryotic taxa showing the strongest correlation with the pattern of AM hyphal proliferation in the organic patches as per the 454-sequencing. The hyphal density of both AM fungi increased due to nitrogen (N)-containing organic amendments (i.e., chitin, DNA, albumin, and clover biomass), while no responses as compared to the non-amended soil patch were recorded for cellulose, phytate, or inorganic phosphate amendments. Abundances of several prokaryotes, including Nitrosospira sp. (an ammonium oxidizer) and an unknown prokaryote with affiliation to Acanthamoeba endosymbiont, which were frequently recorded in the 454-sequencing profiles, correlated positively with the hyphal responses of R. irregularis to the soil amendments. Strong correlation between abundance of these two prokaryotes and the hyphal responses to organic soil amendments by both AM fungi was then confirmed by qPCR analyses using all individual replicate patch samples. Further

  9. Organic Nitrogen-Driven Stimulation of Arbuscular Mycorrhizal Fungal Hyphae Correlates with Abundance of Ammonia Oxidizers

    PubMed Central

    Bukovská, Petra; Gryndler, Milan; Gryndlerová, Hana; Püschel, David; Jansa, Jan

    2016-01-01

    Large fraction of mineral nutrients in natural soil environments is recycled from complex and heterogeneously distributed organic sources. These sources are explored by both roots and associated mycorrhizal fungi. However, the mechanisms behind the responses of arbuscular mycorrhizal (AM) hyphal networks to soil organic patches of different qualities remain little understood. Therefore, we conducted a multiple-choice experiment examining hyphal responses to different soil patches within the root-free zone by two AM fungal species (Rhizophagus irregularis and Claroideoglomus claroideum) associated with Medicago truncatula, a legume forming nitrogen-fixing root nodules. Hyphal colonization of the patches was assessed microscopically and by quantitative real-time PCR (qPCR) using AM taxon-specific markers, and the prokaryotic and fungal communities in the patches (pooled per organic amendment treatment) were profiled by 454-amplicon sequencing. Specific qPCR markers were then designed and used to quantify the abundance of prokaryotic taxa showing the strongest correlation with the pattern of AM hyphal proliferation in the organic patches as per the 454-sequencing. The hyphal density of both AM fungi increased due to nitrogen (N)-containing organic amendments (i.e., chitin, DNA, albumin, and clover biomass), while no responses as compared to the non-amended soil patch were recorded for cellulose, phytate, or inorganic phosphate amendments. Abundances of several prokaryotes, including Nitrosospira sp. (an ammonium oxidizer) and an unknown prokaryote with affiliation to Acanthamoeba endosymbiont, which were frequently recorded in the 454-sequencing profiles, correlated positively with the hyphal responses of R. irregularis to the soil amendments. Strong correlation between abundance of these two prokaryotes and the hyphal responses to organic soil amendments by both AM fungi was then confirmed by qPCR analyses using all individual replicate patch samples. Further

  10. Elucidating Turnover Pathways of Bioactive Small Molecules by Isotopomer Analysis: The Persistent Organic Pollutant DDT

    PubMed Central

    Ehlers, Ina; Betson, Tatiana R.; Vetter, Walter; Schleucher, Jürgen

    2014-01-01

    The persistent organic pollutant DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane) is still indispensable in the fight against malaria, although DDT and related compounds pose toxicological hazards. Technical DDT contains the dichloro congener DDD (1-chloro-4-[2,2-dichloro-1-(4-chlorophenyl)ethyl]benzene) as by-product, but DDD is also formed by reductive degradation of DDT in the environment. To differentiate between DDD formation pathways, we applied deuterium NMR spectroscopy to measure intramolecular deuterium distributions (2H isotopomer abundances) of DDT and DDD. DDD formed in the technical DDT synthesis was strongly deuterium-enriched at one intramolecular position, which we traced back to 2H/1H fractionation of a chlorination step in the technical synthesis. In contrast, DDD formed by reductive degradation was strongly depleted at the same position, which was due to the incorporation of 2H-depleted hydride equivalents during reductive degradation. Thus, intramolecular isotope distributions give mechanistic information on reaction pathways, and explain a puzzling difference in the whole-molecule 2H/1H ratio between DDT and DDD. In general, our results highlight that intramolecular isotope distributions are essential to interpret whole-molecule isotope ratios. Intramolecular isotope information allows distinguishing pathways of DDD formation, which is important to identify polluters or to assess DDT turnover in the environment. Because intramolecular isotope data directly reflect isotope fractionation of individual chemical reactions, they are broadly applicable to elucidate transformation pathways of small bioactive molecules in chemistry, physiology and environmental science. PMID:25350380

  11. Spectroscopy of a Major Complex Organic Molecule: Mono-Deuterated Dimethyl Ether

    NASA Astrophysics Data System (ADS)

    Richard, C.; Margulès, L.; Motiyenko, R. A.; Groner, P.; Coudert, L. H.; Guillemin, J.-C.

    2012-06-01

    Dimethyl ether is one of the most abundant molecule in star-forming regions. Like other complex organic molecules, its formation process is not yet clearly established. The study of deuteration may provide crucial hints. The mono-deuterated species (CH_2DOCH3) is still a relatively light molecule; its spectrum is the most intense in the THz domain even at ISM temperatures (100--150 K). Therefore, it is is necessary to measure and assign its transitions in this range in order to be able to compute accurate predictions which should allow us to detect it with ALMA, expected to be a powerful tool to observe such isotopic species. In this context, spectra between 50 and 950 GHz were recorded in Lille with a solid-state submillimeter-wave spectrometer. The starting point of the analysis was the centimeter-wave measurements carried out in 2003 for almost all isotopic species. Results concerning the symmetric conformer of the mono-deuterated species will be presented in the paper. The fits performed with the ERHAM code will be discussed. Theoretical development are in progress in order to treat the case of the asymmetric conformer. This work is supported by the CNES and the Action sur Projets de l'INSU, PCMI. This work is also funded by the ANR-08-BLAN-0054 and ANR-08-BLAN-0225 contracts. [1]Ceccarelli, Caselli, Herbst, et al., (eds.), University of Arizona Press, Tucson, 951 (2007) 47 [2]Niide et al., J. Mol.Spectrosc. 220 (2003) 65 [3]Groner, J. Chem. Phys. 107 (1997) 4483

  12. Chemoselective single-site Earth-abundant metal catalysts at metal-organic framework nodes.

    PubMed

    Manna, Kuntal; Ji, Pengfei; Lin, Zekai; Greene, Francis X; Urban, Ania; Thacker, Nathan C; Lin, Wenbin

    2016-01-01

    Earth-abundant metal catalysts are critically needed for sustainable chemical synthesis. Here we report a simple, cheap and effective strategy of producing novel earth-abundant metal catalysts at metal-organic framework (MOF) nodes for broad-scope organic transformations. The straightforward metalation of MOF secondary building units (SBUs) with cobalt and iron salts affords highly active and reusable single-site solid catalysts for a range of organic reactions, including chemoselective borylation, silylation and amination of benzylic C-H bonds, as well as hydrogenation and hydroboration of alkenes and ketones. Our structural, spectroscopic and kinetic studies suggest that chemoselective organic transformations occur on site-isolated, electron-deficient and coordinatively unsaturated metal centres at the SBUs via σ-bond metathesis pathways and as a result of the steric environment around the catalytic site. MOFs thus provide a novel platform for the development of highly active and affordable base metal catalysts for the sustainable synthesis of fine chemicals. PMID:27574182

  13. Organic Materials in the Undergraduate Laboratory: Microscale Synthesis and Investigation of a Donor-Acceptor Molecule

    ERIC Educational Resources Information Center

    Pappenfus, Ted M.; Schliep, Karl B.; Dissanayake, Anudaththa; Ludden, Trevor; Nieto-Ortega, Belen; Lopez Navarrete, Juan T.; Ruiz Delgado, M. Carmen; Casado, Juan

    2012-01-01

    A series of experiments for undergraduate courses (e.g., organic, physical) have been developed in the area of small molecule organic materials. These experiments focus on understanding the electronic and redox properties of a donor-acceptor molecule that is prepared in a convenient one-step microscale reaction. The resulting intensely colored…

  14. High-resolution NMR of hydrogen in organic solids by DNP enhanced natural abundance deuterium spectroscopy

    NASA Astrophysics Data System (ADS)

    Rossini, Aaron J.; Schlagnitweit, Judith; Lesage, Anne; Emsley, Lyndon

    2015-10-01

    We demonstrate that high field (9.4 T) dynamic nuclear polarization (DNP) at cryogenic (∼100 K) sample temperatures enables the rapid acquisition of natural abundance 1H-2H cross-polarization magic angle spinning (CPMAS) solid-state NMR spectra of organic solids. Spectra were obtained by impregnating substrates with a solution of the stable DNP polarizing agent TEKPol in tetrachloroethane. Tetrachloroethane is a non-solvent for the solids, and the unmodified substrates are then polarized through spin diffusion. High quality natural abundance 2H CPMAS spectra of histidine hydrochloride monohydrate, glycylglycine and theophylline were acquired in less than 2 h, providing direct access to hydrogen chemical shifts and quadrupolar couplings. The spectral resolution of the 2H solid-state NMR spectra is comparable to that of 1H spectra obtained with state of the art homonuclear decoupling techniques.

  15. High-resolution NMR of hydrogen in organic solids by DNP enhanced natural abundance deuterium spectroscopy.

    PubMed

    Rossini, Aaron J; Schlagnitweit, Judith; Lesage, Anne; Emsley, Lyndon

    2015-10-01

    We demonstrate that high field (9.4 T) dynamic nuclear polarization (DNP) at cryogenic (∼100 K) sample temperatures enables the rapid acquisition of natural abundance (1)H-(2)H cross-polarization magic angle spinning (CPMAS) solid-state NMR spectra of organic solids. Spectra were obtained by impregnating substrates with a solution of the stable DNP polarizing agent TEKPol in tetrachloroethane. Tetrachloroethane is a non-solvent for the solids, and the unmodified substrates are then polarized through spin diffusion. High quality natural abundance (2)H CPMAS spectra of histidine hydrochloride monohydrate, glycylglycine and theophylline were acquired in less than 2h, providing direct access to hydrogen chemical shifts and quadrupolar couplings. The spectral resolution of the (2)H solid-state NMR spectra is comparable to that of (1)H spectra obtained with state of the art homonuclear decoupling techniques. PMID:26363582

  16. A human interactome in three quantitative dimensions organized by stoichiometries and abundances.

    PubMed

    Hein, Marco Y; Hubner, Nina C; Poser, Ina; Cox, Jürgen; Nagaraj, Nagarjuna; Toyoda, Yusuke; Gak, Igor A; Weisswange, Ina; Mansfeld, Jörg; Buchholz, Frank; Hyman, Anthony A; Mann, Matthias

    2015-10-22

    The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connected proteins, both of which span orders of magnitude. However, these aspects have not yet been analyzed globally. Here, we have generated a library of HeLa cell lines expressing 1,125 GFP-tagged proteins under near-endogenous control, which we used as input for a next-generation interaction survey. Using quantitative proteomics, we detect specific interactions, estimate interaction stoichiometries, and measure cellular abundances of interacting proteins. These three quantitative dimensions reveal that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topology. The minority of stable complexes can be identified by their unique stoichiometry signature. This study provides a rich interaction dataset connecting thousands of proteins and introduces a framework for quantitative network analysis. PMID:26496610

  17. Probabilisitc Geobiological Classification Using Elemental Abundance Distributions and Lossless Image Compression in Recent and Modern Organisms

    NASA Technical Reports Server (NTRS)

    Storrie-Lombardi, Michael C.; Hoover, Richard B.

    2005-01-01

    Last year we presented techniques for the detection of fossils during robotic missions to Mars using both structural and chemical signatures[Storrie-Lombardi and Hoover, 2004]. Analyses included lossless compression of photographic images to estimate the relative complexity of a putative fossil compared to the rock matrix [Corsetti and Storrie-Lombardi, 2003] and elemental abundance distributions to provide mineralogical classification of the rock matrix [Storrie-Lombardi and Fisk, 2004]. We presented a classification strategy employing two exploratory classification algorithms (Principal Component Analysis and Hierarchical Cluster Analysis) and non-linear stochastic neural network to produce a Bayesian estimate of classification accuracy. We now present an extension of our previous experiments exploring putative fossil forms morphologically resembling cyanobacteria discovered in the Orgueil meteorite. Elemental abundances (C6, N7, O8, Na11, Mg12, Ai13, Si14, P15, S16, Cl17, K19, Ca20, Fe26) obtained for both extant cyanobacteria and fossil trilobites produce signatures readily distinguishing them from meteorite targets. When compared to elemental abundance signatures for extant cyanobacteria Orgueil structures exhibit decreased abundances for C6, N7, Na11, All3, P15, Cl17, K19, Ca20 and increases in Mg12, S16, Fe26. Diatoms and silicified portions of cyanobacterial sheaths exhibiting high levels of silicon and correspondingly low levels of carbon cluster more closely with terrestrial fossils than with extant cyanobacteria. Compression indices verify that variations in random and redundant textural patterns between perceived forms and the background matrix contribute significantly to morphological visual identification. The results provide a quantitative probabilistic methodology for discriminating putatitive fossils from the surrounding rock matrix and &om extant organisms using both structural and chemical information. The techniques described appear applicable

  18. Protostellar Interferometric Line Survey (PILS): Constraining the formation of complex organic molecules with ALMA

    NASA Astrophysics Data System (ADS)

    Jorgensen, Jes K.; Coutens, Audrey; Bourke, Tyler L.; Favre, Cecile; Garrod, Robin; Lykke, Julie; Mueller, Holger; Oberg, Karin I.; Schmalzl, Markus; van der Wiel, Matthijs; van Dishoeck, Ewine; Wampfler, Susanne F.

    2015-08-01

    Understanding how, when and where complex organic and potentially prebiotic molecules are formed is a fundamental goal of astrochemistry and an integral part of origins of life studies. Already now ALMA is showing its capabilities for studies of the chemistry of solar-type stars with its high sensitivity for faint lines, high spectral resolution which limits line confusion, and high angular resolution making it possible to study the structure of young protostars on solar-system scales. We here present the first results from a large unbiased survey “Protostellar Interferometric Line Survey (PILS)” targeting one of the astrochemical template sources, the low-mass protostellar binary IRAS 16293-2422. The survey is more than an order of magnitude more sensitive than previous surveys of the source and provide imaging down to 25 AU scales (radius) around each of the two components of the binary. An example of one of the early highlights from the survey is unambiguous detections of the (related) prebiotic species glycolaldehyde, ethylene glycol (two lowest energy conformers), methyl formate and acetic acid. The glycolaldehyde-ethylene glycol abundance ratio is high in comparison to comets and other protostars - but agrees with previous measurements, e.g., in the Galactic Centre clouds possibly reflecting different environments and/or evolutionary histories. Complete mapping of this and other chemical networks in comparison with detailed chemical models and laboratory experiments will reveal the origin of complex organic molecules in a young protostellar system and investigate the link between these protostellar stages and the early Solar System.

  19. Selective laser photolysis of organic molecules in complex matrices

    NASA Astrophysics Data System (ADS)

    Moulin, Christophe; Petit, Alain D.

    1995-03-01

    Natural extracts or essences are largely used in several fields (farm- produce industry, cosmetic, perfumery, biochemistry, etc.). However, most of these complex extracts contain also toxic, carcinogenic or non desirable molecules. By using a laser directly tuned to an absorption band of the unwanted molecules, selective elimination is obtained. Advantages of this procedure are the rapidity, in situ reaction and the possibility to perform quantitative elimination. Examples such as the destruction of thujone in extract of Salvia, bergaptene in essence of Bergamote, phycocyanin in Porphyridium Cruentum or simply dye will be presented and discussed.

  20. Prediction of nonlinear optical properties of large organic molecules

    NASA Technical Reports Server (NTRS)

    Cardelino, Beatriz H.

    1992-01-01

    The preparation of materials with large nonlinear responses usually requires involved synthetic processes. Thus, it is very advantageous for materials scientists to have a means of predicting nonlinear optical properties. The prediction of nonlinear optical properties has to be addressed first at the molecular level and then as bulk material. For relatively large molecules, two types of calculations may be used, which are the sum-over-states and the finite-field approach. The finite-field method was selected for this research, because this approach is better suited for larger molecules.

  1. Preservation of Organic Molecules at Mars' Near-Surface

    NASA Astrophysics Data System (ADS)

    Freissinet, C.; Glavin, D. P.; Buch, A.; Szopa, C.; Archer, P. D.; Brinckerhoff, W. B.; Brunner, A. E.; Eigenbrode, J. L.; Franz, H. B.; Kashyap, S.; Malespin, C. A.; Millan, M.; Miller, K. E.; Navarro-Gonzalez, R.; Prats, B. D.; Summons, R. E.; Teinturier, S.; Mahaffy, P. R.

    2016-05-01

    Detection of organics at Mars' surface is challenged by its degradation. Curiosity rover was able to detect some organics in a martian mudstone, providing a context for a habitable environment and raising the possibility for detecting biosignatures.

  2. Effect of nontronite smectite clay on the chemical evolution of several organic molecules under simulated Mars surface UV radiation conditions

    NASA Astrophysics Data System (ADS)

    Poch, Olivier; Dequaire, Tristan; Stalport, Fabien; Jaber, Maguy; Lambert, Jean-François; Szopa, Cyril; Coll, Patrice

    2015-04-01

    The search for organic carbon-containing molecules at the surface of Mars, as clues of past habitability or remnants of life, is a major scientific goal for Mars exploration. Several lines of evidence, including the detection of phyllosilicates, suggest that early Mars offered favorable conditions for long-term sustaining of water. As a consequence, we can assume that in those days, endogenous chemical processes, or even primitive life, may have produced organic matter on Mars. Moreover, exogenous delivery from small bodies or dust particles is likely to have brought fresh organic molecules to the surface of Mars up today. Organic matter is therefore expected to be present at the surface/subsurface of the planet. But the current environmental conditions at the surface - UV radiation, oxidants and energetic particles - generate physico-chemical processes that may affect organic molecules. On the other hand, on Earth, phyllosilicates are known to accumulate and preserve organic matter. But are phyllosilicates efficient at preserving organic molecules under the current environmental conditions at the surface of Mars? We have monitored the qualitative and quantitative evolutions of glycine, urea and adenine interacting with the Fe3+-smectite clay nontronite, one of the most abundant phyllosilicates present at the surface of Mars, under simulated Martian surface ultraviolet light (190-400 nm), mean temperature (218 ± 2 K) and pressure (6 ± 1 mbar) in a laboratory simulation setup. We have tested organic-rich samples which may be representative of the evaporation of a warm little pond of liquid water having concentrated organics on Mars. For each molecule, we have observed how the nontronite influences the quantum efficiency of its photodecomposition and the nature of its solid evolution products. The results reveal a pronounced photoprotective effect of nontronite on the evolution of glycine and adenine: their efficiencies of photodecomposition are reduced by a factor

  3. Evolution of complex organic molecules in hot molecular cores. Synthetic spectra at (sub-)mm wavebands

    NASA Astrophysics Data System (ADS)

    Choudhury, R.; Schilke, P.; Stéphan, G.; Bergin, E.; Möller, T.; Schmiedeke, A.; Zernickel, A.

    2015-03-01

    Context. Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich chemical reservoirs and emission line spectra at (sub-)mm wavebands. Complex organic molecules (COMs) such as methanol (CH3OH), ethanol (C2H5OH), dimethyl ether (CH3OCH3), and methyl formate (HCOOCH3) produce most of these observed lines. The observed spectral feature of HMCs such as total number of emission lines and associated line intensities are also found to vary with evolutionary stages. Aims: We aim to investigate the spectral evolution of these COMs to explore the initial evolutionary stages of high-mass star formation including HMCs. Methods: We developed various 3D models for HMCs guided by the evolutionary scenarios proposed by recent empirical and modeling studies. We then investigated the spatio-temporal variation of temperature and molecular abundances in HMCs by consistently coupling gas-grain chemical evolution with radiative transfer calculations. We explored the effects of varying physical conditions on molecular abundances including density distribution and luminosity evolution of the central protostar(s) among other parameters. Finally, we simulated the synthetic spectra for these models at different evolutionary timescales to compare with observations. Results: Temperature has a profound effect on the formation of COMs through the depletion and diffusion on grain surface to desorption and further gas-phase processing. The time-dependent temperature structure of the hot core models provides a realistic framework for investigating the spatial variation of ice mantle evaporation as a function of evolutionary timescales. We find that a slightly higher value (15 K) than the canonical dark cloud temperature (10 K) provides a more productive environment for COM formation on grain surface. With increasing protostellar luminosity, the water ice evaporation font (~100 K) expands and the spatial distribution of gas phase abundances of

  4. Study of Martian Organic Molecules Irradiation and Evolution: The Momie Experiment

    NASA Astrophysics Data System (ADS)

    Coll, Patrice; Stalport, F.; Szopa, C.; Cottin, H.

    2007-12-01

    The life on Mars remains an open question despite the Viking landers results and the ALH84001 possible terrestrial contamination. However recent data of Mars Express orbiter and the twin rovers Spirit and Opportunity seem show different proofs of a past environment with liquid water and mild temperatures favorable for life. Among the biomarkers we seek, the organic molecules are primordial because they are necessary to the origin of life as we know it. However, these molecules (except methane recently discovered) have never been detected on Mars by the in situ analyzes of the Viking landers. A key question is to know if organic molecules are indeed present, in which concentration and under which form. Indeed, even if endogenous organic molecules were never synthesized, those brought by exogenous sources, like interplanetary dust, should be present in detectable amount. Moreover, the track of the endogenous organic molecules should not be dropped out because these molecules are able to resist over periods of several billion years without being degraded. It thus appears that organic molecules could be present at the surface of Mars, even if they have significant chances to undergo a partial or total chemical evolution. Within the framework of a search for organic molecules by present or future space experiments , we are developing the MOMIE project (Martian Organic Material Irradiation and Evolution) in order to determine how the organic species evolve on the Martian surface. We thus propose to implement this type of research with the assistance of an experimental setup designed for the study of the behavior of organic molecules under conditions simulating as close as possible conditions of Mars surface, and plan to present at 39th DPS our first results.

  5. From Halogen to Superhalogen Behavior of Organic Molecules Created by Functionalizing Benzene.

    PubMed

    Zhao, Hongmin; Zhou, Jian; Fang, Hong; Jena, Puru

    2016-01-01

    Benzene, the classic organic molecule obeying Hückel's rule of aromaticity, has negative electron affinity (EA), namely -1.15 eV. By using density functional theory with hybrid functional for exchange and correlation potential, we show that a series of organic molecules created by changing either the benzene core or the ligands, or both, result in species with EAs that range from 2.15 to 5.37 eV. This shows that ligand substitution is more effective than aromaticity in increasing the EA of organic molecules. The ability to create highly electronegative organic molecules by functionalizing benzene may provide new opportunities for synthesizing organic oxidizing agents with potential new applications. PMID:26467557

  6. Single-Molecule Magnet Behavior of Individual Polyoxometalate Molecules Incorporated within Biopolymer or Metal-Organic Framework Matrices.

    PubMed

    Salomon, William; Lan, Yanhua; Rivière, Eric; Yang, Shu; Roch-Marchal, Catherine; Dolbecq, Anne; Simonnet-Jégat, Corine; Steunou, Nathalie; Leclerc-Laronze, Nathalie; Ruhlmann, Laurent; Mallah, Talal; Wernsdorfer, Wolfgang; Mialane, Pierre

    2016-05-01

    The chemically and structurally highly stable polyoxometalate (POM) single-molecule magnet (SMM) [(FeW9 O34 )2 Fe4 (H2 O)2 ](10-) (Fe6 W18 ) has been incorporated by direct or post-synthetic approaches into a biopolymer gelatin (Gel) matrix and two crystalline metal-organic frameworks (MOFs), including one diamagnetic (UiO-67) and one magnetic (MIL-101(Cr)). Integrity of the POM in the Fe6 W18 @Gel, Fe6 W18 @UiO-67 and Fe6 W18 @MIL-101(Cr) composites was confirmed by a set of complementary techniques. Magnetic studies indicate that the POMs are magnetically well isolated. Remarkably, in Fe6 W18 @Gel, the SMM properties of the embedded molecules are close to those of the crystals, with clear quantum tunneling steps in the hysteresis loops. For the Fe6 W18 @UiO-67 composite, the molecules retain their SMM properties, the energy barrier being slightly reduced in comparison to the crystalline material and the molecules exhibiting a tunneling rate of magnetization significantly faster than for Fe6 W18 @Gel. When Fe6 W18 is introduced into MIL-101(Cr), the width of the hysteresis loops is drastically reduced and the quantum tunneling steps are smeared out because of the magnetic interactions between the antiferromagnetic matrix and the SMM guest molecules. PMID:27080557

  7. Atomic-scale surface roughness of rutile and implications for organic molecule adsorption.

    PubMed

    Livi, Kenneth J T; Schaffer, Bernhard; Azzolini, David; Seabourne, Che R; Hardcastle, Trevor P; Scott, Andrew J; Hazen, Robert M; Erlebacher, Jonah D; Brydson, Rik; Sverjensky, Dimitri A

    2013-06-11

    Crystal surfaces provide physical interfaces between the geosphere and biosphere. It follows that the arrangement of atoms at the surfaces of crystals profoundly influences biological components at many levels, from cells through biopolymers to single organic molecules. Many studies have focused on the crystal-molecule interface in water using large, flat single crystals. However, little is known about atomic-scale surface structures of the nanometer- to micrometer-sized crystals of simple metal oxides typically used in batch adsorption experiments under conditions relevant to biogeochemistry and the origins of life. Here, we present atomic-resolution microscopy data with unprecedented detail of the circumferences of nanosized rutile (α-TiO2) crystals previously used in studies of the adsorption of protons, cations, and amino acids. The data suggest that one-third of the {110} faces, the largest faces on individual crystals, consist of steps at the atomic scale. The steps have the orientation to provide undercoordinated Ti atoms of the type and abundance for adsorption of amino acids as inferred from previous surface complexation modeling of batch adsorption data. A remarkably uniform pattern of step proportions emerges: the step proportions are independent of surface roughness and reflect their relative surface energies. Consequently, the external morphology of rutile nanometer- to micrometer-sized crystals imaged at the coarse scale of scanning electron microscope images is not an accurate indicator of the atomic smoothness or of the proportions of the steps present. Overall, our data strongly suggest that amino acids attach at these steps on the {110} surfaces of rutile. PMID:23675906

  8. Effect of organic molecules on hydrolysis of peptide bond: A DFT study

    NASA Astrophysics Data System (ADS)

    Makshakova, Olga; Ermakova, Elena

    2013-03-01

    The activation and inhibition effects of small organic molecules on peptide hydrolysis have been studied using a model compound dialanine and DFT approach. Solvent-assisted and non-assisted concerted mechanisms were analyzed. Several transition states for the systems: alanine dipeptide-water molecule in complexes with alcohol molecules, acetonitrile, dimethylsulfoxide, propionic, lactic and pyruvic acids and water molecules were localized. The formation of hydrogen bonds between dipeptide, reactive water molecule and molecules of solvents influences the activation energy barrier of the peptide bond hydrolytic reaction. Strong effect of organic acids on the activation energy barrier correlates with their electronegativity. Acetonitrile can act as an inhibitor of reaction. Mechanisms of regulation of the activation energy barrier are discussed in the terms of donor-acceptor interactions.

  9. Formation of complex organic molecules in cold objects: the role of gas-phase reactions

    NASA Astrophysics Data System (ADS)

    Balucani, Nadia; Ceccarelli, Cecilia; Taquet, Vianney

    2015-04-01

    While astrochemical models are successful in reproducing many of the observed interstellar species, they have been struggling to explain the observed abundances of complex organic molecules. Current models tend to privilege grain surface over gas-phase chemistry in their formation. One key assumption of those models is that radicals trapped in the grain mantles gain mobility and react on lukewarm ( ≳ 30 K) dust grains. Thus, the recent detections of methyl formate (MF) and dimethyl ether (DME) in cold objects represent a challenge and may clarify the respective role of grain-surface and gas-phase chemistry. We propose here a new model to form DME and MF with gas-phase reactions in cold environments, where DME is the precursor of MF via an efficient reaction overlooked by previous models. Furthermore, methoxy, a precursor of DME, is also synthesized in the gas phase from methanol, which is desorbed by a non-thermal process from the ices. Our new model reproduces fairly well the observations towards L1544. It also explains, in a natural way, the observed correlation between DME and MF. We conclude that gas-phase reactions are major actors in the formation of MF, DME and methoxy in cold gas. This challenges the exclusive role of grain-surface chemistry and favours a combined grain-gas chemistry.

  10. Separation of rare gases and chiral molecules by selective binding in porous organic cages.

    PubMed

    Chen, Linjiang; Reiss, Paul S; Chong, Samantha Y; Holden, Daniel; Jelfs, Kim E; Hasell, Tom; Little, Marc A; Kewley, Adam; Briggs, Michael E; Stephenson, Andrew; Thomas, K Mark; Armstrong, Jayne A; Bell, Jon; Busto, Jose; Noel, Raymond; Liu, Jian; Strachan, Denis M; Thallapally, Praveen K; Cooper, Andrew I

    2014-10-01

    The separation of molecules with similar size and shape is an important technological challenge. For example, rare gases can pose either an economic opportunity or an environmental hazard and there is a need to separate these spherical molecules selectively at low concentrations in air. Likewise, chiral molecules are important building blocks for pharmaceuticals, but chiral enantiomers, by definition, have identical size and shape, and their separation can be challenging. Here we show that a porous organic cage molecule has unprecedented performance in the solid state for the separation of rare gases, such as krypton and xenon. The selectivity arises from a precise size match between the rare gas and the organic cage cavity, as predicted by molecular simulations. Breakthrough experiments demonstrate real practical potential for the separation of krypton, xenon and radon from air at concentrations of only a few parts per million. We also demonstrate selective binding of chiral organic molecules such as 1-phenylethanol, suggesting applications in enantioselective separation. PMID:25038731

  11. Development of high harmonic generation spectroscopy of organic molecules and biomolecules

    NASA Astrophysics Data System (ADS)

    Marangos, J. P.

    2016-07-01

    In this review we will discuss the topic of high order harmonic generation (HHG) from samples of organic and bio-molecules. The possibility to extract useful dynamical and structural information from the measurement of the HHG emission, a technique termed high harmonic generation spectroscopy (HHGS), will be the special focus of our discussions. We will begin by introducing the salient facts of HHG from atoms and simple molecules and explaining the principles behind HHGS. Next the technical difficulties associated with HHG from samples of organic molecules and biomolecules, principally the low sample density and the low ionization potential, will be examined. Then we will present some recent experiments where HHG spectra from samples of these molecules have been measured and discuss what has been learned from these measurements. Finally we will look at the future prospects for HHG spectroscopy of organic molecules, discussing some of the technical and in principle limits of the technique and methods that may ameliorate these limits.

  12. Separation of rare gases and chiral molecules by selective binding in porous organic cages

    NASA Astrophysics Data System (ADS)

    Chen, Linjiang; Reiss, Paul S.; Chong, Samantha Y.; Holden, Daniel; Jelfs, Kim E.; Hasell, Tom; Little, Marc A.; Kewley, Adam; Briggs, Michael E.; Stephenson, Andrew; Thomas, K. Mark; Armstrong, Jayne A.; Bell, Jon; Busto, Jose; Noel, Raymond; Liu, Jian; Strachan, Denis M.; Thallapally, Praveen K.; Cooper, Andrew I.

    2014-10-01

    The separation of molecules with similar size and shape is an important technological challenge. For example, rare gases can pose either an economic opportunity or an environmental hazard and there is a need to separate these spherical molecules selectively at low concentrations in air. Likewise, chiral molecules are important building blocks for pharmaceuticals, but chiral enantiomers, by definition, have identical size and shape, and their separation can be challenging. Here we show that a porous organic cage molecule has unprecedented performance in the solid state for the separation of rare gases, such as krypton and xenon. The selectivity arises from a precise size match between the rare gas and the organic cage cavity, as predicted by molecular simulations. Breakthrough experiments demonstrate real practical potential for the separation of krypton, xenon and radon from air at concentrations of only a few parts per million. We also demonstrate selective binding of chiral organic molecules such as 1-phenylethanol, suggesting applications in enantioselective separation.

  13. Exploring molecular complexity with ALMA (EMoCA): Deuterated complex organic molecules in Sagittarius B2(N2)

    NASA Astrophysics Data System (ADS)

    Belloche, A.; Müller, H. S. P.; Garrod, R. T.; Menten, K. M.

    2016-03-01

    Context. Deuteration is a powerful tracer of the history of the cold prestellar phase in star-forming regions. Apart from methanol, little is known about deuterium fractionation of complex organic molecules in the interstellar medium, especially in regions forming high-mass stars. Aims: Our goal is to detect deuterated complex organic molecules toward the high mass star-forming region Sagittarius B2 (Sgr B2) and derive the level of deuteration for these molecules. Methods: We use a complete 3-mm spectral line survey performed with the Atacama Large Millimeter/submillimeter Array (ALMA) to search for deuterated complex organic molecules toward the hot molecular core Sgr B2(N2). We constructed population diagrams and integrated intensity maps to fit rotational temperatures and emission sizes for each molecule. Column densities are derived by modeling the full spectrum under the assumption of local thermodynamic equilibrium. We compare the results to predictions of two astrochemical models that treat the deuteration process. Results: We report the detection of CH2DCN toward Sgr B2(N2) with a deuteration level of 0.4%, and tentative detections of CH2DOH, CH2DCH2CN, the chiral molecule CH3CHDCN, and DC3N with levels in the range 0.05%-0.12%. A stringent deuteration upper limit is obtained for CH3OD (<0.07%). Upper limits in the range 0.5-1.8% are derived for the three deuterated isotopologues of vinyl cyanide, the four deuterated species of ethanol, and CH2DOCHO. Ethyl cyanide is less deuterated than methyl cyanide by at least a factor five. The [CH2DOH]/[CH3OD] abundance ratio is higher than 1.8. It may still be consistent with the value obtained in Orion KL. Except for methyl cyanide, the measured deuteration levels lie at least a factor four below the predictions of current astrochemical models. The deuteration levels in Sgr B2(N2) are also lower than in Orion KL by a factor of a few up to a factor ten. Conclusions: The discrepancy between the deuteration levels of

  14. Adsorption of two gas molecules at a single metal site in a metal-organic framework.

    PubMed

    Runčevski, Tomče; Kapelewski, Matthew T; Torres-Gavosto, Rodolfo M; Tarver, Jacob D; Brown, Craig M; Long, Jeffrey R

    2016-07-01

    One strategy to markedly increase the gas storage capacity of metal-organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules-specifically hydrogen, methane, or carbon dioxide. PMID:27284590

  15. Adsorption of two gas molecules at a single metal site in a metal–organic framework

    SciTech Connect

    Runčevski, Tomče; Kapelewski, Matthew T.; Torres-Gavosto, Rodolfo M.; Tarver, Jacob D.; Brown, Craig M.; Long, Jeffrey R.

    2016-01-01

    One strategy to markedly increase the gas storage capacity of metal-organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules--specifically hydrogen, methane, or carbon dioxide.

  16. Inorganic-Organic Molecules and Solids with Nanometer-Sized Pores

    SciTech Connect

    Maverick, Andrew W

    2011-12-17

    We are constructing porous inorganic-organic hybrid molecules and solids, many of which contain coordinatively unsaturated metal centers. In this work, we use multifunctional ²-diketone ligands as building blocks to prepare extended-solid and molecular porous materials that are capable of reacting with a variety of guest molecules.

  17. Tunneling spectroscopy of organic monolayers and single molecules.

    PubMed

    Hipps, K W

    2012-01-01

    Basic concepts in tunneling spectroscopy applied to molecular systems are presented. Junctions of the form M-A-M, M-I-A-M, and M-I-A-I'-M, where A is an active molecular layer, are considered. Inelastic electron tunneling spectroscopy (IETS) is found to be readily applied to all the above device types. It can provide both vibrational and electron spectroscopic data about the molecules comprising the A layer. In IETS there are no strong selection rules (although there are preferences) so that transitions that are normally IR, Raman, or even photon-forbidden can be observed. In the electronic transition domain, spin and Laporte forbidden transitions may be observed. Both vibrational and electronic IETS can be acquired from single molecules. The negative aspect of this seemingly ideal spectroscopic method is the thermal line width of about 5 k(B)T. This limits the useful measurement of vibrational IETS to temperatures below about 10 K. In the case of most electronic transitions where the intrinsic linewidth is much broader, useful experiments above 100 K are possible. One further limitation of electronic IETS is that it is generally limited to transitions with energy less than about 20,000 cm(-1). IETS can be identified by peaks in d(2) I/dV (2) vs bias voltage plots that occur at the same position (but not necessarily same intensity) in either bias polarity.Elastic tunneling spectroscopy is discussed in the context of processes involving molecular ionization and electron affinity states, a technique we call orbital mediated tunneling spectroscopy, or OMTS. OMTS can be applied readily to M-I-A-M and M-I-A-I'-M systems, but application to M-A-M junctions is problematic. Spectra can be obtained from single molecules. Ionization state results correlate well with UPS spectra obtained from the same systems in the same environment. Both ionization and affinity levels measured by OMTS can usually be correlated with one electron oxidation and reduction potentials for the

  18. Preservation of Organic Molecules Under Cosmic Rays in Martian Surface Rocks

    NASA Astrophysics Data System (ADS)

    Pavlov, A. A.; Glavin, D.; McLain, H.; Dworkin, J.; Elsila-Cook, J.; Eigenbrode, J.

    2016-05-01

    Organic molecules are destroyed in the surface rocks of Mars by cosmic rays at faster rates than was assumed in previous studies. Only surface rocks, with an exposure age of less than 50 million years, might contain unaltered amino acids.

  19. PICOSECOND IR MALDI MASS SPECTROMETRY OF ORGANIC MOLECULES ON NITRATE CRYSTALLITES

    EPA Science Inventory

    A critical problem in environmental science and engineering is tracking organic molecules and metal complexes in soils and other poorly characterized systems. We have extended the technique of MALDI mass spectrometry (MS), largely the province of biomolecular characterization, t...

  20. Predators alter community organization of coral reef cryptofauna and reduce abundance of coral mutualists

    NASA Astrophysics Data System (ADS)

    Stier, A. C.; Leray, M.

    2014-03-01

    Coral reefs are the most diverse marine systems in the world, yet our understanding of the processes that maintain such extraordinary diversity remains limited and taxonomically biased toward the most conspicuous species. Cryptofauna that live deeply embedded within the interstitial spaces of coral reefs make up the majority of reef diversity, and many of these species provide important protective services to their coral hosts. However, we know very little about the processes governing the diversity and composition of these less conspicuous but functionally important species. Here, we experimentally quantify the role of predation in driving the community organization of small fishes and decapods that live embedded within Pocillopora eydouxi, a structurally complex, reef-building coral found widely across the Indo-Pacific. We use surveys to describe the natural distribution of predators, and then, factorially manipulate two focal predator species to quantify the independent and combined effects of predator density and identity on P. eydouxi-dwelling cryptofauna. Predators reduced abundance (34 %), species richness (20 %), and modified species composition. Rarefaction revealed that observed reductions in species richness were primarily driven by changes in abundance. Additionally, the two predator species uniquely affected the beta diversity and composition of the prey assemblage. Predators reduced the abundance and modified the composition of a number of mutualist fishes and decapods, whose benefit to the coral is known to be both diversity- and density-dependent. We predict that the density and identity of predators present within P. eydouxi may substantially alter coral performance in the face of an increased frequency and intensity of natural and anthropogenic stressors.

  1. Growth of Ammonium Bisulfate Clusters by Adsorption of Oxygenated Organic Molecules.

    PubMed

    DePalma, Joseph W; Wang, Jian; Wexler, Anthony S; Johnston, Murray V

    2015-11-12

    Quantum chemical calculations were employed to model the interactions of the [(NH4(+))4(HSO4(-))4] ammonium bisulfate cluster with one or more molecular products of monoterpene oxidation. A strong interaction was found between the bisulfate ion of this cluster and a carboxylic acid, aldehyde, or ketone functionality of the organic molecule. Free energies of adsorption for carboxylic acids were in the -70 to -73 kJ/mol range, while those for aldehydes and ketones were in the -46 to -50 kJ/mol range. These values suggest that a small ambient [(NH4(+))4(SO4(-))4]cluster is able to adsorb an oxygenated organic molecule. While adsorption of the first molecule is highly favorable, adsorption of subsequent molecules is less so, suggesting that sustained uptake of organic molecules does not occur, and thus is not a pathway for continuing growth of the cluster. This result is consistent with ambient measurements showing that particles below ∼1 nm grow slowly, while those above 1 nm grow at an increasing rate presumably due to a lower surface energy barrier enabling the uptake of organic molecules. This work provides insight into the molecular level interactions which affect sustained cluster growth by uptake of organic molecules. PMID:26488562

  2. Growth of Ammonium Bisulfate Clusters by Adsorption of Oxygenated Organic Molecules

    SciTech Connect

    DePalma, Joseph W.; Wang, Jian; Wexler, Anthony S.; Johnston, Murray V.

    2015-10-21

    Quantum chemical calculations were employed to model the interactions of the [(NH4+)4(HSO4-)4] ammonium bisulfate cluster with one or more molecular products of monoterpene oxidation. A strong interaction was found between the bisulfate ion of the cluster and a carboxylic acid, aldehyde or ketone functionality of the organic molecule. Free energies of adsorption for carboxylic acids were in the -70 to -73 kJ/mol range, while those for aldehydes and ketones were in the -46 to -50 kJ/mol range. These values suggest that a small ambient ammonium bisulfate cluster, such as the [(NH4+)4(SO4-)4] cluster, is able to adsorb an oxygenated organic molecule. Although adsorption of the first molecule is highly favorable, adsorption of subsequent molecules is not, suggesting that sustained uptake of organic molecules does not occur, and thus is not a pathway for continuing growth of the cluster. This result is consistent with ambient measurements showing that particles below ~1 nm grow slowly, while those above 1 nm grow at an increasing rate presumably due to a lower surface energy barrier enabling the uptake of organic molecules. This work provides insight into the molecular level interactions which affect sustained cluster growth by uptake of organic molecules.

  3. Growth of Ammonium Bisulfate Clusters by Adsorption of Oxygenated Organic Molecules

    DOE PAGESBeta

    DePalma, Joseph W.; Wang, Jian; Wexler, Anthony S.; Johnston, Murray V.

    2015-10-21

    Quantum chemical calculations were employed to model the interactions of the [(NH4+)4(HSO4-)4] ammonium bisulfate cluster with one or more molecular products of monoterpene oxidation. A strong interaction was found between the bisulfate ion of the cluster and a carboxylic acid, aldehyde or ketone functionality of the organic molecule. Free energies of adsorption for carboxylic acids were in the -70 to -73 kJ/mol range, while those for aldehydes and ketones were in the -46 to -50 kJ/mol range. These values suggest that a small ambient ammonium bisulfate cluster, such as the [(NH4+)4(SO4-)4] cluster, is able to adsorb an oxygenated organic molecule.more » Although adsorption of the first molecule is highly favorable, adsorption of subsequent molecules is not, suggesting that sustained uptake of organic molecules does not occur, and thus is not a pathway for continuing growth of the cluster. This result is consistent with ambient measurements showing that particles below ~1 nm grow slowly, while those above 1 nm grow at an increasing rate presumably due to a lower surface energy barrier enabling the uptake of organic molecules. This work provides insight into the molecular level interactions which affect sustained cluster growth by uptake of organic molecules.« less

  4. Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities

    SciTech Connect

    Podar, Mircea; Abulencia, Carl; Walcher, Marion; Hutchinson, Don; Zengler, Karsten; Garcia, Joseph; Holland, Trevin; Cotton, Dave; Hauser, Loren John; Keller, Martin

    2007-01-01

    Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism, and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequency, especially those representing yet uncultured taxa-which includes the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms directly isolated from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community metabolic potential.

  5. Magnesium sulfate as a key mineral for the detection of organic molecules on Mars using pyrolysis

    NASA Astrophysics Data System (ADS)

    François, P.; Szopa, C.; Buch, A.; Coll, P.; McAdam, A. C.; Mahaffy, P. R.; Freissinet, C.; Glavin, D. P.; Navarro-Gonzalez, R.; Cabane, M.

    2016-01-01

    Pyrolysis of soil or rock samples is the preferred preparation technique used on Mars to search for organic molecules up today. During pyrolysis, oxichlorines present in the soil of Mars release oxidant species that alter the organic molecules potentially contained in the samples collected by the space probes. This process can explain the difficulty experienced by in situ exploration probes to detect organic materials in Mars soil samples until recently. Within a few months, the Curiosity rover should reach and analyze for the first time soils rich in sulfates which could induce a different behavior of the organics during the pyrolysis compared with the types of soils analyzed up today. For this reason, we systematically studied the pyrolysis of organic molecules trapped in magnesium sulfate, in the presence or absence of calcium perchlorate. Our results show that organics trapped in magnesium sulfate can undergo some oxidation and sulfuration during the pyrolysis. But these sulfates are also shown to protect organics trapped inside the crystal lattice and/or present in fluid inclusions from the oxidation induced by the decomposition of calcium perchlorate and probably other oxychlorine phases currently detected on Mars. Trapped organics may also be protected from degradation processes induced by other minerals present in the sample, at least until these organics are released from the pyrolyzed sulfate mineral (~700°C in our experiment). Hence, we suggest magnesium sulfate as one of the minerals to target in priority for the search of organic molecules by the Curiosity and ExoMars 2018 rovers.

  6. Organic Molecules in the Sheepbed Mudstone, Gale Crater, Mars

    NASA Technical Reports Server (NTRS)

    Freissinet, C.; Glavin, D. P.; Mahaffy, P. R.; Miller, K. E.; Eigenbrode, J. L.; Summons, R. E.; Brunner, A. E.; Buch, A.; Szopa, C.; Archer, P. D.; Franz, H. B.; Steele, A.

    2014-01-01

    The Sample Analysis at Mars (SAM) instrument on the Curiosity rover is designed to determine the inventory of organic and inorganic volatiles thermally released from solid samples using a combination of evolved gas analysis (EGA), gas chromatography mass spectrometry (GCMS), and tunable laser spectroscopy. Here we report on various chlorinated hydrocarbons (chloromethanes, chlorobenzene and dichloroalkanes) detected at elevated levels above instrument background at the Cumberland (CB) drill site, and discuss their possible sources.

  7. Differential adsorption of complex organic molecules isomers at interstellar ice surfaces

    NASA Astrophysics Data System (ADS)

    Lattelais, M.; Bertin, M.; Mokrane, H.; Romanzin, C.; Michaut, X.; Jeseck, P.; Fillion, J.-H.; Chaabouni, H.; Congiu, E.; Dulieu, F.; Baouche, S.; Lemaire, J.-L.; Pauzat, , F.; Pilmé, J.; Minot, C.; Ellinger, Y.

    2011-08-01

    Context. Over 20 of the ~150 different species detected in the interstellar and circumstellar media have also been identified in icy environments. For most of the species observed so far in the interstellar medium (ISM), the most abundant isomer of a given generic chemical formula is the most stable one (minimum energy principle - MEP) with few exceptions such as, for example, CH3COOH/HCOOCH3 and CH3CH2OH/CH3OCH3, whose formation is thought to occur on the icy mantles of interstellar grains. Aims: We investigate whether differences found in the compositions of molecular ices and the surrounding gas phase could originate from differences between the adsorption of one isomer from that of another at the ice surface. Methods: We performed a coherent and concerted theoretical/experimental study of the adsorption energies of the four molecules mentioned above, i.e. acetic acid (AA)/methyl formate (MF) and ethanol (EtOH)/dimethyl ether (DME) on the surface of water ice at low temperature. The question was first addressed theoretically at LCT using solid state periodic density functional theory (DFT) to represent the organized solid support. The experimental determination of the ice/molecule interaction energies was then carried out independently by two teams at LPMAA and LERMA/LAMAp using temperature programmed desorption (TPD) under an ultra-high vacuum (UHV) between 70 and 160 K. Results: For each pair of isomers, theory and experiments both agree that the most stable isomer (AA or EtOH) interacts more efficiently with the water ice than the higher energy isomer (MF or DME). This differential adsorption can be clearly seen in the different desorption temperatures of the isomers. It is not related to their intrinsic stability but instead to both AA and EtOH producing more and stronger hydrogen bonds with the ice surface. Conclusions: We show that hydrogen bonding may play an important role in the release of organic species from grains and propose that, depending on the

  8. EVAPORATION: a new vapour pressure estimation methodfor organic molecules including non-additivity and intramolecular interactions

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Ceulemans, K.; Müller, J.-F.

    2011-09-01

    We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict (subcooled) liquid pure compound vapour pressure p0 of organic molecules that requires only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: aldehydes, ketones, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

  9. Complex organic molecules in the interstellar medium: IRAM 30 m line survey of Sagittarius B2(N) and (M)

    NASA Astrophysics Data System (ADS)

    Belloche, A.; Müller, H. S. P.; Menten, K. M.; Schilke, P.; Comito, C.

    2013-11-01

    Context. The discovery of amino acids in meteorites fallen to Earth and the detection of glycine, the simplest of them, in samples returned from a comet to Earth strongly suggest that the chemistry of the interstellar medium is capable of producing such complex organic molecules and that they may be widespread in our Galaxy. Aims: Our goal is to investigate the degree of chemical complexity that can be reached in the interstellar medium, in particular in dense star-forming regions. Methods: We performed an unbiased, spectral line survey toward Sgr B2(N) and (M), two regions where high-mass stars are formed, with the IRAM 30 m telescope in the 3 mm atmospheric transmission window. Partial surveys at 2 and 1.3 mm were performed in parallel. The spectra were analyzed with a simple radiative transfer model that assumes local thermodynamic equilibrium but takes optical depth effects into account. Results: About 3675 and 945 spectral lines with a peak signal-to-noise ratio higher than 4 are detected at 3 mm toward Sgr B2(N) and (M), i.e. about 102 and 26 lines per GHz, respectively. This represents an increase by about a factor of two over previous surveys of Sgr B2. About 70% and 47% of the lines detected toward Sgr B2(N) and (M) are identified and assigned to 56 and 46 distinct molecules as well as to 66 and 54 less abundant isotopologues of these molecules, respectively. In addition, we report the detection of transitions from 59 and 24 catalog entries corresponding to vibrationally or torsionally excited states of some of these molecules, respectively, up to a vibration energy of 1400 cm-1 (2000 K). Excitation temperatures and column densities were derived for each species but should be used with caution. The rotation temperatures of the detected complex molecules typically range from ~50 to 200 K. Among the detected molecules, aminoacetonitrile, n-propyl cyanide, and ethyl formate were reported for the first time in space based on this survey, as were five rare

  10. All organic memory devices utilizing fullerene molecules and insulating polymers

    NASA Astrophysics Data System (ADS)

    Kanwal, Alokik Paul

    The convergence of mobile technologies combined with stricter power requirements and increasing demands have strained the current memory technology. Newer technologies such as phase changing, ferroelectric, and magnetic random access memories are unsatisfactory in meeting the new requirements. We propose a new memory technology based on our initial discovery of charge storage in C60 molecules within poly (4-vinyl phenol) (PVP). To understand the memory potential, we created single-layer devices consisting of ˜30nm films of PVP+C60 sandwiched between aluminum (Al) electrodes. Current versus voltage (I-V) sweeps showed a significant hysteresis of 75nA, with distinguishable memory states. Room temperature charging of C60 was confirmed indirectly through capacitance versus voltage measurements and directly by monitoring the A1g characteristic peak of C60 during Raman measurements. We demonstrated memory operations by applying read-write-erase (RWE) pulses. The PVP+C60 devices exhibited memory retention for over 1 hour and response times of around 10ns. Characteristic hysteresis was demonstrated at the nanoscale. Conduction models were fitted at room temperature to the I-V curves. It was found that combination of direct and Fowler-Nordheim tunneling were the principle conduction mechanisms. For a more technologically viable memory device, we developed a multi-layer device structure, consisting of a polystyrene (PS) capping layer. The resulting asymmetrical I-V curve exhibited a hysteresis ratio of 103 . RWE cycles were measured with clearly distinguishable states. The memory retentions were measured over 2 hours and the response time around 10ns. The stability of the multi-layer devices was improved. I-V measurements at temperatures varying from 4.2 K to 298 K were performed to construct a theoretical model. The I-V curves were found to be temperature independent and exhibited similar tunneling behaviors as the single-layer devices. A simple model for conduction and

  11. UV and VUV Ionization of Organic Molecules, Clusters, and Complexes

    NASA Astrophysics Data System (ADS)

    Marksteiner, Markus; Haslinger, Philipp; Sclafani, Michele; Ulbricht, Hendrik; Arndt, Markus

    2009-08-01

    The generation of organic particle beams is studied in combination with photoionization using UV radiation at 266 nm and vacuum ultraviolet (VUV) light at 157 nm. Single-photon ionization with pulsed VUV light turns out to be sensitive enough to detect various large neutral biomolecular complexes ranging from metal-amino acid complexes to nucleotide clusters and aggregates of polypeptides. Different biomolecular clusters are shown to exhibit rather specific binding characteristics with regard to the various metals that are codesorbed in the source. We also find that the ion signal of gramicidin can be increased by a factor of 15 when the photon energy is increased from 4.66 to 7.9 eV.

  12. Orbital tomography: Deconvoluting photoemission spectra of organic molecules

    NASA Astrophysics Data System (ADS)

    Puschnig, Peter; Reinisch, Eva-Maria; Ules, Thomas; Koller, Georg; Soubatch, Sergey; Ostler, Markus; Romaner, Lorenz; Tautz, F. Stefan; Ambrosch-Draxl, Claudia; Ramsey, Michael G.

    2012-02-01

    We study the interface of an organic monolayer with a metallic surface, i. e., PTCDA (3,4,9,10-perylene-tetracarboxylic-dianhydride) on Ag(110), by means of angle-resolved photoemission spectroscopy (ARPES) and ab initio electronic structure calculations. We present a tomographic method which uses the energy and momentum dependence of ARPES data to deconvolute spectra into individual orbital contributions beyond the limits of energy resolution. This provides an orbital-by-orbital characterization of large adsorbate systems without the need to invoke sophisticated theory of photoemission, allowing us to directly estimate the effects of bonding on individual orbitals. Moreover, this experimental data serves as a most stringent test necessary for the further development of ab initio electronic structure theory.

  13. Quinone-Catalyzed Selective Oxidation of Organic Molecules.

    PubMed

    Wendlandt, Alison E; Stahl, Shannon S

    2015-12-01

    Quinones are common stoichiometric reagents in organic chemistry. Para-quinones with high reduction potentials, such as DDQ and chloranil, are widely used and typically promote hydride abstraction. In recent years, many catalytic applications of these methods have been achieved by using transition metals, electrochemistry, or O2 to regenerate the oxidized quinone in situ. Complementary studies have led to the development of a different class of quinones that resemble the ortho-quinone cofactors in copper amine oxidases and mediate the efficient and selective aerobic and/or electrochemical dehydrogenation of amines. The latter reactions typically proceed by electrophilic transamination and/or addition-elimination reaction mechanisms, rather than hydride abstraction pathways. The collective observations show that the quinone structure has a significant influence on the reaction mechanism and has important implications for the development of new quinone reagents and quinone-catalyzed transformations. PMID:26530485

  14. Effects of multiple levels of social organization on survival and abundance.

    PubMed

    Ward, Eric J; Semmens, Brice X; Holmes, Elizabeth E; Balcomb Iii, Ken C

    2011-04-01

    Identifying how social organization shapes individual behavior, survival, and fecundity of animals that live in groups can inform conservation efforts and improve forecasts of population abundance, even when the mechanism responsible for group-level differences is unknown. We constructed a hierarchical Bayesian model to quantify the relative variability in survival rates among different levels of social organization (matrilines and pods) of an endangered population of killer whales (Orcinus orca). Individual killer whales often participate in group activities such as prey sharing and cooperative hunting. The estimated age-specific survival probabilities and survivorship curves differed considerably among pods and to a lesser extent among matrilines (within pods). Across all pods, males had lower life expectancy than females. Differences in survival between pods may be caused by a combination of factors that vary across the population's range, including reduced prey availability, contaminants in prey, and human activity. Our modeling approach could be applied to demographic rates for other species and for parameters other than survival, including reproduction, prey selection, movement, and detection probabilities. PMID:21054527

  15. Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses.

    PubMed

    Voget, Sonja; Wemheuer, Bernd; Brinkhoff, Thorsten; Vollmers, John; Dietrich, Sascha; Giebel, Helge-Ansgar; Beardsley, Christine; Sardemann, Carla; Bakenhus, Insa; Billerbeck, Sara; Daniel, Rolf; Simon, Meinhard

    2015-02-01

    The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene sequence similarity of >98%, is the largest cluster of the marine Roseobacter clade and most abundant in temperate to (sub)polar oceans, constituting up to 35% of total bacterioplankton. The genome analysis of the first described species of the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of homologous genes with any other organism of this clade. The genome is the smallest of all closed genomes of the Roseobacter clade, exhibits various features of genome streamlining and encompasses genes for aerobic anoxygenic photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical significance of the RCA cluster we investigated a phytoplankton spring bloom in the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean 18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some variations during day and night. The genome of P. temperata RCA23 was also retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82% from stations of the Global Ocean Sampling expedition in the northwestern Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of P. temperata RCA23. This abundant taxon appears to be a major player in ocean biogeochemistry. PMID:25083934

  16. Effect of nontronite smectite clay on the chemical evolution of several organic molecules under simulated martian surface ultraviolet radiation conditions.

    PubMed

    Poch, Olivier; Jaber, Maguy; Stalport, Fabien; Nowak, Sophie; Georgelin, Thomas; Lambert, Jean-François; Szopa, Cyril; Coll, Patrice

    2015-03-01

    Most of the phyllosilicates detected at the surface of Mars today are probably remnants of ancient environments that sustained long-term bodies of liquid water at the surface or subsurface and were possibly favorable for the emergence of life. Consequently, phyllosilicates have become the main mineral target in the search for organics on Mars. But are phyllosilicates efficient at preserving organic molecules under current environmental conditions at the surface of Mars? We monitored the qualitative and quantitative evolutions of glycine, urea, and adenine in interaction with the Fe(3+)-smectite clay nontronite, one of the most abundant phyllosilicates present at the surface of Mars, under simulated martian surface ultraviolet light (190-400 nm), mean temperature (218 ± 2 K), and pressure (6 ± 1 mbar) in a laboratory simulation setup. We tested organic-rich samples that were representative of the evaporation of a small, warm pond of liquid water containing a high concentration of organics. For each molecule, we observed how the nontronite influences its quantum efficiency of photodecomposition and the nature of its solid evolution products. The results reveal a pronounced photoprotective effect of nontronite on the evolution of glycine and adenine; their efficiencies of photodecomposition were reduced by a factor of 5 when mixed at a concentration of 2.6 × 10(-2) mol of molecules per gram of nontronite. Moreover, when the amount of nontronite in the sample of glycine was increased by a factor of 2, the gain of photoprotection was multiplied by a factor of 5. This indicates that the photoprotection provided by the nontronite is not a purely mechanical shielding effect but is also due to stabilizing interactions. No new evolution product was firmly identified, but the results obtained with urea suggest a particular reactivity in the presence of nontronite, leading to an increase of its dissociation rate. PMID:25734356

  17. Highly Crystalline Films of Organic Small Molecules with Alkyl Chains Fabricated by Weak Epitaxy Growth.

    PubMed

    Zhu, Yangjie; Chen, Weiping; Wang, Tong; Wang, Haibo; Wang, Yue; Yan, Donghang

    2016-05-12

    Because side-chain engineering of organic conjugated molecules has been widely utilized to tune organic solid-state optoelectronic properties, the achievement of their high-quality films is important for realizing high-performance devices. Here, highly crystalline films of an organic molecule with short alkyl chains, 5,8,15,18-tetrabutyl-5,8,15,18-tetrahydroindolo[3,2-a]indole[30,20:5,6]quinacridone (C4-IDQA), are fabricated by weak epitaxy growth, and highly oriented, large-area, and continuous films are obtained. Because of the soft matter properties, the C4-IDQA molecules can adjust themselves to realize commensurate epitaxy growth on the inducing layers and exhibited good lattice matching in the thin film phase. The crystalline phase is also observed in thicker C4-IDQA films. The growth behavior of C4-IDQA on the inducing layer is further investigated, including the strong dependence of film morphologies on substrate temperatures and deposition rates due to the poor diffusion ability of C4-IDQA molecules. Moreover, highly crystalline films and high electron field-effect mobility are also obtained for the small molecule N,N'-dioctyl-3,4:9,10-perylene tetracarboxylic diimide (C8-PTCDI), which demonstrate that the weak epitaxy growth method could be an effective way to fabricate highly crystalline films of organic small molecules with flexible side chains. PMID:27116036

  18. Intramolecular Long-Distance Electron Transfer in Organic Molecules

    NASA Astrophysics Data System (ADS)

    Closs, Gerhard L.; Miller, John R.

    1988-04-01

    Intramolecular long-distance electron transfer (ET) has been actively studied in recent years in order to test existing theories in a quantitative way and to provide the necessary constants for predicting ET rates from simple structural parameters. Theoretical predictions of an ``inverted region,'' where increasing the driving force of the reaction will decrease its rate, have begun to be experimentally confirmed. A predicted nonlinear dependence of ET rates on the polarity of the solvent has also been confirmed. This work has implications for the design of efficient photochemical charge-separation devices. Other studies have been directed toward determining the distance dependence of ET reactions. Model studies on different series of compounds give similar distance dependences. When different stereochemical structures are compared, it becomes apparent that geometrical factors must be taken into account. Finally, the mechanism of coupling between donor and acceptor in weakly interacting systems has become of major importance. The theoretical and experimental evidence favors a model in which coupling is provided by the interaction with the orbitals of the intervening molecular fragments, although more experimental evidence is needed. Studies on intramolecular ET in organic model compounds have established that current theories give an adequate description of the process. The separation of electronic from nuclear coordinates is only a convenient approximation applied to many models, but in long-distance ET it works remarkably well. It is particularly gratifying to see Marcus' ideas finally confirmed after three decades of skepticism. By obtaining the numbers for quantitative correlations between rates and distances, these experiments have shown that saturated hydrocarbon fragments can ``conduct'' electrons over tens of angstroms. A dramatic demonstration of this fact has recently been obtained by tunneling electron microscopy on Langmuir-Blodgett films, showing in a

  19. Self-organizing ontology of biochemically relevant small molecules

    PubMed Central

    2012-01-01

    Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology can ease the burden of

  20. Atmospheric Aerosols: Cloud Condensation Nucleus Activity of Selected Organic Molecules

    NASA Astrophysics Data System (ADS)

    Rosenorn, T.; Henning, S.; Hartz, K. H.; Kiss, G.; Pandis, S.; Bilde, M.

    2005-12-01

    Gas/particle partitioning of vapors in the atmosphere plays a major role in both climate through micro meteorology and in the physical and chemical processes of a single particle. This work has focused on the cloud droplet activation of a number of pure and mixed compounds. The means used to investigate these processes have been the University of Copenhagen cloud condensation nucleus counter setup and the Carnegie Mellon University CCNC setup. The importance of correct water activity modeling has been addressed and it has been pointed out that the molecular mass is an important parameter to consider when choosing model compounds for cloud activation models. It was shown that both traditional Kohler theory and Kohler theory modified to account for limited solubility reproduce measurements of soluble compounds well. For less soluble compounds it is necessary to use Kohler theory modified to account for limited solubility. It was also shown that this works for mixtures of compounds containing both inorganic salts and dicarboxylic acids. It has also been shown that particle phase and humidity history is important for activation behavior of particles consisting of two slightly soluble organic substances (succinic and adipic acid) and a soluble salt (NaCl). Model parameters for terpene oxidation product cloud activation have been derived. These are based on two sets of average parameters covering monoterpene oxidation products and sesquiterpene oxidation products. All parameters except the solubility were estimated and an effective solubility was calculated as the fitting parameter. The average solubility of the model compound found for mono terpene oxidation products is similar to those of sodium chloride and ammonium sulfate; however the higher molecular weight leads to a slightly higher activation diameter at fixed supersaturation. On a molar basis the monoterpene oxidation products show a 1.5 times higher effective solubility than the sesquiterpene oxidation products.

  1. Analysis of the Molecules Structure and Vertical Electron Affinity of Organic Gas Impact on Electric Strength

    NASA Astrophysics Data System (ADS)

    Jiao, Juntao; Xiao, Dengming; Zhao, Xiaoling; Deng, Yunkun

    2016-05-01

    It is necessary to find an efficient selection method to pre-analyze the gas electric strength from the perspective of molecule structure and the properties for finding the alternative gases to sulphur hexafluoride (SF6). As the properties of gas are determined by the gas molecule structure, the research on the relationship between the gas molecule structure and the electric strength can contribute to the gas pre-screening and new gas development. In this paper, we calculated the vertical electron affinity, molecule orbits distribution and orbits energy of gas molecules by the means of density functional theory (DFT) for the typical structures of organic gases and compared their electric strengths. By this method, we find part of the key properties of the molecule which are related to the electric strength, including the vertical electron affinity, the lowest unoccupied molecule orbit (LUMO) energy, molecule orbits distribution and negative-ion system energy. We also listed some molecule groups such as unsaturated carbons double bonds (C=C) and carbonitrile bonds (C≡N) which have high electric strength theoretically by this method. supported by National Natural Science Foundation of China (Nos. 51177101 and 51337006)

  2. Seasonal abundance of organic molecular markers in urban particulate matter from Philadelphia, PA

    NASA Astrophysics Data System (ADS)

    Li, Min; McDow, Stephen R.; Tollerud, David J.; Mazurek, Monica A.

    Organic molecular markers were measured in airborne particulate matter (PM10) from the City of Philadelphia North Broad Street air quality monitoring site to identify the seasonal abundance of key tracer compounds together with their dominant sources. Daily PM10 samples were collected seasonally in 2000 for four 2-week periods (January, April, August, and October). The North Broad Street site is within a heavily populated location in Philadelphia, PA. A suite of 52 individual organic marker compounds was monitored in the PM10 samples. Molecular markers, homologous compound series, and nonpolar and polar organic compounds were detected at ng m -3 ambient concentrations using gas chromatography/ion trap mass spectrometry (GC/IT MS). Organic diacids (C 3-C 9) and monoacids (C 10-C 30) had seasonal mass concentrations ranging from 91.0 (winter) to 261.8 ng m -3 (summer). Total n-alkanes (C 25-C 33) ranged from 25.9 (spring) to 49.5 ng m -3 (fall), total PAHs from 2.1 ng m -3 (summer) to 4.1 ng m -3 (winter), and total hopanes ranged from 4.0 ng m -3 (winter) to 7.4 ng m -3 (fall). The molecular marker ambient mass concentrations were normalized by the annual average mass of PM10 elemental carbon (EC) for the central Philadelphia area. The ambient mass concentrations to EC and OC ratios ranged from 2.6×10 -3 for total PAHs to EC to 115.3×10 -3 for total n-alkanoic acids to EC, 0.5×10 -3 for total PAHs to OC to 23.8×10 -3 for total n-alkanoic acids to OC. Ambient concentrations of individual markers are similar to other reported levels for metropolitan Los Angeles, CA and Atlanta, GA. Seasonal and daily variations of marker compounds are consistent with motor vehicle exhaust, particularly in winter. Summer concentration patterns indicate the importance of secondary organic aerosol to the PM10 ambient mass.

  3. Selective transformation of carbonyl ligands to organic molecules

    SciTech Connect

    Cutler, A.R.

    1992-05-12

    Studies on the carbonylation of ({eta}{sup 5}-indenyl)(L)(CO)Ru-R complexes (L = CO, PPh{sub 3}; R = CH{sub 2}OMe, CH{sub 3}) have been completed. Particularly noteworthy is that the methoxymethyl complexes readily transform to their acyl derivatives under mild conditions that leave their iron congeners inert towards CO. Surprisingly, even ({eta}{sup 5}-indenyl)(PPh{sub 3}){sub 2}Ru-CH{sub 3} carbonylates and gives ({eta}{sup 5}-indenyl)(PPh{sub 3})(CO)Ru-C(O)CH{sub 3}. Mechanistic studies on the non catalyzed'' hydrosilation of the manganese acyls (CO){sub 5}Mn-C(O)CH{sub 2}R (R = H, OCH{sub 3}, CH{sub 3}) with Et{sub 3}SiH and of cobalt acetyls (CO){sub 3}(PR{sub 3})CoC(O)CH{sub 3} with several monohydrosilanes have been completed. The cobalt acetyls cleanly give ethoxysilanes (not acetaldehyde), and the manganese acyls provide {alpha}-siloxyvinyl complexes Z-(CO){sub 5}Mn-C(OSiEt{sub 3})=CHR (R = H, CH{sub 3}, OCH{sub 3}). Carbonylation and protolytic cleavage of the latter generate pyruvoyl complexes (CO){sub 5}Mn-COCOR (R = CH{sub 3}, CH{sub 2}CH{sub 3}), formally the products of net double carbonylation'' sequences. Studies in progress are concerned with how manganese complexes as diverse as (CO){sub 5}Mn-Y (Y = C(O)R, R, BR - but not SiMe{sub 3} or Mn(CO){sub 5}) and ({eta}{sup 3}-C{sub 3}H{sub 5})Mn(CO){sub 2}L (but not CpMn(CO){sub 3} or CpMn(CO){sub 2}({eta}{sup 2}HSiR{sub 3})) function as efficient hydrosilation catalysts towards Cp(CO){sub 2}FeC(O)CH{sub 3}, for example. These reactions cleanly afford fully characterized {alpha}-siloxyethyl complexes Fp-CH(OSiR{sub 3})CH{sub 3} under conditions where typically Rh(1) hydrosilation catalysts are inactive. Several of these manganese complexes also catalytically hydrosilate organic esters, including lactones, to their ethers R-CH{sub 2}OR; these novel ester reductions occur quantitatively at room temperature and appear to be general in scope.

  4. Current complexity: a tool for assessing the complexity of organic molecules.

    PubMed

    Li, Jun; Eastgate, Martin D

    2015-07-14

    Molecular complexity for a synthetic organic chemist is difficult to define, though intuitively known. Despite the importance of this concept, the quantitative assessment of complexity within organic chemistry has remained a challenge. We report here on the development of an approach for generating a unique complexity index, which is reflective of both intrinsic molecular complexity and extrinsic synthetic complexity. This index is based on a community's perception of complexity, within the context of current technology, calculating a molecule's current complexity. Our approach allows for a direct comparison between molecules, the analysis of trends within research programs, it enables an assessment (and comparison) of new synthetic approaches to known molecules and is capable of following a molecule's apparent complexity as it changes over time. PMID:25962620

  5. Exchange Coupling Inversion in a High-Spin Organic Triradical Molecule.

    PubMed

    Gaudenzi, R; Burzurí, E; Reta, D; Moreira, I de P R; Bromley, S T; Rovira, C; Veciana, J; van der Zant, H S J

    2016-03-01

    The magnetic properties of a nanoscale system are inextricably linked to its local environment. In adatoms on surfaces and inorganic layered structures, the exchange interactions result from the relative lattice positions, layer thicknesses, and other environmental parameters. Here, we report on a sample-dependent sign inversion of the magnetic exchange coupling between the three unpaired spins of an organic triradical molecule embedded in a three-terminal device. This ferro-to-antiferromagnetic transition is due to structural distortions and results in a high-to-low spin ground-state change in a molecule traditionally considered to be a robust high-spin quartet. Moreover, the flexibility of the molecule yields an in situ electric tunability of the exchange coupling via the gate electrode. These findings open a route to the controlled reversal of the magnetic states in organic molecule-based nanodevices by mechanical means, electrical gating, or chemical tailoring. PMID:26862681

  6. Attachment limited versus diffusion limited nucleation of organic molecules: Hexaphenyl on sputter-modified mica.

    PubMed

    Tumbek, L; Winkler, A

    2012-08-01

    The nucleation and growth of organic molecules is usually discussed in the framework of diffusion limited aggregation (DLA). In this letter we demonstrate for the rod-like organic molecules hexaphenyl (6P) on sputter-modified mica, that under specific experimental conditions the nucleation has to be described by attachment limited aggregation (ALA). The crucial parameter for the growth mode is the roughness of the substrate surface, as induced by ion sputtering. With decreasing surface roughness the diffusion probability of the molecules increases and the growth mode changes from DLA to ALA. This was derived from the deposition rate dependence of the island density. A critical size of i = 7 molecules was determined for the nucleation of 6P on a moderately sputtered mica surface. PMID:23470898

  7. Attachment limited versus diffusion limited nucleation of organic molecules: Hexaphenyl on sputter-modified mica

    NASA Astrophysics Data System (ADS)

    Tumbek, L.; Winkler, A.

    2012-08-01

    The nucleation and growth of organic molecules is usually discussed in the framework of diffusion limited aggregation (DLA). In this letter we demonstrate for the rod-like organic molecules hexaphenyl (6P) on sputter-modified mica, that under specific experimental conditions the nucleation has to be described by attachment limited aggregation (ALA). The crucial parameter for the growth mode is the roughness of the substrate surface, as induced by ion sputtering. With decreasing surface roughness the diffusion probability of the molecules increases and the growth mode changes from DLA to ALA. This was derived from the deposition rate dependence of the island density. A critical size of i = 7 molecules was determined for the nucleation of 6P on a moderately sputtered mica surface.

  8. Organic soluble and uniform film forming oligoethylene glycol substituted BODIPY small molecules with improved hole mobility.

    PubMed

    Singh, Saumya; Venugopalan, Vijay; Krishnamoorthy, Kothandam

    2014-07-14

    Judiciously chosen side chains of conjugated molecules have a positive impact on charge transport properties when used as the active material in organic electronic devices. Amongst the side chains, oligoethylene glycols (OEGs) have been relatively unexplored due to their hydrophilic nature. OEGs also affect the smooth film formation of conjugated molecules, which preclude device fabrication. However, X-ray diffraction studies have shown that OEGs facilitate intermolecular contact, which is a desirable property for the fabrication of organic electronic devices. Thus the challenge is to design and synthesize organic solvent soluble and uniform film forming conjugated molecules with OEG side chains. We have designed and synthesized conjugated small molecules (CSMs) comprising BODIPY as acceptor and triphenylamine as donor with an OEG side chain. This molecule forms smooth films when processed from organic solvents. In order to understand the impact of the OEG side chain, we have also synthesized alkyl chain analogs. All the molecules exhibit exactly the same HOMO and LUMO energy levels, but the packing in the solid state is different. CSM with methyl side chains exhibit an inter planar distance of 4.15 Å. Contrary to this, the OEG side chain containing CSM showed an inter planar spacing of 4.30 Å, which is 0.2 Å less than the alkyl side chain comprising CSMs. Please note that the length of the hydrophobic and hydrophilic side chains is the same. Interestingly, the OEG side chain comprising CSM showed two orders of higher hole carrier mobilities compared to all the other derivatives. The same molecule also showed an extremely low threshold voltage of -0.27 V indicating the OEG side chains' favourable interaction between substrate as well as between molecules. PMID:24874914

  9. Laser induced fluorescence monitoring of the transport of small organic molecules in an organic vapor phase deposition system

    NASA Astrophysics Data System (ADS)

    Rolin, Cedric; Vartanian, Garen; Forrest, Stephen R.

    2012-12-01

    Laser-induced fluorescence is employed for the accurate and real-time in-situ monitoring of the concentration of organic molecules in an organic vapor phase deposition (OVPD) chamber. We investigate the transport dynamics of organic species in a hot N2 carrier gas from the evaporation source to the substrate. Based on the time-dependent concentration of organic molecules obtained from their fluorescence intensity near the substrate, we find that carrier gas transport is accurately described by Poiseuille flow. The interplay between convective and diffusive forces gives rise to dispersion of organic molecules in the carrier gas, resulting in the development of plug flow as described by Taylor-Aris theory. Retention of molecules in chamber dead volumes delays transport and introduces tailing of the concentration transients. Our study indicates how OVPD system design and operating conditions can be optimized to limit the duration of transport transients, ultimately leading to precise control over the growth of complex multilayer thin film structures.

  10. Doping of Metal-Organic Frameworks with Functional Guest Molecules and Nanoparticles

    NASA Astrophysics Data System (ADS)

    Schröder, Felicitas; Fischer, Roland A.

    Nanoparticle synthesis within metal-organic frameworks (MOFs) is performed by the adsorption of suitable precursor molecules for the metal component and subsequent decomposition to the composite materials nanoparticles@MOF. This chapter will review different approaches of loading MOFs with more complex organic molecules and metal-organic precursor molecules. The related reactions inside MOFs are discussed with a focus on stabilizing reactive intermediates in the corresponding cavities. The syntheses of metal and metal oxide nanoparticles inside MOFs are reviewed, and different synthetic routes compared. Emphasis is placed on the micro structural characterization of the materials nanoparticles@MOF with a particular focus on the location of embedded nanoparticles using TEM methods. Some first examples of applications of the doped MOFs in heterogeneous catalysis and hydrogen storage are described.

  11. Structural Evolution of an Organic Semiconducting Molecule onto a Soft Substrate.

    PubMed

    Martínez-Tong, Daniel E; Ruzié, Christian; Geerts, Yves H; Sferrazza, Michele

    2016-04-18

    The structural organization and evolution of the organic semiconducting molecule 2,7-dioctyloxy[1]benzothieno[3,2-b]-benzothiophene on a soft matrix is studied. Thin films of a blend formed from polystyrene and the molecule were prepared by spin-coating onto silicon substrates, which were subsequently studied by using a combination of microscopy and scattering techniques. The organic semiconducting molecule segregated to the surface and developed a phase with a different structure to the bulk, as in the case of a substrate induced phase observed previously. Under a solvent vapor annealing procedure, the growth of micrometer-sized tetragonal crystals onto the polymer surface was observed, which was not evidenced for the silicon substrates. PMID:26853087

  12. Bismuth Interfacial Doping of Organic Small Molecules for High Performance n-type Thermoelectric Materials.

    PubMed

    Huang, Dazhen; Wang, Chao; Zou, Ye; Shen, Xingxing; Zang, Yaping; Shen, Hongguang; Gao, Xike; Yi, Yuanping; Xu, Wei; Di, Chong-An; Zhu, Daoben

    2016-08-26

    Development of chemically doped high performance n-type organic thermoelectric (TE) materials is of vital importance for flexible power generating applications. For the first time, bismuth (Bi) n-type chemical doping of organic semiconductors is described, enabling high performance TE materials. The Bi interfacial doping of thiophene-diketopyrrolopyrrole-based quinoidal (TDPPQ) molecules endows the film with a balanced electrical conductivity of 3.3 S cm(-1) and a Seebeck coefficient of 585 μV K(-1) . The newly developed TE material possesses a maximum power factor of 113 μW m(-1)  K(-2) , which is at the forefront for organic small molecule-based n-type TE materials. These studies reveal that fine-tuning of the heavy metal doping of organic semiconductors opens up a new strategy for exploring high performance organic TE materials. PMID:27496293

  13. Adsorption of organic molecules on the TiO2(011) surface: STM study.

    PubMed

    Godlewski, Szymon; Tekiel, Antoni; Prauzner-Bechcicki, Jakub S; Budzioch, Janusz; Gourdon, Andre; Szymonski, Marek

    2011-06-14

    High resolution scanning tunneling microscopy has been applied to investigate adsorption and self-assembly of large organic molecules on the TiO(2)(011) surface. The (011) face of the rutile titania has been rarely examined in this context. With respect to possible industrial applications of rutile, quite often in a powder form, knowledge on behavior of organic molecules on that face is required. In the presented study we fill in the gap and report on experiments focused on the self-assembly of organic nanostructures on the TiO(2)(011) surface. We use three different kinds of organic molecules of potential interest in various applications, namely, PTCDA and CuPc representing flat, planar stacking species, and Violet Landers specially designed for new applications in molecular electronics. In order to reach a complete picture of molecular behavior, extended studies with different surface coverage ranging from single molecule up to 2 monolayer (ML) thick films are performed. Our results show that the adsorption behavior is significantly different from previously observed for widely used metallic templates. Creation of highly ordered molecular lines, quasi-ordered wetting layers, controlled geometrical reorientation upon thermal treatment, existence of specific adsorption geometries, and prospects for tip-induced molecule ordering and manipulation provide better understanding and add new phenomena to the knowledge on the (011) face of rutile titania. PMID:21682527

  14. Rational Design of Diketopyrrolopyrrole-Based Small Molecules as Donating Materials for Organic Solar Cells

    PubMed Central

    Jin, Ruifa; Wang, Kai

    2015-01-01

    A series of diketopyrrolopyrrole-based small molecules have been designed to explore their optical, electronic, and charge transport properties as organic solar cell (OSCs) materials. The calculation results showed that the designed molecules can lower the band gap and extend the absorption spectrum towards longer wavelengths. The designed molecules own the large longest wavelength of absorption spectra, the oscillator strength, and absorption region values. The optical, electronic, and charge transport properties of the designed molecules are affected by the introduction of different π-bridges and end groups. We have also predicted the mobility of the designed molecule with the lowest total energies. Our results reveal that the designed molecules are expected to be promising candidates for OSC materials. Additionally, the designed molecules are expected to be promising candidates for electron and/or hole transport materials. On the basis of our results, we suggest that molecules under investigation are suitable donors for [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and its derivatives as acceptors of OSCs. PMID:26343640

  15. Characterization of Antibiotic Resistance Gene Abundance and Microbiota Composition in Feces of Organic and Conventional Pigs from Four EU Countries.

    PubMed

    Gerzova, Lenka; Babak, Vladimir; Sedlar, Karel; Faldynova, Marcela; Videnska, Petra; Cejkova, Darina; Jensen, Annette Nygaard; Denis, Martine; Kerouanton, Annaelle; Ricci, Antonia; Cibin, Veronica; Österberg, Julia; Rychlik, Ivan

    2015-01-01

    One of the recent trends in animal production is the revival of interest in organic farming. The increased consumer interest in organic animal farming is mainly due to concerns about animal welfare and the use of antibiotics in conventional farming. On the other hand, providing animals with a more natural lifestyle implies their increased exposure to environmental sources of different microorganisms including pathogens. To address these concerns, we determined the abundance of antibiotic resistance and diversity within fecal microbiota in pigs kept under conventional and organic farming systems in Sweden, Denmark, France and Italy. The abundance of sul1, sul2, strA, tet(A), tet(B) and cat antibiotic resistance genes was determined in 468 samples by real-time PCR and the fecal microbiota diversity was characterized in 48 selected samples by pyrosequencing of V3/V4 regions of 16S rRNA. Contrary to our expectations, there were no extensive differences between the abundance of tested antibiotic resistance genes in microbiota originating from organic or conventionally housed pigs within individual countries. There were also no differences in the microbiota composition of organic and conventional pigs. The only significant difference was the difference in the abundance of antibiotic resistance genes in the samples from different countries. Fecal microbiota in the samples originating from southern European countries (Italy, France) exhibited significantly higher antibiotic resistance gene abundance than those from northern parts of Europe (Denmark, Sweden). Therefore, the geographical location of the herd influenced the antibiotic resistance in the fecal microbiota more than farm's status as organic or conventional. PMID:26218075

  16. Development of new methods in modern selective organic synthesis: preparation of functionalized molecules with atomic precision

    NASA Astrophysics Data System (ADS)

    Ananikov, V. P.; Khemchyan, L. L.; Ivanova, Yu V.; Bukhtiyarov, V. I.; Sorokin, A. M.; Prosvirin, I. P.; Vatsadze, S. Z.; Medved'ko, A. V.; Nuriev, V. N.; Dilman, A. D.; Levin, V. V.; Koptyug, I. V.; Kovtunov, K. V.; Zhivonitko, V. V.; Likholobov, V. A.; Romanenko, A. V.; Simonov, P. A.; Nenajdenko, V. G.; Shmatova, O. I.; Muzalevskiy, V. M.; Nechaev, M. S.; Asachenko, A. F.; Morozov, O. S.; Dzhevakov, P. B.; Osipov, S. N.; Vorobyeva, D. V.; Topchiy, M. A.; Zotova, M. A.; Ponomarenko, S. A.; Borshchev, O. V.; Luponosov, Yu N.; Rempel, A. A.; Valeeva, A. A.; Stakheev, A. Yu; Turova, O. V.; Mashkovsky, I. S.; Sysolyatin, S. V.; Malykhin, V. V.; Bukhtiyarova, G. A.; Terent'ev, A. O.; Krylov, I. B.

    2014-10-01

    The challenges of the modern society and the growing demand of high-technology sectors of industrial production bring about a new phase in the development of organic synthesis. A cutting edge of modern synthetic methods is introduction of functional groups and more complex structural units into organic molecules with unprecedented control over the course of chemical transformation. Analysis of the state-of-the-art achievements in selective organic synthesis indicates the appearance of a new trend — the synthesis of organic molecules, biologically active compounds, pharmaceutical substances and smart materials with absolute selectivity. Most advanced approaches to organic synthesis anticipated in the near future can be defined as 'atomic precision' in chemical reactions. The present review considers selective methods of organic synthesis suitable for transformation of complex functionalized molecules under mild conditions. Selected key trends in the modern organic synthesis are considered including the preparation of organofluorine compounds, catalytic cross-coupling and oxidative cross-coupling reactions, atom-economic addition reactions, methathesis processes, oxidation and reduction reactions, synthesis of heterocyclic compounds, design of new homogeneous and heterogeneous catalytic systems, application of photocatalysis, scaling up synthetic procedures to industrial level and development of new approaches to investigation of mechanisms of catalytic reactions. The bibliography includes 840 references.

  17. The IRAM-30 m line survey of the Horsehead PDR. III. High abundance of complex (iso-)nitrile molecules in UV-illuminated gas

    NASA Astrophysics Data System (ADS)

    Gratier, P.; Pety, J.; Guzmán, V.; Gerin, M.; Goicoechea, J. R.; Roueff, E.; Faure, A.

    2013-09-01

    Context. Complex (iso-)nitrile molecules, such as CH3CN and HC3N, are relatively easily detected in our Galaxy and in other galaxies. Aims: We aim at constraining their chemistry through observations of two positions in the Horsehead edge: the photo-dissociation region (PDR) and the dense, cold, and UV-shielded core just behind it. Methods: We systematically searched for lines of CH3CN, HC3N, C3N, and some of their isomers in our sensitive unbiased line survey at 3, 2, and 1 mm. We stacked the lines of C3N to improve the detectability of this species. We derived column densities and abundances through Bayesian analysis using a large velocity gradient radiative transfer model. Results: We report the first clear detection of CH3NC at millimeter wavelength. We detected 17 lines of CH3CN at the PDR and 6 at the dense core position, and we resolved its hyperfine structure for 3 lines. We detected 4 lines of HC3N, and C3N is clearly detected at the PDR position. We computed new electron collisional rate coefficients for CH3CN, andwe found that including electron excitation reduces the derived column density by 40% at the PDR position, where the electron density is 1-5 cm-3. While CH3CN is 30 times more abundant in the PDR (2.5 × 10-10) than in the dense core (8 × 10-12), HC3N has similar abundance at both positions (8 × 10-12). The isomeric ratio CH3NC/CH3CN is 0.15 ± 0.02. Conclusions: The significant amount of complex (iso-)nitrile molecule in the UV illuminated gas is puzzling as the photodissociation is expected to be efficient. This is all the more surprising in the case of CH3CN, which is 30 times more abundant in the PDR than in the dense core. In this case, pure gas phase chemistry cannot reproduce the amount of CH3CN observed in the UV-illuminated gas. We propose that CH3CN gas phase abundance is enhanced when ice mantles of grains are destroyed through photo-desorption or thermal-evaporation in PDRs, and through sputtering in shocks. Based on observations

  18. Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules

    PubMed Central

    Schobesberger, Siegfried; Junninen, Heikki; Bianchi, Federico; Lönn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K.; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, João; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J.; Dunne, Eimear M.; Flagan, Richard C.; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kürten, Andreas; Kurtén, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P.; Rondo, Linda; Santos, Filipe D.; Schallhart, Simon; Schnitzhofer, Ralf; Sipilä, Mikko; Tomé, António; Tsagkogeorgas, Georgios; Vehkamäki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S.; Curtius, Joachim; Hansel, Armin; Petäjä, Tuukka; Kulmala, Markku; Donahue, Neil M.; Worsnop, Douglas R.

    2013-01-01

    Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molecules and then form growing clusters of one to three sulfuric acid molecules plus one to four oxidized organics. Most of these organic compounds retain 10 carbon atoms, and some of them are remarkably highly oxidized (oxygen-to-carbon ratios up to 1.2). The average degree of oxygenation of the organic compounds decreases while the clusters are growing. Our measurements therefore connect oxidized organics directly, and in detail, with the very first steps of new particle formation and their growth between 1 and 2 nm in a controlled environment. Thus, they confirm that oxidized organics are involved in both the formation and growth of particles under ambient conditions. PMID:24101502

  19. Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules.

    PubMed

    Schobesberger, Siegfried; Junninen, Heikki; Bianchi, Federico; Lönn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, João; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J; Dunne, Eimear M; Flagan, Richard C; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kürten, Andreas; Kurtén, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P; Rondo, Linda; Santos, Filipe D; Schallhart, Simon; Schnitzhofer, Ralf; Sipilä, Mikko; Tomé, António; Tsagkogeorgas, Georgios; Vehkamäki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S; Curtius, Joachim; Hansel, Armin; Petäjä, Tuukka; Kulmala, Markku; Donahue, Neil M; Worsnop, Douglas R

    2013-10-22

    Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molecules and then form growing clusters of one to three sulfuric acid molecules plus one to four oxidized organics. Most of these organic compounds retain 10 carbon atoms, and some of them are remarkably highly oxidized (oxygen-to-carbon ratios up to 1.2). The average degree of oxygenation of the organic compounds decreases while the clusters are growing. Our measurements therefore connect oxidized organics directly, and in detail, with the very first steps of new particle formation and their growth between 1 and 2 nm in a controlled environment. Thus, they confirm that oxidized organics are involved in both the formation and growth of particles under ambient conditions. PMID:24101502

  20. Solution processable organic polymers and small molecules for bulk-heterojunction solar cells: A review

    SciTech Connect

    Sharma, G. D.

    2011-10-20

    Solution processed bulk heterojunction (BHJ) organic solar cells (OSCs) have gained wide interest in past few years and are established as one of the leading next generation photovoltaic technologies for low cost power production. Power conversion efficiencies up to 6% and 6.5% have been reported in the literature for single layer and tandem solar cells, respectively using conjugated polymers. A recent record efficiency about 8.13% with active area of 1.13 cm{sup 2} has been reported. However Solution processable small molecules have been widely applied for photovoltaic (PV) devices in recent years because they show strong absorption properties, and they can be easily purified and deposited onto flexible substrates at low cost. Introducing different donor and acceptor groups to construct donor--acceptor (D--A) structure small molecules has proved to be an efficient way to improve the properties of organic solar cells (OSCs). The power conversion efficiency about 4.4 % has been reported for OSCs based on the small molecules. This review deals with the recent progress of solution processable D--A structure small molecules and discusses the key factors affecting the properties of OSCs based on D--A structure small molecules: sunlight absorption, charge transport and the energy level of the molecules.

  1. Interfacial energy level shifts in few-molecule clusters of the organic semiconductor PTCDA

    NASA Astrophysics Data System (ADS)

    Burke, Sarah; Cochrane, Katherine; Schiffrin, Agustin; Roussy, Tanya

    2014-03-01

    Detailed knowledge of the local electronic structure of organic semiconductors near interfaces is crucial for the understanding of a variety of electronic and optoelectronic applications of these emerging materials. However, organic molecules are highly sensitive to the local environment, which abruptly changes at an interface. Here, we present a study on the prototypical organic semiconductor PTCDA by scanning tunneling microscopy and spectroscopic mapping. Nanoscale clusters of varying size and geometry were probed on a bilayer NaCl film on Ag(111). The molecular states, while decoupled from the underlying metal surface, are relatively delocalized within these monolayer islands. Depending on the size of the cluster and arrangement of molecules within the cluster, edge molecules exhibit varying energy level shifts relative to the central molecules, both of which differ from the isolated molecule. For well ordered islands, this leads to a type-1 heterojunction, with a larger band gap at the edge of the cluster differing by as much as 0.5eV. In considering nanoscale structures within multicomponent device architectures, such internal heterostructures established by differences in the local environment are an important consideration, and could even be exploited.

  2. Organic crystals bearing both channels and cavities formed from tripodal adamantane molecules

    NASA Astrophysics Data System (ADS)

    Tominaga, Masahide; Iekushi, Akitaka; Katagiri, Kosuke; Ohara, Kazuaki; Yamaguchi, Kentaro; Azumaya, Isao

    2013-08-01

    Three adamantane-based tripodal molecules bearing either a benzene, pyridine, or toluene unit (1-3) form molecular organic networks (1a-3a) with internal spaces, via intermolecular non-covalent interactions such as CH/π, CH/N, and CH/O interactions in the solid state. Crystals of 1a and 2a formed both one-dimensional channels and cavities, where guest molecules were encapsulated. The channels were derived from the alignment of the hexagonal cavities formed from six component molecules, while cavities formed between the 2D layers. In contrast, 3a contained only cavities built from the six component molecules, which correspond to the spaces which connected to form channels in 1a and 2a.

  3. Dipole-driven self-organization of zwitterionic molecules on alkali halide surfaces.

    PubMed

    Nony, Laurent; Bocquet, Franck; Para, Franck; Chérioux, Frédéric; Duverger, Eric; Palmino, Frank; Luzet, Vincent; Loppacher, Christian

    2012-01-01

    We investigated the adsorption of 4-methoxy-4'-(3-sulfonatopropyl)stilbazolium (MSPS) on different ionic (001) crystal surfaces by means of noncontact atomic force microscopy. MSPS is a zwitterionic molecule with a strong electric dipole moment. When deposited onto the substrates at room temperature, MSPS diffuses to step edges and defect sites and forms disordered assemblies of molecules. Subsequent annealing induces two different processes: First, at high coverage, the molecules assemble into a well-organized quadratic lattice, which is perfectly aligned with the <110> directions of the substrate surface (i.e., rows of equal charges) and which produces a Moiré pattern due to coincidences with the substrate lattice constant. Second, at low coverage, we observe step edges decorated with MSPS molecules that run along the <110> direction. These polar steps most probably minimize the surface energy as they counterbalance the molecular dipole by presenting oppositely charged ions on the rearranged step edge. PMID:22497002

  4. Dipole-driven self-organization of zwitterionic molecules on alkali halide surfaces

    PubMed Central

    Nony, Laurent; Bocquet, Franck; Para, Franck; Chérioux, Frédéric; Duverger, Eric; Palmino, Frank; Luzet, Vincent

    2012-01-01

    Summary We investigated the adsorption of 4-methoxy-4′-(3-sulfonatopropyl)stilbazolium (MSPS) on different ionic (001) crystal surfaces by means of noncontact atomic force microscopy. MSPS is a zwitterionic molecule with a strong electric dipole moment. When deposited onto the substrates at room temperature, MSPS diffuses to step edges and defect sites and forms disordered assemblies of molecules. Subsequent annealing induces two different processes: First, at high coverage, the molecules assemble into a well-organized quadratic lattice, which is perfectly aligned with the <110> directions of the substrate surface (i.e., rows of equal charges) and which produces a Moiré pattern due to coincidences with the substrate lattice constant. Second, at low coverage, we observe step edges decorated with MSPS molecules that run along the <110> direction. These polar steps most probably minimize the surface energy as they counterbalance the molecular dipole by presenting oppositely charged ions on the rearranged step edge. PMID:22497002

  5. Solution-grown small-molecule organic semiconductor with enhanced crystal alignment and areal coverage for organic thin film transistors

    DOE PAGESBeta

    Bi, Sheng; He, Zhengran; Chen, Jihua; Li, Dawen

    2015-07-24

    Drop casting of small-molecule organic semiconductors typically forms crystals with random orientation and poor areal coverage, which leads to significant performance variations of organic thin-film transistors (OTFTs). In this study, we utilize the controlled evaporative self-assembly (CESA) method combined with binary solvent system to control the crystal growth. A small-molecule organic semiconductor,2,5-Di-(2-ethylhexyl)-3,6-bis(5"-n-hexyl-2,2',5',2"]terthiophen-5-yl)-pyrrolo[3,4-c]pyrrole-1,4-dione (SMDPPEH), is used as an example to demonstrate the effectiveness of our approach. By optimizing the double solvent ratios, well-aligned SMDPPEH crystals with significantly improved areal coverage were achieved. As a result, the SMDPPEH based OTFTs exhibit a mobility of 1.6 × 10-2 cm2/V s, which is themore » highest mobility from SMDPPEH ever reported.« less

  6. Solution-grown small-molecule organic semiconductor with enhanced crystal alignment and areal coverage for organic thin film transistors

    SciTech Connect

    Bi, Sheng; He, Zhengran; Chen, Jihua; Li, Dawen

    2015-07-24

    Drop casting of small-molecule organic semiconductors typically forms crystals with random orientation and poor areal coverage, which leads to significant performance variations of organic thin-film transistors (OTFTs). In this study, we utilize the controlled evaporative self-assembly (CESA) method combined with binary solvent system to control the crystal growth. A small-molecule organic semiconductor,2,5-Di-(2-ethylhexyl)-3,6-bis(5"-n-hexyl-2,2',5',2"]terthiophen-5-yl)-pyrrolo[3,4-c]pyrrole-1,4-dione (SMDPPEH), is used as an example to demonstrate the effectiveness of our approach. By optimizing the double solvent ratios, well-aligned SMDPPEH crystals with significantly improved areal coverage were achieved. As a result, the SMDPPEH based OTFTs exhibit a mobility of 1.6 × 10-2 cm2/V s, which is the highest mobility from SMDPPEH ever reported.

  7. Self-Powered Electrochemistry for the Oxidation of Organic Molecules by a Cross-Linked Triboelectric Nanogenerator.

    PubMed

    Zheng, Xin; Su, Jingzhen; Wei, Xianjun; Jiang, Tao; Gao, Shuyan; Wang, Zhong Lin

    2016-07-01

    A cross-linked triboelectric nanogenerator with high performance is designed for the first time, which harvests vibrational energy to self-power the electrochemical oxidation of organic molecules. This system lays the groundwork for applications to an environmentally friendly production of important organic molecules and the waste treatment of organic pollutants. PMID:27145038

  8. EPOXIDATION OF SMALL ORGANIC MOLECULES USING A SPINNING TUBE-IN-TUBE REACTOR

    EPA Science Inventory

    The commodity-scale epoxidation of several organic molecules has been carried out using a Spinning Tube-in-Tube (STTr) reactor (manufactured by Kreido Laboratories). This reactor, which embodies and facilitates the use of Green Chemistry principles and Process Intensification, a...

  9. Adsorption of two gas molecules at a single metal site in a metal–organic framework

    SciTech Connect

    Runčevski, Tomče; Kapelewski, Matthew T.; Torres-Gavosto, Rodolfo M.; Tarver, Jacob D.; Brown, Craig M.; Long, Jeffrey R.

    2016-01-01

    One strategy to markedly increase the gas storage capacity of metal–organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules—specifically hydrogen, methane, or carbon dioxide.

  10. Enantiospecific spin polarization of electrons photoemitted through layers of homochiral organic molecules.

    PubMed

    Niño, Miguel Ángel; Kowalik, Iwona Agnieszka; Luque, Francisco Jesús; Arvanitis, Dimitri; Miranda, Rodolfo; de Miguel, Juan José

    2014-11-26

    Electrons photoemitted through layers of purely organic chiral molecules become strongly spin-polarized even at room temperature and for double-monolayer thicknesses. The substitution of one enantiomer for its mirror image does not revert the sign of the spin polarization, rather its direction in space. These findings might lead to the obtention of highly efficient spin filters for spintronic applications. PMID:25183637

  11. Kondo effect in a neutral and stable all organic radical single molecule break junction

    NASA Astrophysics Data System (ADS)

    Burzuri, Enrique; Gaudenzi, Rocco; Frisenda, Riccardo; Franco, Carlos; Mas-Torrent, Marta; Rovira, Concepcio; Veciana, Jaume; Alcon, Isaac; Bromley, Stefan T.; van der Zant, Herre S. J.

    Organic radicals are neutral, purely organic molecules exhibiting an intrinsic magnetic moment due to the presence of an unpaired electron in the molecule in its ground state. This property, added to the low spin-orbit coupling makes organic radicals good candidates for molecular spintronics insofar as the radical character is stable in solid state electronic devices. We show that the paramagnetism of the PTM radical molecule, in the shape of a Kondo anomaly is preserved in two- and three-terminal solid-state devices, regardless of mechanical and electrostatic changes. Indeed, our results demonstrate that the Kondo anomaly is robust under electrodes displacement and changes of the electrostatic environment, pointing to a localized orbital in the radical as the source of magnetism. Strong support to this picture is provided by density functional calculations and measurements of the corresponding nonradical specie. We further study polyradical systems, where several unpaired spins interact in the same molecule. This work was supported by the EU FP7 program through project 618082 ACMOL and ERC grant advanced Mols@Mols. It was also supported by the Dutch funding organization NWO (VENI).

  12. Covalent organic frameworks with spatially confined guest molecules in nanochannels and their impacts on crystalline structures.

    PubMed

    Gao, Jia; Jiang, Donglin

    2016-01-25

    We demonstrate the profound effects of spatially confined guest molecules in one-dimensional nanochannels on X-ray diffraction behaviors of covalent organic frameworks. Our results give insights into the abnormal X-ray diffraction patterns and suggest a novel molecular dynamic strategy for resolving crystalline structures. PMID:26658526

  13. Sampling and Analysis of Organic Molecules in the Plumes of Enceladus

    NASA Astrophysics Data System (ADS)

    Monroe, A. A.; Williams, P.; Anbar, A. D.; Tsou, P.

    2012-12-01

    The recent detection of organic molecules in the plumes of Enceladus, which also contain water and nitrogen (Waite et al., 2006; Matson et al., 2007), suggests that the geologically active South polar region contains habitable, subsurface water (McKay et al., 2008). Characterizing these molecules will be a high priority for any future mission to Enceladus. Sample return is highly desirable, but can it capture useful samples at Enceladus? Using Stardust mission parameters for comparison, we consider the survival of complex organic molecules during collection to assess the feasibility of one aspect of a sample return mission. A successful sample return mission must include the capability to capture and recover intact or partly intact molecules of particular astrobiological interest: lipids, amino and nucleic acids, polypeptides, and polynucleotides. The Stardust mission to comet Wild 2 successfully captured amino acids, amines, and PAHs using a combination of aerogel and Al foil (Sandford et al., 2006, 2010). For larger and more fragile molecules, particularly polypeptides and polynucleotides, low collisional damage is achieved by impact on low molecular weight surfaces. A particularly intriguing possibility is a capture surface pre-coated with organic matrices identified as ideal for analysis of various biomolecules using MALDI-MS (matrix-assisted laser desorption/ionization mass spectrometry) (Hillenkamp and Karas, 2007). MALDI is a standard technique with attomole sensitivity, exceptional mass resolution, and (bio)molecular specificity (Vestal, 2011). Capture surfaces appropriate for MALDI-MS analysis could be analyzed directly without post-return manipulation, minimizing post-capture damage to these molecules and the risk of contamination during handling. A hypothetical sample collection encounter speed of ~ 5 km/s corresponds to ~0.13 eV kinetic energy per amu. Studies of molecule survival and fragmentation exist for free hexapeptides impacting hydrocarbon

  14. The formation of organic molecules in solar system environments: The Miller-Urey Experiment in Space preflight overview

    NASA Astrophysics Data System (ADS)

    Kotler, J.; Ehrenfreund, P.; Martins, Z.; Ricco, A.; Blum, J.; Schraepler, R.; van Dongen, J.; Palmans, A.; Sephton, M.; Cleaves, H. J.

    2011-12-01

    The Miller-Urey Experiment in space (MUE) will investigate the formation of prebiotic organic compounds in the early solar system environment when it is sent to, and later retrieved from, the International Space Station in 2012. The dynamic environment of the solar nebula with the simultaneous presence of gas, particles, and energetic processes, including shock waves, electrical discharges, and radiation may trigger a rich organic chemistry leading to organic molecules. Two gas mixture compositions (CH4, NH3, H2 and N2, H2, CO) will be tested and subjected to continuous spark discharges for 48, 96, and 192 hours. Silicate particles will serve as surfaces on which thin water ice mantles can accrete. The experiment will be performed at low temperatures (-5 °C), slowing hydrolysis and improving chances of detection of initial products, intermediates and their abundances. Conducting the Miller-Urey experiment in the space environment (microgravity) allows us to simulate conditions that could have prevailed in the low gravity, energetic early solar nebula and provides insights into the chemical pathways that may occur as planetary systems form.

  15. The nature and possible roles of larger organic molecules in the atmosphere of Titan

    NASA Astrophysics Data System (ADS)

    Imanaka, Hiroshi; Smith, Mark A.; McKay, Chris

    Active organic chemistry in the thick N2 /CH4 atmosphere of Titan leads eventually to heavy organic gaseous species and aerosol particles. Recent observations by the Cassini Ion Neutral Mass Spectrometer (INMS) and the Cassini Plasma Spectrometer (CAPS) clearly demonstrate the formation of large organic molecules and organic aerosols in the ionosphere. The efficient formation of organic aerosol in the ionosphere may affect the chemistry, dynamics, and radia-tive balance in the mesosphere and stratosphere. We have conducted laboratory simulations in order to understand the chemistry of aerosol nucleation and their chemical growth via hetero-geneous reactions. The mass spectrum of C2 H2 plasma polymer shows a reasonable match with the CAPS positive ion mass spectrum. This implies the initial growth of large hydrocarbon molecules via ion-molecule reactions in the ionosphere. In the dusty environment of the upper atmosphere, the further nitrogen and hydrogen incorporation to aerosol particles via heteroge-neous reactions is plausible and significantly affects the C/H/N budgets in the atmosphere of Titan.

  16. Surface Enhanced Raman Spectroscopy of Organic Molecules on Magnetite (Fe3O4) Nanoparticles.

    PubMed

    Lee, Namhey; Schuck, P James; Nico, Peter S; Gilbert, Benjamin

    2015-03-19

    Surface-enhanced Raman spectroscopy (SERS) of species bound to environmentally relevant oxide nanoparticles is largely limited to organic molecules structurally related to catechol that facilitate a chemical enhancement of the Raman signal. Here, we report that magnetite (Fe3O4) nanoparticles provide a SERS signal from oxalic acid and cysteine via an electric field enhancement. Magnetite thus likely provides an oxide substrate for SERS study of any adsorbed organic molecule. This substrate combines benefits from both metal-based and chemical SERS by providing an oxide surface for studies of environmentally and catalytically relevant detailed chemical bonding information with fewer restrictions of molecular structure or binding mechanisms. Therefore, the magnetite-based SERS demonstrated here provides a new approach to establishing the surface interactions of environmentally relevant organic ligands and mineral surfaces. PMID:26262854

  17. Luminescent zinc metal-organic framework (ZIF-90) for sensing metal ions, anions and small molecules.

    PubMed

    Liu, Chang; Yan, Bing

    2015-09-26

    We synthesize a zinc zeolite-type metal-organic framework, the zeolitic imidazolate framework (ZIF-90), which exhibits an intense blue luminescence excited under visible light. Luminescent studies indicate that ZIF-90 could be an efficient multifunctional fluorescence material for high sensitivity metal ions, anions and organic small molecules, especially for Cd(2+), Cu(2+), CrO4(2-) and acetone. The luminescence intensity of ZIF-90 increases with the concentration of Cd(2+) and decreases proportionally with the concentration of Cu(2+), while the same quenched experimental phenomena appear in the sensing of CrO4(2-). With the increase of the amount of acetone, the luminescence intensity decreases gradually in the emulsions of ZIF-90. The mechanism of the sensing properties is studied in detail as well. This study shows that ZIF-90 could be a useful luminescent sensor for metal ions, anions and organic small molecules. PMID:26123790

  18. Nucleation of Organic Molecules via a Hot Precursor State: Pentacene on Amorphous Mica.

    PubMed

    Winkler, Adolf; Tumbek, Levent

    2013-12-01

    Organic thin films have attracted considerable interest due to their applicability in organic electronics. The classical scenario for thin film nucleation is the diffusion-limited aggregation (DLA). Recently, it has been shown that organic thin film growth is better described by attachment-limited aggregation (ALA). However, in both cases, an unusual relationship between the island density and the substrate temperature was observed. Here, we present an aggregation model that goes beyond the classical DLA or ALA models to explain this behavior. We propose that the (hot) molecules impinging on the surface cannot immediately equilibrate to the substrate temperature but remain in a hot precursor state. In this state, the molecules can migrate considerable distances before attaching to a stable or unstable island. This results in a significantly smaller island density than expected by assuming fast equilibration and random diffusion. We have applied our model to pentacene film growth on amorphous Muscovite mica. PMID:24340130

  19. Nucleation of Organic Molecules via a Hot Precursor State: Pentacene on Amorphous Mica

    PubMed Central

    2013-01-01

    Organic thin films have attracted considerable interest due to their applicability in organic electronics. The classical scenario for thin film nucleation is the diffusion-limited aggregation (DLA). Recently, it has been shown that organic thin film growth is better described by attachment-limited aggregation (ALA). However, in both cases, an unusual relationship between the island density and the substrate temperature was observed. Here, we present an aggregation model that goes beyond the classical DLA or ALA models to explain this behavior. We propose that the (hot) molecules impinging on the surface cannot immediately equilibrate to the substrate temperature but remain in a hot precursor state. In this state, the molecules can migrate considerable distances before attaching to a stable or unstable island. This results in a significantly smaller island density than expected by assuming fast equilibration and random diffusion. We have applied our model to pentacene film growth on amorphous Muscovite mica. PMID:24340130

  20. Enhancing the low frequency THz resonances (< 1 THz) of organic molecules via electronegative atom substitution

    NASA Astrophysics Data System (ADS)

    Dash, Jyotirmayee; Ray, Shaumik; Pesala, Bala

    2015-03-01

    Terahertz (THz) technology is an active area of research with various applications in non-intrusive imaging and spectroscopy. Very few organic molecules have significant resonances below 1 THz. Understanding the origin of low frequency THz modes in these molecules and their absence in other molecules could be extremely important in design and engineering molecules with low frequency THz resonances. These engineered molecules can be used as THz tags for anti-counterfeiting applications. Studies show that low frequency THz resonances are commonly observed in molecules having higher molecular mass and weak intermolecular hydrogen bonds. In this paper, we have explored the possibility of enhancing the strength of THz resonances below 1 THz through electronegative atom substitution. Adding an electronegative atom helps in achieving higher hydrogen bond strength to enhance the resonances below 1 THz. Here acetanilide has been used as a model system. THz-Time Domain Spectroscopy (THz-TDS) results show that acetanilide has a small peak observed below 1 THz. Acetanilide can be converted to 2-fluoroacetanilide by adding an electronegative atom, fluorine, which doesn't have any prominent peak below 1 THz. However, by optimally choosing the position of the electronegative atom as in 4-fluoroacetanilide, a significant THz resonance at 0.86 THz is observed. The origin of low frequency resonances can be understood by carrying out Density Functional Theory (DFT) simulations of full crystal structure. These studies show that adding an electronegative atom to the organic molecules at an optimized position can result in significantly enhanced resonances below 1 THz.

  1. Use of Rigid Liquid Crystalline Polypeptides as Alignment Matrices for Organic Nonlinear Optical Molecules.

    NASA Astrophysics Data System (ADS)

    Tokarski, Zbigniew

    The orientation of nonlinear optical (NLO) organic molecules is crucial for the existence of high values for the macroscopic susceptibilities. The orientation and interaction of several smaller NLO active molecules with an easily alignable polypeptide host was investigated to determine which functional groups and molecular shapes would produce the largest orientation with the host material; these parameters included aromatic vs aliphatic, polar vs nonpolar, saturate vs unsaturated hydrocarbons and the length of the guest molecule. The host materials were either poly ( gamma-benzyl-l-glutamate) (PBLG) or poly ( gamma-ethyl-l-glutamate) (PELG) lyotropic liquid crystals. These host polymers formed pseudo-hexagonal crystalline structures with long rigid alpha -helical backbones. The interstitial alignment of the guest molecules was dictated by the overall alignment of the host polypeptide rigid rods. Within these films many of the guest molecules existed in a metastable state that delayed phase separation for several hours. The rate of phase separation was influenced by the concentration of the guest molecule and on the side chain moiety of the polypeptide. Guest phase separation to a solid or a liquid occurred at a faster rate in PELG films, due to the lack of the side chain induced hindrance, than in PBLG films. An indicator of the occurrence of phase separation was with the onset of opaqueness in the films. The thin polypeptide films containing the aligned guest molecules became optically opaque as the incompatibilities between the side chains of the polypeptides and the guest molecules increased. The nonlinear optical susceptibility measurements were hampered by either the low guest solubility or the low concentration level required to avoid the guest -host incompatibility. Electro-optic and degenerate two and four wave mixing were done and produced signals in solutions but not in the doped films. The semiflexible aromatic guest molecules, such as the derivatives

  2. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    SciTech Connect

    Osiry, H.; Cano, A.; Lemus-Santana, A.A.; Rodríguez, A.; Carbonio, R.E.; Reguera, E.

    2015-10-15

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.

  3. Doped thin films of two organic molecules for light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Giovanella, Umberto; Botta, Chiara; Pasini, Mariacecilia; Porzio, William; Destri, Silvia

    2003-11-01

    The photoluminescence and electroluminescence of doped organic materials are reported for thin films prepared by ultrahigh-vacuum coevaporation and by spin coating from solution of two emitting molecules. For both films, efficient energy transfer from the donor to the acceptor molecules is observed without relevant dopant segregation for molar concentrations up to 10%. In spin-coated films the energy transfer from the matrix to the dopant is due to purely resonant energy transfer processes while the cosublimated films show the presence of additional thermally activated hopping processes. Light-emitting diodes fabricated with coevaporated films yield electroluminescence with higher efficiency and stability.

  4. Indistinguishable near-infrared single photons from an individual organic molecule

    NASA Astrophysics Data System (ADS)

    Trebbia, Jean-Baptiste; Tamarat, Philippe; Lounis, Brahim

    2010-12-01

    By using the zero-phonon line emission of an individual organic molecule, we realized a source of indistinguishable single photons in the near infrared. A Hong-Ou-Mandel interference experiment is performed and a two-photon coalescence probability higher than 50% at 2 K is obtained. The contribution of the temperature-dependent dephasing processes to the two-photon interference contrast is studied. We show that the molecule delivers nearly ideal indistinguishable single photons at the lowest temperatures when the dephasing is nearly lifetime limited. This source is used to generate postselected polarization-entangled photon pairs as a test bench for applications in quantum information.

  5. Effects of vibrational motion on core-level spectra of prototype organic molecules

    SciTech Connect

    Uejio, Janel S.; Schwartz, Craig P.; Saykally, Richard J.; Prendergast, David

    2008-08-21

    A computational approach is presented for prediction and interpretation of core-level spectra of complex molecules. Applications are presented for several isolated organic molecules, sampling a range of chemical bonding and structural motifs. Comparison with gas phase measurements indicate that spectral lineshapes are accurately reproduced both above and below the ionization potential, without resort to ad hoc broadening. Agreement with experiment is significantly improved upon inclusion of vibrations via molecular dynamics sampling. We isolate and characterize spectral features due to particular electronic transitions enabled by vibrations, noting that even zero-point motion is sufficient in some cases.

  6. Chemical methods for degradation of target proteins using designed light-activatable organic molecules.

    PubMed

    Tanimoto, Shuho; Takahashi, Daisuke; Toshima, Kazunobu

    2012-08-11

    Molecular design, chemical synthesis, and biological evaluation of several designed organic molecules, which target-selectively degrade proteins upon photo-irradiation, are introduced. The designed molecules for protein photo-degradation include 2-phenylquinoline-steroid hormone hybrids and porphyrin derivatives, both of which selectively photo-degrade estrogen receptor-α, and fullerene-sugar and -sulfonic acid hybrids, which selectively photo-degrade HIV-1 protease and amyloid β, respectively. The information will provide a novel and effective way to control specific functions of proteins, and contribute to the molecular design of novel protein photo-degrading agents, which should find wide application in chemistry, biology, and medicine. PMID:22739361

  7. Electrochemical assembly of organic molecules by the reduction of iodonium salts

    DOEpatents

    Dirk, Shawn M.; Howell, Stephen W.; Wheeler, David R.

    2009-06-23

    Methods are described for the electrochemical assembly of organic molecules on silicon, or other conducting or semiconducting substrates, using iodonium salt precursors. Iodonium molecules do not assemble on conducting surfaces without a negative bias. Accordingly, the iodonium salts are preferred for patterning applications that rely on direct writing with negative bias. The stability of the iodonium molecule to acidic conditions allows them to be used with standard silicon processing. As a directed assembly process, the use of iodonium salts provides for small features while maintaining the ability to work on a surface and create structures on a wafer level. Therefore, the process is amenable for mass production. Furthermore, the assembled monolayer (or multilayer) is chemically robust, allowing for subsequent chemical manipulations and the introduction of various molecular functionalities for various chemical and biological applications.

  8. Spin-boson theory for charge photogeneration in organic molecules: Role of quantum coherence

    NASA Astrophysics Data System (ADS)

    Yao, Yao

    2015-01-01

    The charge photogeneration process in organic molecules is investigated by a quantum heat engine model, in which two molecules are modeled by a two-spin system sandwiched between two bosonic baths. The two baths represent the high-temperature photon emission source and the low-temperature phonon environment, respectively. We utilize the time-dependent density matrix renormalization group algorithm to investigate the quantum dynamics of the model. It is found that the transient energy current flowing through the two molecules exhibits two stages. In the first stage the energy current is of a coherent feature and represents the ultrafast delocalization of the charge-transfer state, and in the second stage a steady incoherent current is established. The power conversion efficiency is significantly high and may reach the maximum value of 93 % with optimized model parameters. The long-lived quantum entanglement between the two spins is found to be primarily responsible for the hyperefficiency.

  9. Controlling the Spin Texture of Topological Insulators by Rational Design of Organic Molecules.

    PubMed

    Jakobs, Sebastian; Narayan, Awadhesh; Stadtmüller, Benjamin; Droghetti, Andrea; Rungger, Ivan; Hor, Yew S; Klyatskaya, Svetlana; Jungkenn, Dominik; Stöckl, Johannes; Laux, Martin; Monti, Oliver L A; Aeschlimann, Martin; Cava, Robert J; Ruben, Mario; Mathias, Stefan; Sanvito, Stefano; Cinchetti, Mirko

    2015-09-01

    We present a rational design approach to customize the spin texture of surface states of a topological insulator. This approach relies on the extreme multifunctionality of organic molecules that are used to functionalize the surface of the prototypical topological insulator (TI) Bi2Se3. For the rational design we use theoretical calculations to guide the choice and chemical synthesis of appropriate molecules that customize the spin texture of Bi2Se3. The theoretical predictions are then verified in angular-resolved photoemission experiments. We show that, by tuning the strength of molecule-TI interaction, the surface of the TI can be passivated, the Dirac point can energetically be shifted at will, and Rashba-split quantum-well interface states can be created. These tailored interface properties-passivation, spin-texture tuning, and creation of hybrid interface states-lay a solid foundation for interface-assisted molecular spintronics in spin-textured materials. PMID:26262825

  10. Enzymatic activities and prokaryotic abundance in relation to organic matter along a West-East Mediterranean transect (TRANSMED cruise).

    PubMed

    Zaccone, R; Boldrin, A; Caruso, G; La Ferla, R; Maimone, G; Santinelli, C; Turchetto, M

    2012-07-01

    The distribution of extracellular enzymatic activities (EEA) [leucine aminopeptidase (LAP), ß-glucosidase (GLU), alkaline phosphatase (AP)], as well as that of prokaryotic abundance (PA) and biomass (PB), dissolved organic carbon (DOC), particulate organic carbon and particulate total nitrogen (POC, PTN), was determined in the epi-, meso-, and bathypelagic waters of the Mediterranean Sea along a West-East transect and at one Atlantic station located outside the Strait of Gibraltar. This study represents a synoptical evaluation of the microbial metabolism during early summer. Decreasing trends with depth were observed for most of the parameters (PA, PB, AP, DOC, POC, PTN). Significant differences between the western and eastern basins of the Mediterranean Sea were found, displaying higher rates of LAP and GLU and lower C/N ratios more in the eastern than in the western areas. Conversely, in the epipelagic layer, PA and PB were found to be higher in the western than in the eastern basins. PB was significantly related to DOC concentration (all data, n = 145, r = 0.53, P < 0.01), while significant correlations of EEA with POC and PTN were found in the epipelagic layer, indicating an active response of microbial metabolism to organic substrates. Specific enzyme activities normalized to cell abundance pointed out high values of LAP and GLU in the bathypelagic layer, especially in the eastern basin, while cell-specific AP was high in the epi- and bathypelagic zone of the eastern basin indicating a rapid regeneration of inorganic P for both prokaryotes and phytoplankton needs. Low activity and abundance characterized the Atlantic station, while opposite trends of these parameters were observed along the Mediterranean transect, showing the uncoupling between abundance and activity data. In the east Mediterranean Sea, decomposition processes increased probably in response to mesoscale structures which lead to organic matter downwelling. PMID:22349935

  11. Difficulties in Laboratory Studies and Astronomical Observations of Organic Molecules: Hydroxyacetone and Lactic Acid

    NASA Technical Reports Server (NTRS)

    Apponi, A. J.; Brewster, M. A.; Hoy, J.; Ziurys, L. M.

    2006-01-01

    For the past 35 years, radio astronomy has revealed a rich organic chemistry in the interstellar gas, which is exceptionally complex towards active star-forming regions. New solar systems condense out of this gas and may influence the evolution of life on newly formed planets. Much of the biologically important functionality is present among the some 130 gas-phase molecules found to date, including alcohols, aldehydes, ketones, acids, amines, amides and even the simplest sugar - glycolaldehyde. Still, many unidentified interstellar radio signals remain, and their identification relies on further laboratory study. The molecules hydroxyacetone and lactic acid are relatively small organic molecules, but possess rather complex rotational spectra owing to their high asymmetry. Hydroxyacetone is particularly problematic because it possess a very low barrier to internal rotation, and exhibits strong coupling of the free-rotor states with the overall rotation of the molecule. As in the case of acetamide, a full decomposition method was employed to order the resultant eigenstates onto normal asymmetric top eigenvectors.

  12. Laser-induced desorption of organic molecules from front- and back-irradiated metal foils

    SciTech Connect

    Zinovev, Alexander V.; Veryovkin, Igor V.; Pellin, Michael J.

    2009-03-17

    Laser-Induced Acoustic Desorption (LIAD) from thin metal foils is a promising technique for gentle and efficient volatilization of intact organic molecules from surfaces of solid substrates. Using the Single Photon Ionization (SPI) method combined with time-of-flight mass-spectrometry (TOF MS), desorbed flux in LIAD was examined and compared to that from direct laser desorption (LD). Molecules of various organic dyes were used in experiments. Translational velocities of the desorbed intact molecules did not depend on the desorbing laser intensity, which implies the presence of more sophisticated mechanism of energy transfer than the direct mechanical or thermal coupling between the laser pulse and the adsorbed molecules. The results of our experiments indicate that the LIAD phenomenon cannot be described in terms of a simple mechanical shake-off nor the direct laser desorption. Rather, they suggest that multi-step energy transfer processes are involved. Possible qualitative mechanism of LIAD that are based on formation of non-equilibrium energy states in the adsorbate-substrate system are proposed and discussed.

  13. Laser-induced desorption of organic molecules from front- and back-irradiated metal foils.

    SciTech Connect

    Zinovev, A. V.; Veryovkin, I. V.; Pellin, M. J.; Materials Science Division

    2009-01-01

    Laser-Induced Acoustic Desorption (LIAD) from thin metal foils is a promising technique for gentle and efficient volatilization of intact organic molecules from surfaces of solid substrates. Using the Single Photon Ionization (SPI) method combined with time-of-flight mass-spectrometry (TOF MS), desorbed flux in LIAD was examined and compared to that from direct laser desorption (LD). Molecules of various organic dyes were used in experiments. Translational velocities of the desorbed intact molecules did not depend on the desorbing laser intensity, which implies the presence of more sophisticated mechanism of energy transfer than the direct mechanical or thermal coupling between the laser pulse and the adsorbed molecules. The results of our experiments indicate that the LIAD phenomenon cannot be described in terms of a simple mechanical shake-off nor the direct laser desorption. Rather, they suggest that multi-step energy transfer processes are involved. Possible qualitative mechanism of LIAD that are based on formation of non-equilibrium energy states in the adsorbate-substrate system are proposed and discussed.

  14. High-resolution electrohydrodynamic jet printing of small-molecule organic light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Kim, Kukjoo; Kim, Gyeomuk; Lee, Bo Ram; Ji, Sangyoon; Kim, So-Yun; An, Byeong Wan; Song, Myoung Hoon; Park, Jang-Ung

    2015-08-01

    The development of alternative organic light-emitting diode (OLED) fabrication technologies for high-definition and low-cost displays is an important research topic as conventional fine metal mask-assisted vacuum evaporation has reached its limit to reduce pixel sizes and manufacturing costs. Here, we report an electrohydrodynamic jet (e-jet) printing method to fabricate small-molecule OLED pixels with high resolution (pixel width of 5 μm), which significantly exceeds the resolutions of conventional inkjet or commercial OLED display pixels. In addition, we print small-molecule emitting materials which provide a significant advantage in terms of device efficiency and lifetime compared to those with polymers.The development of alternative organic light-emitting diode (OLED) fabrication technologies for high-definition and low-cost displays is an important research topic as conventional fine metal mask-assisted vacuum evaporation has reached its limit to reduce pixel sizes and manufacturing costs. Here, we report an electrohydrodynamic jet (e-jet) printing method to fabricate small-molecule OLED pixels with high resolution (pixel width of 5 μm), which significantly exceeds the resolutions of conventional inkjet or commercial OLED display pixels. In addition, we print small-molecule emitting materials which provide a significant advantage in terms of device efficiency and lifetime compared to those with polymers. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03034j

  15. Ordered quantum dot molecules and single quantum dots formed by self-organized anisotropic strain engineering

    SciTech Connect

    Lippen, T. van; Noetzel, R.; Hamhuis, G.J.; Wolter, J.H.

    2005-02-15

    An ordered lattice of lateral InAs quantum dot (QD) molecules is created by self-organized anisotropic strain engineering of an (In,Ga)As/GaAs superlattice (SL) template on GaAs(311)B by molecular-beam epitaxy, constituting a Turing pattern in solid state. The SL template and InAs QD growth conditions, such as the number of SL periods, growth temperatures, amount and composition of deposited (In,Ga)As, and insertion of Al-containing layers, are studied in detail for an optimized QD ordering within and among the InAs QD molecules on the SL template nodes, which is evaluated by atomic force microscopy. The average number of InAs QDs within the molecules is controlled by the thickness of the upper GaAs separation layer on the SL template and the (In,Ga)As growth temperature in the SL. The strain-correlated growth in SL template formation and QD ordering is directly confirmed by high-resolution x-ray diffraction. Ordered arrays of single InAs QDs on the SL template nodes are realized for elevated SL template and InAs QD growth temperatures together with the insertion of a second InAs QD layer. The InAs QD molecules exhibit strong photoluminescence (PL) emission up to room temperature. Temperature-dependent PL measurements exhibit an unusual behavior of the full width at half maximum, indicating carrier redistribution solely within the QD molecules.

  16. Organic crystals: properties, devices, functionalization and bridges to bio-molecules.

    PubMed

    Brooks, James S

    2010-07-01

    The purpose of this critical review is twofold: first, to review organic "small molecule" crystalline materials in terms of structure and function; and second, to consider if and how such materials might eventually enter the realm of device applicability. This area, one of the most interdisciplinary fields of research in contemporary materials science, embraces chemistry, physics, engineering, biology, theory and computation. The review therefore attempts to treat a relatively large number of examples including fundamental physical and electronic structure, single component and charge transfer complexes, physical properties of single crystalline materials, thin film and single crystal electronic and photonic devices, functional materials, and bio-inspired structures. The point of view is that of an experimental physicist, and in this context, challenges and possible routes to further advances in the development and utilization of organic small molecule materials are discussed for both fundamental and applied purposes (153 references). PMID:20505863

  17. Hot OH and CN: Evidence for organic molecules close to the nucleus of comet Halley

    NASA Astrophysics Data System (ADS)

    Clairemidi, J.; Moreels, G.

    1989-12-01

    During the encounter session of Vega 2 with comet Halley on 6 Mar. 1986, advantage was taken of the approach motion and of the resulting zoom effect to assemble the monochromatic charts produced by a three channel spectrometer in composite images at selected wavelengths. Two jets are clearly apparent in most of the monochromatic images. The OH and CN emission originating from the jets exhibit a pronounced peculiarity. The bands located at 309 and 388 nm show an excess of emission at 305 and 383 nm. The proposed mechanism, specific to the jets, is the photodissociation of one or several organic molecules of the type A-OH or B-CN which would release hot OH and CN when submitted to the solar UV flux. These organic molecules would be a component of the envelope of the CHON submicronic grains dragged by the gaseous jets. They provide an additional argument in favor of the similarity between cometary and interstellar matter.

  18. Oxidative addition of C--H bonds in organic molecules to transition metal centers

    SciTech Connect

    Bergman, R.G.

    1989-04-01

    Alkanes are among the most chemically inert organic molecules. They are reactive toward a limited range of reagents, such as highly energetic free radicals and strongly electrophilic and oxidizing species. This low reactivity is a consequence of the C--H bond energies in most saturated hydrocarbons. These values range from 90 to 98 kcal/mole for primary and secondary C--H bonds; in methane, the main constituent of natural gas, the C--H bond energy is 104 kcal/mole. This makes methane one of the most common but least reactive organic molecules in nature. This report briefly discusses the search for metal complexes capable of undergoing the C--H oxidative addition process allowing alkane chemistry to be more selective than that available using free radical reagents. 14 refs.

  19. Exploiting Metallophilicity for the Assembly of Inorganic Nanocrystals and Conjugated Organic Molecules.

    PubMed

    Dalmases, Mariona; Aguiló, Elisabet; Llorca, Jordi; Rodríguez, Laura; Figuerola, Albert

    2016-07-18

    The accurate engineering of interfaces between inorganic nanocrystals and semiconducting organic molecules is currently viewed as key for further developments in critical fields such as photovoltaics and photocatalysis. In this work, a new and unconventional source of interface interaction based on metal-metal bonds is presented. With this aim, an Au(I) organometallic gelator was exploited for the formation of hydrogel-like nanocomposites containing inorganic nanoparticles and conjugated organic molecules. Noteworthy, the establishment of metallophilic interactions at the interface between the two moieties greatly enhances interparticle coupling in the composites. Thus, we believe that this new hybrid system might represent a promising alternative in several fields, such as in the fabrication of improved light-harvesting devices. PMID:26973083

  20. Nature of chalcogen hor ellipsis chalcogen contact interactions in organic donor-molecule salts

    SciTech Connect

    Novoa, J.J.; Whangbo, Myung-Hwan . Dept. of Chemistry); Williams, J.M. )

    1990-01-01

    The nature of chalcogen{hor ellipsis}chalcogen contact interactions in organic donor-molecule salts was examined by performing ab initio SCF-MO/MP2 calculations on H{sub 2}X{hor ellipsis}XH{sub 2}(X = O, S, SE, Te) and MM2 calculations on donor dimers (TXF){sub 2} (X = S, SE, Te) and (BEDX-TTF){sub 2} (X = O, S). 14 refs., 4 figs., 4 tabs.

  1. Bis(haloBODIPYs) with Labile Helicity: Valuable Simple Organic Molecules That Enable Circularly Polarized Luminescence.

    PubMed

    Ray, César; Sánchez-Carnerero, Esther M; Moreno, Florencio; Maroto, Beatriz L; Agarrabeitia, Antonia R; Ortiz, María J; López-Arbeloa, Íñigo; Bañuelos, Jorge; Cohovi, Komlan D; Lunkley, Jamie L; Muller, Gilles; de la Moya, Santiago

    2016-06-20

    Simple organic molecules (SOM) based on bis(haloBODIPY) are shown to enable circularly polarized luminescence (CPL), giving rise to a new structural design for technologically valuable CPL-SOMs. The established design comprises together synthetic accessibility, labile helicity, possibility of reversing the handedness of the circularly polarized emission, and reactive functional groups, making it unique and attractive as advantageous platform for the development of smart CPL-SOMs. PMID:27123965

  2. Semiempirical evaluation of post-Hartree-Fock diagonal-Born-Oppenheimer corrections for organic molecules.

    PubMed

    Mohallem, José R

    2008-04-14

    Recent post-Hartree-Fock calculations of the diagonal-Born-Oppenheimer correction empirically show that it behaves quite similar to atomic nuclear mass corrections. An almost constant contribution per electron is identified, which converges with system size for specific series of organic molecules. This feature permits pocket-calculator evaluation of the corrections within thermochemical accuracy (10(-1) mhartree or kcal/mol). PMID:18412429

  3. Organic molecules in protoplanetary disks around T Tauri and Herbig Ae stars

    NASA Astrophysics Data System (ADS)

    Thi, W.-F.; van Zadelhoff, G.-J.; van Dishoeck, E. F.

    2004-10-01

    The results of single-dish observations of low- and high-J transitions of selected molecules from protoplanetary disks around two T Tauri stars (LkCa 15 and TW Hya) and two Herbig Ae stars (HD 163296 and MWC 480) are reported. Simple molecules such as CO, 13CO, HCO+, CN and HCN are detected. Several lines of H2CO are found toward the T Tauri star LkCa 15 but not in other objects. No CH3OH has been detected down to abundances of 10-9-10-8 with respect to H2. SO and CS lines have been searched for without success. Line ratios indicate that the molecular emission arises from dense (106-108 cm-3) and moderately warm (T ˜ 20-40 K) intermediate height regions of the disk atmosphere between the midplane and the upper layer, in accordance with predictions from models of the chemistry in disks. The sizes of the disks were estimated from model fits to the 12CO 3-2 line profiles. The abundances of most species are lower than in the envelope around the solar-mass protostar IRAS 16293-2422. Freeze-out in the cold midplane and photodissociation by stellar and interstellar ultraviolet photons in the upper layers are likely causes of the depletion. CN is strongly detected in all disks, and the CN/HCN abundance ratio toward the Herbig Ae stars is even higher than that found in galactic photon-dominated regions, testifying to the importance of photodissociation by radiation from the central object in the upper layers. DCO+ is detected toward TW Hya, but not in other objects. The high inferred DCO+/HCO+ ratio of ˜0.035 is consistent with models of the deuterium fractionation in disks which include strong depletion of CO. The inferred ionization fraction in the intermediate height regions as deduced from HCO+ is at least 10-11-10-10, comparable to that derived for the midplane from recent H2D+ observations. Comparison with the abundances found in cometary comae is made. Tables 3-5 are only available in electronic form at http://www.edpsciences.org

  4. Investigation of Multiconfigurational Short-Range Density Functional Theory for Electronic Excitations in Organic Molecules.

    PubMed

    Hubert, Mickaël; Hedegård, Erik D; Jensen, Hans Jørgen Aa

    2016-05-10

    Computational methods that can accurately and effectively predict all types of electronic excitations for any molecular system are missing in the toolbox of the computational chemist. Although various Kohn-Sham density-functional methods (KS-DFT) fulfill this aim in some cases, they become inadequate when the molecule has near-degeneracies and/or low-lying double-excited states. To address these issues we have recently proposed multiconfiguration short-range density-functional theory-MC-srDFT-as a new tool in the toolbox. While initial applications for systems with multireference character and double excitations have been promising, it is nevertheless important that the accuracy of MC-srDFT is at least comparable to the best KS-DFT methods also for organic molecules that are typically of single-reference character. In this paper we therefore systematically investigate the performance of MC-srDFT for a selected benchmark set of electronic excitations of organic molecules, covering the most common types of organic chromophores. This investigation confirms the expectation that the MC-srDFT method is accurate for a broad range of excitations and comparable to accurate wave function methods such as CASPT2, NEVPT2, and the coupled cluster based CC2 and CC3. PMID:27058733

  5. Synthesis of carbon nano-structures using organic-molecule intercalated taeniolite layered silicates

    NASA Astrophysics Data System (ADS)

    Maezumi, Takaaki; Wada, Noboru

    2015-03-01

    By calcinating organic-molecule intercalated taeniolite layered silicates, carbon nano-structures were made between the 2:1 layered silicate sheets. Raman scattering, XRD, TGA and SEM were used to characterize the samples. Large taeniolite crystals (NaLiMg2Si4O10F) were first prepared by melting appropriate chemicals at high temperatures using a platinum crucible. Then, the taeniolite crystals made were cation-exchanged with Li+, K+, NH4+,Ca2+ + and Mg2+ in salt solution. Finally, various organic molecules such as ethylene glycol, pyridine and so on were intercalated into the taeniolite crystals, and calcinated under a N2 atmosphere at about 1000K. The resulting crystals are usually gray or black. X-ray (00l) diffraction patterns suggested that the carbon structures may be monolayer thick (i.e., graphene-like). Raman scattering spectra which exhibited a sharp G-band peak with a high G-band/D-band ratio indicated that the carbon structures were relatively well crystallized. Cation and organic-molecule dependence on the carbon structures will be discussed. In addition, evidence for stage-2 taeniolite will be presented.

  6. Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program.

    PubMed

    Izumi, Hiroshi; Nafie, Laurence A; Dukor, Rina K

    2016-05-01

    Searching the 3D structural fragments of organic molecules is challenging because of structural differences between X-ray and theoretically calculated geometries and the conformational flexibility of substituents. The codification program called Conformational Code for Organic Molecules (CCOM) can be used to unambiguously convert 3D conformational data for various molecules to 1D data. Two deviations from Rule E-5.6 of the International Union of Pure and Applied Chemistry (IUPAC) Rules for Nomenclature of Organic Chemistry were introduced to the CCOM program for 3D fragment searching. First, the search for the highest priority atom was limited to a distance of two bonds from the center bond for dihedral angle determination. Second, for indistinguishable atoms in experimentally observed solution structures, the smallest number of atom index in the molecular model was chosen as the priority atom for dihedral angle determination. A search of the 3D conformational fragment mb_3a6c4c of mevastatin () in combination with the SMiles ARbitrary Target Specification (SMARTS) description suggested that a change in the conformation of this fragment may be the driving force for dissociation of mevastatin from its target protein. Chirality 28:370-375, 2016. © 2016 Wiley Periodicals, Inc. PMID:27040870

  7. Non-basic high-performance molecules for solution-processed organic solar cells.

    PubMed

    van der Poll, Thomas S; Love, John A; Nguyen, Thuc-Quyen; Bazan, Guillermo C

    2012-07-17

    A new small molecule, p-DTS(FBTTh(2))(2), is designed for incorporation into solution-fabricated high-efficiency organic solar cells. Of primary importance is the incorporation of electron poor heterocycles that are not prone to protonation and thereby enable the incorporation of commonly used interlayers between the organic semiconductor and the charge collecting electrodes. These features have led to the creation of p-DTS(FBTTh(2))(2)/PC(71)BM solar cells with power conversion efficiencies of up to 7%. PMID:22674636

  8. Laser-driven acoustic desorption of organic molecules from back-irradiated solid foils.

    SciTech Connect

    Zinovev, A. V.; Veryovkin, I. V.; Moore, J. F.; Pellin, M. J.; Materials Science Division; Mass Think

    2007-11-01

    Laser-induced acoustic desorption (LIAD) from thin metal foils is a promising technique for gentle and efficient volatilization of intact organic molecules from surfaces of solid substrates. Using the single-photon ionization method combined with time-of-flight mass spectrometry, we have examined the neutral component of the desorbed flux in LIAD and compared it to that from direct laser desorption. These basic studies of LIAD, conducted for molecules of various organic dyes (rhodamine B, fluorescein, anthracene, coumarin, BBQ), have demonstrated detection of intact parent molecules of the analyte even at its surface concentrations corresponding to a submonolayer coating. In some cases (rhodamine B, fluorescein, BBQ), the parent molecular ion peak was accompanied by a few fragmentation peaks of comparable intensity, whereas for others, only peaks corresponding to intact parent molecules were detected. At all measured desorbing laser intensities (from 100 to 500 MW/cm{sup 2}), the total amount of desorbed parent molecules depended exponentially on the laser intensity. Translational velocities of the desorbed intact molecules, determined for the first time in this work, were of the order of hundreds of meters per second, less than what has been observed in our experiments for direct laser desorption, but substantially greater than the possible perpendicular velocity of the substrate foil surface due to laser-generated acoustic waves. Moreover, these velocities did not depend on the desorbing laser intensity, which implies the presence of a more sophisticated mechanism of energy transfer than direct mechanical or thermal coupling between the laser pulse and the adsorbed molecules. Also, the total flux of desorbed intact molecules as a function of the total number of desorbing laser pulses, striking the same point on the target, decayed following a power law rather than an exponential function, as would have been predicted by the shake-off model. To summarize, the

  9. COMPLEX ORGANIC MOLECULES AT HIGH SPATIAL RESOLUTION TOWARD ORION-KL. I. SPATIAL SCALES

    SciTech Connect

    Widicus Weaver, Susanna L.; Friedel, Douglas N. E-mail: friedel@astro.illinois.edu

    2012-08-01

    Here we present high spatial resolution (<1'') observations of molecular emission in Orion-KL conducted using the Combined Array for Research in Millimeter-wave Astronomy. This work was motivated by recent millimeter continuum imaging studies of this region conducted at a similarly high spatial resolution, which revealed that the bulk of the emission arises from numerous compact sources, rather than the larger-scale extended structures typically associated with the Orion Hot Core and Compact Ridge. Given that the spatial extent of molecular emission greatly affects the determination of molecular abundances, it is important to determine the true spatial scale for complex molecules in this region. Additionally, it has recently been suggested that the relative spatial distributions of complex molecules in a source might give insight into the chemical mechanisms that drive complex chemistry in star-forming regions. In order to begin to address these issues, this study seeks to determine the spatial distributions of ethyl cyanide [C{sub 2}H{sub 5}CN], dimethyl ether [(CH{sub 3}){sub 2}O], methyl formate [HCOOCH{sub 3}], formic acid [HCOOH], acetone [(CH{sub 3}){sub 2}CO], SiO, methanol [CH{sub 3}OH], and methyl cyanide [CH{sub 3}CN] in Orion-KL at {lambda} = 3 mm. We find that for all observed molecules, the molecular emission arises from multiple components of the cloud that include a range of spatial scales and physical conditions. Here, we present the results of these observations and discuss the implications for studies of complex molecules in star-forming regions.

  10. Near-Unity Mass Accommodation Coefficient of Organic Molecules of Varying Structure

    PubMed Central

    2014-01-01

    Atmospheric aerosol particles have a significant effect on global climate, air quality, and consequently human health. Condensation of organic vapors is a key process in the growth of nanometer-sized particles to climate relevant sizes. This growth is very sensitive to the mass accommodation coefficient α, a quantity describing the vapor uptake ability of the particles, but knowledge on α of atmospheric organics is lacking. In this work, we have determined α for four organic molecules with diverse structural properties: adipic acid, succinic acid, naphthalene, and nonane. The coefficients are studied using molecular dynamics simulations, complemented with expansion chamber measurements. Our results are consistent with α = 1 (indicating nearly perfect accommodation), regardless of the molecular structural properties, the phase state of the bulk condensed phase, or surface curvature. The results highlight the need for experimental techniques capable of resolving the internal structure of nanoparticles to better constrain the accommodation of atmospheric organics. PMID:25260072

  11. Metal-organic frameworks with functional pores for recognition of small molecules.

    PubMed

    Chen, Banglin; Xiang, Shengchang; Qian, Guodong

    2010-08-17

    Molecular recognition, an important process in biological and chemical systems, governs the diverse functions of a variety of enzymes and unique properties of some synthetic receptors. Because molecular recognition is based on weak interactions between receptors and substrates, the design and assembly of synthetic receptors to mimic biological systems and the development of novel materials to discriminate different substrates for selective recognition of specific molecules has proved challenging. The extensive research on synthetic receptors for molecular recognition, particularly on noncovalent complexes self-assembled by hydrogen bonding and metal-organic coordination, has revealed some underlying principles. In particular, these studies have demonstrated that the shapes of the supramolecular receptors play significant roles in their specific and selective recognition of substrates: receptors can offer concave surfaces that complement their convex targets. This Account describes our research to develop a synthetic molecular recognition platform using porous metal-organic frameworks (MOFs). These materials contain functional pores to direct their specific and unique recognition of small molecules through several types of interactions: van der Waals interactions of the framework surface with the substrate, metal-substrate interactions, and hydrogen bonding of the framework surface with the substrate. These materials have potential applications for gas storage, separation, and sensing. We demonstrate a simple strategy to construct a primitive cubic net of interpenetrated microporous MOFs from the self-assembly of the paddle-wheel clusters M(2)(CO(2))(4) (M = Cu(2+), Zn(2+), and Co(2+)) with two types of organic dicarboxylic acid and pillar bidentate linkers. This efficient method allows us to rationally tune the micropores to size-exclusively sort different small gas molecules, leading to the highly selective separation and purification of gases. By optimizing the

  12. Formation and Destruction Processes of Interstellar Dust: From Organic Molecules to carbonaceous Grains

    NASA Technical Reports Server (NTRS)

    Salama, F.; Biennier, L.

    2004-01-01

    The study of the formation and destruction processes of cosmic dust is essential to understand and to quantify the budget of extraterrestrial organic molecules. interstellar dust presents a continuous size distribution from large molecules, radicals and ions to nanometer-sized particles to micron-sized grains. The lower end of the dust size distribution is thought to be responsible for the ubiquitous spectral features that are seen in emission in the IR (UIBs) and in absorption in the visible (DIBs). The higher end of the dust-size distribution is thought to be responsible for the continuum emission plateau that is seen in the IR and for the strong absorption seen in the interstellar UV extinction curve. All these spectral signatures are characteristic of cosmic organic materials that are ubiquitous and present in various forms from gas-phase molecules to solid-state grains. Although dust with all its components plays an important role in the evolution of interstellar chemistry and in the formation of organic molecules, little is known on the formation and destruction processes of dust. Recent space observations in the UV (HST) and in the IR (ISO) help place size constraints on the molecular component of carbonaceous IS dust and indicate that small (ie., subnanometer) PAHs cannot contribute significantly to the IS features in the UV and in the IR. Studies of large molecular and nano-sized IS dust analogs formed from PAH precursors have been performed in our laboratory under conditions that simulate diffuse ISM environments (the particles are cold -100 K vibrational energy, isolated in the gas phase and exposed to a high-energy discharge environment in a cold plasma). The species (molecules, molecular fragments, ions, nanoparticles, etc) formed in the pulsed discharge nozzle (PDN) plasma source are detected with a high-sensitivity cavity ring-down spectrometer (CRDS). We will present new experimental results that indicate that nanoparticles are generated in the

  13. Factors controlling the abundance of organic sulfur in flash pyrolyzates of Upper Cretaceous kerogens from Sergipe Basin, Brazil

    USGS Publications Warehouse

    Carmo, A.M.; Stankiewicz, B.A.; Mastalerz, Maria; Pratt, L.M.

    1997-01-01

    The molecular and elemental composition of immature kerogens isolated from Upper Cretaceous marine carbonates from Sergipe Basin, Brazil were investigated using combined pyrolysis-gas chromatography/mass spectrometry and organic petrographic techniques. The kerogens are predominantly composed of reddish-fluorescing amorphous organic matter (AOM) and variable amounts of yellow-fluorescing alginite and liptodetrinite. The abundance of organic sulfur in the kerogens inferred from the ratio 2-ethyl-5-methylthiophene/(1,2-dimethylbenzene + dec-1-ene) in the pyrolyzates is variable and may be related to changes in the type of primary organic input and/or to variations in rates of bacterial sulfate reduction. A concomitant increase in S/C and O/C ratios determined in situ using the electron microprobe is observed in AOM and alginites and may be related to a progressive oxidation of the organic matter during sulfurization. The S/C ratio of the AOM is systematically higher than the S C ratio of the alginites. Combined with a thiophene distribution characteristic of pyrolyzates of Type II organic matter, the higher S/C of AOM in Sergipe kerogens suggests that sulfurization and incorporation of low-molecular weight lipids derived from normal marine organic matter into the kerogen structure predominated over direct sulfurization of highly aliphatic algal biomacromolecules.The molecular and elemental composition of immature kerogens isolated from Upper Cretaceous marine carbonates from Sergipe Basin, Brazil were investigated using combined pyrolysis-gas chromatography/mass spectrometry and organic petrographic techniques. The kerogens are predominantly composed of reddish-fluorescing amorphous organic matter (AOM) and variable amounts of yellow-fluorescing alginite and liptodetrinite. The abundance of organic sulfur in the kerogens inferred from the ratio 2-ethyl-5-methylthiophene/(1,2-dimethylbenzene+dec-1-ene) in the pyrolyzates is variable and may be related to changes in

  14. Single Molecule Spectroelectrochemistry of Interfacial Charge Transfer Dynamics In Hybrid Organic Solar Cell

    SciTech Connect

    Pan, Shanlin

    2014-11-16

    Our research under support of this DOE grant is focused on applied and fundamental aspects of model organic solar cell systems. Major accomplishments are: 1) we developed a spectroelectorchemistry technique of single molecule single nanoparticle method to study charge transfer between conjugated polymers and semiconductor at the single molecule level. The fluorescence of individual fluorescent polymers at semiconductor surfaces was shown to exhibit blinking behavior compared to molecules on glass substrates. Single molecule fluorescence excitation anisotropy measurements showed the conformation of the polymer molecules did not differ appreciably between glass and semiconductor substrates. The similarities in molecular conformation suggest that the observed differences in blinking activity are due to charge transfer between fluorescent polymer and semiconductor, which provides additional pathways between states of high and low fluorescence quantum efficiency. Similar spectroelectrochemistry work has been done for small organic dyes for understand their charge transfer dynamics on various substrates and electrochemical environments; 2) We developed a method of transferring semiconductor nanoparticles (NPs) and graphene oxide (GO) nanosheets into organic solvent for a potential electron acceptor in bulk heterojunction organic solar cells which employed polymer semiconductor as the electron donor. Electron transfer from the polymer semiconductor to semiconductor and GO in solutions and thin films was established through fluorescence spectroscopy and electroluminescence measurements. Solar cells containing these materials were constructed and evaluated using transient absorption spectroscopy and dynamic fluorescence techniques to understand the charge carrier generation and recombination events; 3) We invented a spectroelectorchemistry technique using light scattering and electroluminescence for rapid size determination and studying electrochemistry of single NPs in an

  15. Formation kinetics and abundance of organic nitrates in α-pinene ozonolysis

    NASA Astrophysics Data System (ADS)

    Berkemeier, Thomas; Ammann, Markus; Pöschl, Ulrich; Shiraiwa, Manabu

    2016-04-01

    Formation of organic nitrates affects the total atmospheric budget of oxidized nitrogen (NOy) and alters the total aerosol mass yield from secondary sources. We investigated the formation of organic nitrate species during ozonolysis of α-pinene and subsequent formation of secondary organic aerosols (SOA) using the short-lived radioactive tracer 13N inside an aerosol flow reactor (Ammann et al., 2001). The results represent direct measurements of the organic nitrate content of α-pinene secondary aerosol and give insight into the kinetics of organic nitrate formation. Organic nitrates constituted up to 40 % of aerosol mass with a pronounced influence during the initial period of particle growth. Kinetic modelling, as well as additional experiments using OH scavengers and UV irradiation, suggests that organic peroxy radicals (RO2) from the reaction of α-pinene with secondarily produced OH are important intermediates in the organic nitrate formation process. Direct oxidation of α-pinene by NO3 was found to be a less efficient pathway for formation of particle phase nitrate. The organic nitrate content decreased very slightly with an increase of relative humidity on the experimental time scale. The experiments show a tight correlation between organic nitrate content and SOA number concentrations, implying that organic nitrates play an important role in nucleation and growth of nanoparticles. Since present in large amounts in organic aerosol, organic nitrates deposited in the lung might have implications for human health as they release nitric acid upon hydrolysis, especially in regions influenced by urban pollution and large sources of monoterpene SOA precursors. References Ammann et al. (2001) Radiochimica Acta 89, 831.

  16. Donor-acceptor small molecules for organic photovoltaics: single-atom substitution (Se or S).

    PubMed

    He, Xiaoming; Cao, Bing; Hauger, Tate C; Kang, Minkyu; Gusarov, Sergey; Luber, Erik J; Buriak, Jillian M

    2015-04-22

    Two isostructural low-band-gap small molecules that contain a one-atom substitution, S for Se, were designed and synthesized. The molecule 7,7'-[4,8-bis(2-ethylhexyloxy)benzo[1,2-b:4,5-b']dithiophene]bis[6-fluoro-4-(5'-hexyl-2,2'-bithiophen-5-yl)benzo[c][1,2,5]thiadiazole] (1) and its selenium analogue 7,7'-[4,8-bis(2-ethylhexyloxy)benzo[1,2-b:4,5-b']dithiophene]bis[6-fluoro-4-(5'-hexyl-2,2'-bithiophen-5-yl)benzo[c][1,2,5]selenodiazole] (2) are both based on the electron-rich central unit benzo[1,2-b:4,5-b']dithiophene. The aim of this work was to investigate the effect of one-atom substitution on the optoelectronic properties and photovoltaic performance of devices. Theoretical calculations revealed that this one-atom variation has a small but measurable effect on the energy of frontier molecular orbital (HOMO and LUMO), which, in turn, can affect the absorption profile of the molecules, both neat and when mixed in a bulk heterojunction (BHJ) with PC71BM. The Se-containing variant 2 led to higher efficiencies [highest power conversion efficiency (PCE) of 2.6%] in a standard organic photovoltaic architecture, when combined with PC71BM after a brief thermal annealing, than the S-containing molecule 1 (highest PCE of 1.0%). Studies of the resulting morphologies of BHJs based on 1 and 2 showed that one-atom substitution could engender important differences in the solubilities, which then influenced the crystal orientations of the small molecules within this thin layer. Brief thermal annealing resulted in rotation of the crystalline grains of both molecules to more energetically favorable configurations. PMID:25808481

  17. Noble metal-free hydrogen-evolving photocathodes based on small molecule organic semiconductors

    NASA Astrophysics Data System (ADS)

    Morozan, A.; Bourgeteau, T.; Tondelier, D.; Geffroy, B.; Jousselme, B.; Artero, V.

    2016-09-01

    Organic semiconductors have great potential for producing hydrogen in a sustainable and economically-viable manner because they rely on readily available materials with highly tunable properties. We demonstrate here the relevance of heterojunctions to the construction of H2-evolving photocathodes, exclusively based on earth-abundant elements. Boron subnaphthalocyanine chloride proved a very promising acceptor in that perspective. It absorbs a part of the solar spectrum complementary to α-sexithiophene as a donor, thus generating large photocurrents and providing a record onset potential for light-driven H2 evolution under acidic aqueous conditions using a nanoparticulate amorphous molybdenum sulfide catalyst.

  18. Noble metal-free hydrogen-evolving photocathodes based on small molecule organic semiconductors.

    PubMed

    Morozan, A; Bourgeteau, T; Tondelier, D; Geffroy, B; Jousselme, B; Artero, V

    2016-09-01

    Organic semiconductors have great potential for producing hydrogen in a sustainable and economically-viable manner because they rely on readily available materials with highly tunable properties. We demonstrate here the relevance of heterojunctions to the construction of H2-evolving photocathodes, exclusively based on earth-abundant elements. Boron subnaphthalocyanine chloride proved a very promising acceptor in that perspective. It absorbs a part of the solar spectrum complementary to α-sexithiophene as a donor, thus generating large photocurrents and providing a record onset potential for light-driven H2 evolution under acidic aqueous conditions using a nanoparticulate amorphous molybdenum sulfide catalyst. PMID:27455142

  19. Transformation of Graphitic and Amorphous Carbon Dust to Complex Organic Molecules in a Massive Carbon Cycle in Protostellar Nebulae

    NASA Technical Reports Server (NTRS)

    Nuth, Joseph A., III; Johnson, Natasha M.

    2012-01-01

    More than 95% of silicate minerals and other oxides found in meteorites were melted, or vaporized and recondensed in the Solar Nebula prior to their incorporation into meteorite parent bodies. Gravitational accretion energy and heating via radioactive decay further transformed oxide minerals accreted into planetesimals. In such an oxygen-rich environment the carbonaceous dust that fell into the nebula as an intimate mixture with oxide grains should have been almost completely converted to CO. While some pre-collapse, molecular-cloud carbonaceous dust does survive, much in the same manner as do pre-solar oxide grains, such materials constitute only a few percent of meteoritic carbon and are clearly distinguished by elevated D/H, N-15/N-16, C-13/C-12 ratios or noble gas patterns. Carbonaceous Dust in Meteorites: We argue that nearly all of the carbon in meteorites was synthesized in the Solar Nebula from CO and that this CO was generated by the reaction of carbonaceous dust with solid oxides, water or OH. It is probable that some fraction of carbonaceous dust that is newly synthesized in the Solar Nebula is also converted back into CO by additional thermal processing. CO processing might occur on grains in the outer nebula through irradiation of CO-containing ice coatings or in the inner nebula via Fischer-Tropsch type (FTT) reactions on grain surfaces. Large-scale transport of both gaseous reaction products and dust from the inner nebula out to regions where comets formed would spread newly formed carbonaceous materials throughout the solar nebula. Formation of Organic Carbon: Carbon dust in the ISM might easily be described as inorganic graphite or amorphous carbon, with relatively low structural abundances of H, N, O and S . Products of FTT reactions or organics produced via irradiation of icy grains contain abundant aromatic and aliphatic hydrocarbons. aldehydes, keytones, acids, amines and amides.. The net result of the massive nebular carbon cycle is to convert

  20. Reactions of metal cluster anions with inorganic and organic molecules in the gas phase.

    PubMed

    Zhao, Yan-Xia; Liu, Qing-Yu; Zhang, Mei-Qi; He, Sheng-Gui

    2016-07-28

    The study of gas phase ion-molecule reactions by state-of-the-art mass spectrometric experiments in conjunction with quantum chemistry calculations offers an opportunity to clarify the elementary steps and mechanistic details of bond activation and conversion processes. In the past few decades, a considerable number of publications have been devoted to the ion-molecule reactions of metal clusters, the experimentally and theoretically tractable models for the active phase of condensed phase systems. The focus of this perspective concerns progress on activation and transformation of important inorganic and organic molecules by negatively charged metal clusters. The metal cluster anions cover bare metal clusters as well as ligated systems with oxygen, carbon, and nitrogen, among others. The following important issues have been summarized and discussed: (i) dependence of chemical reactivity and selectivity on cluster structures and sizes, metals and metal oxidation states, odd-even electron numbers, etc. and (ii) effects of doping, ligation, and pre-adsorption on the reactivity of metal clusters toward rather inert molecules. PMID:27346242

  1. Supramolecular organization of pi-conjugated molecules monitored by single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Alvarez, Laurent; Almadori, Yann; Belhboub, Anouar; Le Parc, Rozenn; Aznar, Raymond; Dieudonné-George, Philippe; Rahmani, Abdelali; Hermet, Patrick; Fossard, Frédéric; Loiseau, Annick; Jousselme, Bruno; Campidelli, Stéphane; Saito, Takeshi; Wang, Guillaume; Bantignies, Jean-Louis

    2016-03-01

    Photoactive pi-conjugated molecules (quaterthiophene and phthalocyanine) are either encapsulated into the hollow core of single-walled carbon nanotubes or noncovalently stacked at their outer surface in order to elaborate hybrid nanosystems with new physical properties, providing practical routes to fit different requirements for potential applications. We are interested in the relationship between the structure and the optoelectronic properties. The structural properties are investigated mainly by x-ray diffraction and/or transmission electron microscopy and Raman spectroscopy. We show that the supramolecular organizations of confined quaterthiophenes depend on the nanocontainer size, whereas phthalocyanine encapsulation leads to the formation of a one-dimensional phase for which the angle between the molecule ring and the nanotube axis is close to 32 deg. Confined phthalocyanine molecules display Raman spectra hardly altered with respect to the bulk phase, suggesting a rather weak interaction with the tubes. In contrast, the vibrational properties of the molecules stacked at the outer surface of tubes display important modifications. We assume a significant curvature of the phthalocyanine induced by the interaction with the tube walls and a change of the central atom position within the molecular ring, in good agreement with our density functional theory calculations.

  2. A scale-bridging modeling approach for anisotropic organic molecules at patterned semiconductor surfaces

    NASA Astrophysics Data System (ADS)

    Kleppmann, Nicola; Klapp, Sabine H. L.

    2015-02-01

    Hybrid systems consisting of organic molecules at inorganic semiconductor surfaces are gaining increasing importance as thin film devices for optoelectronics. The efficiency of such devices strongly depends on the collective behavior of the adsorbed molecules. In the present paper, we propose a novel, coarse-grained model addressing the condensed phases of a representative hybrid system, that is, para-sexiphenyl (6P) at zinc-oxide (ZnO). Within our model, intermolecular interactions are represented via a Gay-Berne potential (describing steric and van-der-Waals interactions) combined with the electrostatic potential between two linear quadrupoles. Similarly, the molecule-substrate interactions include a coupling between a linear molecular quadrupole to the electric field generated by the line charges characterizing ZnO(10-10). To validate our approach, we perform equilibrium Monte Carlo simulations, where the lateral positions are fixed to a 2D lattice, while the rotational degrees of freedom are continuous. We use these simulations to investigate orientational ordering in the condensed state. We reproduce various experimentally observed features such as the alignment of individual molecules with the line charges on the surface, the formation of a standing uniaxial phase with a herringbone structure, as well as the formation of a lying nematic phase.

  3. A scale-bridging modeling approach for anisotropic organic molecules at patterned semiconductor surfaces.

    PubMed

    Kleppmann, Nicola; Klapp, Sabine H L

    2015-02-14

    Hybrid systems consisting of organic molecules at inorganic semiconductor surfaces are gaining increasing importance as thin film devices for optoelectronics. The efficiency of such devices strongly depends on the collective behavior of the adsorbed molecules. In the present paper, we propose a novel, coarse-grained model addressing the condensed phases of a representative hybrid system, that is, para-sexiphenyl (6P) at zinc-oxide (ZnO). Within our model, intermolecular interactions are represented via a Gay-Berne potential (describing steric and van-der-Waals interactions) combined with the electrostatic potential between two linear quadrupoles. Similarly, the molecule-substrate interactions include a coupling between a linear molecular quadrupole to the electric field generated by the line charges characterizing ZnO(10-10). To validate our approach, we perform equilibrium Monte Carlo simulations, where the lateral positions are fixed to a 2D lattice, while the rotational degrees of freedom are continuous. We use these simulations to investigate orientational ordering in the condensed state. We reproduce various experimentally observed features such as the alignment of individual molecules with the line charges on the surface, the formation of a standing uniaxial phase with a herringbone structure, as well as the formation of a lying nematic phase. PMID:25681929

  4. Probing the Formation of Complex Organic Molecules in Interstellar Ices - Beyond the FTIR - RGA Limitation

    NASA Astrophysics Data System (ADS)

    Kaiser, Ralf I.

    2015-08-01

    An understanding of the formation of key classes of complex organic molecules (COMs) within interstellar ices is of core value to the laboratory astrophysics community with structural isomers - molecules with the same molecular formula but different connectivities of atoms - serving as a molecular clock and tracers in defining the evolutionary stage of cold molecular clouds and star forming regions. Here, the lack of data on products, branching ratios, and rate constants of their formation and how they depend on the ice temperature and composition limits the understanding how COMs are synthesized. Classically, infrared spectroscopy combined with mass spectrometry of the irradiated and subliming ices have been exploited for the last decades, but the usefulness of these methods has reached the limits when it comes to the identification of CMS in those ices. Here, infrared spectroscopy can only untangle the functional groups of COMs; mass spectrometry coupled with electron impact ionization cannot discriminate structural isomers and suffers from extensive fragmentation. This talk presents a novel approach to elucidate the formation of COMs by exploiting - besides classical infrared, Raman, and ultraviolet-visual spectroscopy - reflectron time-of-flight mass spectrometry (ReTOF) coupled with tunable vacuum ultraviolet (VUV) soft photoionization (ReTOF-PI). This technique has the unique power to identify the molecules based on a cross correlation of their mass-to-charge ratios, their ionization energies (IE), and their sublimation temperatures ultimately unraveling an inventory of individual COMs molecules formed upon interaction of ionizing radiation with interstellar analog ices.

  5. Racemization as a stereochemical measure of dynamics and robustness in shape-shifting organic molecules

    PubMed Central

    He, Maggie; Bode, Jeffrey W.

    2011-01-01

    Bullvalene is a structurally unique dynamic molecule thought to interconvert among 1.2 million degenerate isomers. The incorporation of different chemical substituents onto the bullvalene core should lead to a “shape-shifting” molecule that can interconvert among thousands of discrete structural isomers. Previous NMR spectroscopy and HPLC studies on substituted bullvalenes ascertained the fact that these compounds are dynamic, but they could not attest to whether the molecules are only interconverting among only a few isomers or if a multitude of structures are being accessed. Here we confirm the remarkable shape-shifting property of a tetrasubstituted bullvalene by means of a racemization experiment. We show that a single, though fleeting, chiral, enantioenriched tetrasubstituted bullvalene isomer can spontaneously equilibrate to a racemic population of dynamic compounds. Despite the fact that conversion from one enantiomer of a bullvalene isomer to the other may require dozens or even hundreds of rearrangements and involve many potential pathways, CD spectroscopy and HPLC analysis of different bullvalene populations showed that multiple pathways exist and result in the complete racemization of an initial enantioenriched chiral bullvalene. These oligosubstituted bullvalenes represent a very rare example of an entity that can spontaneously transform itself into different discrete structures using ambient thermal energy. The confirmation that these shape-shifting organic molecules are chemically robust yet structurally dynamic is an important step toward their further use as materials, sensors, and biologically active compounds. PMID:21873220

  6. Accounting for non-independent detection when estimating abundance of organisms with a Bayesian approach

    USGS Publications Warehouse

    Martin, Julien; Royle, J. Andrew; MacKenzie, Darryl I.; Edwards, Holly H.; Kery, Marc; Gardner, Beth

    2011-01-01

    Summary 1. Binomial mixture models use repeated count data to estimate abundance. They are becoming increasingly popular because they provide a simple and cost-effective way to account for imperfect detection. However, these models assume that individuals are detected independently of each other. This assumption may often be violated in the field. For instance, manatees (Trichechus manatus latirostris) may surface in turbid water (i.e. become available for detection during aerial surveys) in a correlated manner (i.e. in groups). However, correlated behaviour, affecting the non-independence of individual detections, may also be relevant in other systems (e.g. correlated patterns of singing in birds and amphibians). 2. We extend binomial mixture models to account for correlated behaviour and therefore to account for non-independent detection of individuals. We simulated correlated behaviour using beta-binomial random variables. Our approach can be used to simultaneously estimate abundance, detection probability and a correlation parameter. 3. Fitting binomial mixture models to data that followed a beta-binomial distribution resulted in an overestimation of abundance even for moderate levels of correlation. In contrast, the beta-binomial mixture model performed considerably better in our simulation scenarios. We also present a goodness-of-fit procedure to evaluate the fit of beta-binomial mixture models. 4. We illustrate our approach by fitting both binomial and beta-binomial mixture models to aerial survey data of manatees in Florida. We found that the binomial mixture model did not fit the data, whereas there was no evidence of lack of fit for the beta-binomial mixture model. This example helps illustrate the importance of using simulations and assessing goodness-of-fit when analysing ecological data with N-mixture models. Indeed, both the simulations and the goodness-of-fit procedure highlighted the limitations of the standard binomial mixture model for aerial

  7. Detecting and Identifying Organic Molecules in Space - The AstroBiology Explorer (ABE) MIDEX Mission Concept

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.

    2001-01-01

    Infrared spectroscopy in the 2.5-16 micron (4000-625/cm) range is a principle means by which organic compounds are detected and identified in space. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Unfortunately, neither the distribution of these materials nor their genetic and evolutionary relationships with each other or their environments are well understood. The Astrobiology Explorer (ABE) is a MIDEX (Medium-class Explorer) mission concept currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corporation. ABE will conduct IR spectroscopic observations to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding (1) the evolution of ices and organic matter in dense molecular clouds and young forming stellar systems, (2) the chemical evolution of organic molecules in the ISM as they transition from AGB outflows to planetary nebulae to the general diffuse ISM to H II regions and dense clouds, (3) the distribution of organics in the diffuse ISM, (4) the nature of organics in the Solar System (in comets, asteroids, satellites), and (5) the nature and distribution of organics in local galaxies. Both the scientific goals of the mission and how they would be achieved will be discussed.

  8. Identifying Organic Molecules in Space: The AstroBiology Explorer (ABE) MIDEX Mission Concept

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; Allamandola, Louis; Bregman, Jesse; Ennico, Kimberly; Greene, Thomas; Hudgins, Douglas; Strecker, Donald; DeVincenzi, Donald (Technical Monitor)

    2001-01-01

    Infrared spectroscopy in the 2.5-16 micron range is a principle means by which organic compounds are detected and identified in space. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Unfortunately, neither the distribution of these materials nor their genetic and evolutionary relationships with each other or their environments are well understood. The Astrobiology Explorer (ABE) is a MIDEX mission concept currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corporation. ABE will conduct IR spectroscopic observations to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding (1) the evolution of ices and organic matter in dense molecular clouds and young forming stellar systems, (2) the chemical evolution of organic molecules in the ISM as they transition from AGB outflows to planetary nebulae to the general diffuse ISM to H II regions and dense clouds, (3) the distribution of organics in the diffuse ISM, (4) the nature of organics in the Solar System (in comets, asteroids, satellites), and (5) the nature and distribution of organics in local galaxies. The technical considerations of achieving these science objectives in a MIDEX-sized mission will be described.

  9. Detecting and Identifying Organic Molecules in Space: The AstroBiology Explorer (ABE) MIDEX Mission Concept

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; DeVincenzi, Donald (Technical Monitor)

    2001-01-01

    Infrared spectroscopy in the 2.5-16 microns (4000-625/cm) range is a principle means by which organic compounds are detected and identified in space. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Unfortunately, neither the distribution of these materials nor their genetic and evolutionary relationships with each other or their environments are well understood. The Astrobiology Explorer (ABE) is a MIDEX (Medium-class Explorer) mission concept currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corporation. ABE will conduct IR spectroscopic observations to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding (1) the evolution of ices and organic matter in dense molecular clouds and young forming stellar systems, (2) the chemical evolution of organic molecules in the ISM as they transition from AGB outflows to planetary nebulae to the general diffuse ISM to H II regions and dense clouds, (3) the distribution of organics in the diffuse ISM, (4) the nature of organics in the Solar System (in comets, asteroids, satellites), and (5) the nature and distribution of organics in local galaxies. Both the scientific goals of the mission and how they would be achieved will be discussed.

  10. Occurrence and abundance of carbohydrates and amino compounds in sequentially extracted labile soil organic matter fractions.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study aimed to investigate the content of carbohydrates and amino compounds in three labile fraction of soil organic matter (SOM). Soil samples were collected from two agricultural fields in southern Italy and the light fraction (LF), the 500–53-µm particulate organic matter (POM) and the mobil...

  11. Weed seed persistence and microbial abundance in long-term organic and conventional cropping systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weed seed persistence in soil can be influenced by many factors, including crop management. This research was conducted to determine whether organic management systems with higher organic amendments and soil microbial biomass could reduce weed seed persistence compared to conventional management sy...

  12. Guest–host interactions of a rigid organic molecule in porous silica frameworks

    PubMed Central

    Wu, Di; Hwang, Son-Jong; Zones, Stacey I.; Navrotsky, Alexandra

    2014-01-01

    Molecular-level interactions at organic–inorganic interfaces play crucial roles in many fields including catalysis, drug delivery, and geological mineral precipitation in the presence of organic matter. To seek insights into organic–inorganic interactions in porous framework materials, we investigated the phase evolution and energetics of confinement of a rigid organic guest, N,N,N-trimethyl-1-adamantammonium iodide (TMAAI), in inorganic porous silica frameworks (SSZ-24, MCM-41, and SBA-15) as a function of pore size (0.8 nm to 20.0 nm). We used hydrofluoric acid solution calorimetry to obtain the enthalpies of interaction between silica framework materials and TMAAI, and the values range from −56 to −177 kJ per mole of TMAAI. The phase evolution as a function of pore size was investigated by X-ray diffraction, IR, thermogravimetric differential scanning calorimetry, and solid-state NMR. The results suggest the existence of three types of inclusion depending on the pore size of the framework: single-molecule confinement in a small pore, multiple-molecule confinement/adsorption of an amorphous and possibly mobile assemblage of molecules near the pore walls, and nanocrystal confinement in the pore interior. These changes in structure probably represent equilibrium and minimize the free energy of the system for each pore size, as indicated by trends in the enthalpy of interaction and differential scanning calorimetry profiles, as well as the reversible changes in structure and mobility seen by variable temperature NMR. PMID:24449886

  13. Photogenerated Intrinsic Free Carriers in Small-molecule Organic Semiconductors Visualized by Ultrafast Spectroscopy

    PubMed Central

    He, Xiaochuan; Zhu, Gangbei; Yang, Jianbing; Chang, Hao; Meng, Qingyu; Zhao, Hongwu; Zhou, Xin; Yue, Shuai; Wang, Zhuan; Shi, Jinan; Gu, Lin; Yan, Donghang; Weng, Yuxiang

    2015-01-01

    Confirmation of direct photogeneration of intrinsic delocalized free carriers in small-molecule organic semiconductors has been a long-sought but unsolved issue, which is of fundamental significance to its application in photo-electric devices. Although the excitonic description of photoexcitation in these materials has been widely accepted, this concept is challenged by recently reported phenomena. Here we report observation of direct delocalized free carrier generation upon interband photoexcitation in highly crystalline zinc phthalocyanine films prepared by the weak epitaxy growth method using ultrafast spectroscopy. Transient absorption spectra spanning the visible to mid-infrared region revealed the existence of short-lived free electrons and holes with a diffusion length estimated to cross at least 11 molecules along the π−π stacking direction that subsequently localize to form charge transfer excitons. The interband transition was evidenced by ultraviolet-visible absorption, photoluminescence and electroluminescence spectroscopy. Our results suggest that delocalized free carriers photogeneration can also be achieved in organic semiconductors when the molecules are packed properly. PMID:26611323

  14. Spintronic and Electronic Phenomena in Organic Molecules Measured with μSR

    NASA Astrophysics Data System (ADS)

    Wang, Ke; Schulz, Leander; Willis, Maureen; Zhang, Sijie; Misquitta, Alston J.; Drew, Alan J.

    2016-09-01

    The use of implanted muons to probe the spin dynamics and electronic excitations in organic materials is reviewed. At first, a brief introduction to the historical context and background of the muon technique is given, followed by an outline of some of the underlying theoretical models needed to quantitatively interpret data taken on organic molecules. Caution is advised when using certain theoretical models for the interpretation of low-field spin relaxation data. The next section deals with spin dynamics in soft materials, and starts with discussing many of the key results in thin films, followed by a review of bulk measurements in three different materials classes — polymers, biologically active molecules, and small molecules. Finally, we present a detailed discussion of the density functional theory methodology when applied to μSR, and present the common issues encountered when trying to perform these calculations to support muon experiments. In particular, we discuss a method for benchmarking to manage the approximations inherent to the technique and common sources of errors that can sometimes fortuitously cancel.

  15. Nanocoating of titanium implant surfaces with organic molecules. Polysaccharides including glycosaminoglycans.

    PubMed

    Gurzawska, Katarzyna; Svava, Rikke; Jørgensen, Niklas Rye; Gotfredsen, Klaus

    2012-12-01

    Long-term stability of titanium implants are dependent on a variety of factors. Nanocoating with organic molecules is one of the method used to improve osseointegration. Nanoscale modification of titanium implants affects surface properties, such as hydrophilicity, biochemical bonding capacity and roughness. This influences cell behaviour on the surface such as adhesion, proliferation and differentiation of cells as well as the mineralization of the extracellular matrix at the implant surfaces. The aim of the present systematic review was to describe organic molecules used for surface nanocoating with focus on polysaccharides including glycosaminoglycans, and how these molecules change surface properties, cell reactions and affect on osseointegartion. The included in vitro studies demonstrated increased cell adhesion, proliferation and mineralization of a number of the tested polysaccharide nanocoatings. The included in vivo studies, showed improvement of bone interface reactions measured as increased Bone-to-Implant Contact length and Bone Mineral Density adjacent to the polysaccharide coated surfaces. Based on existing literature, surface modification with polysaccharide and glycosaminoglycans appears to be an effective way to stimulate bone regeneration on bone-implant interface. PMID:23030010

  16. An investigation of the interrelationships between linear and nonlinear polarizabilities and bond-length alternation in conjugated organic molecules.

    PubMed Central

    Gorman, C B; Marder, S R

    1993-01-01

    A computational method was devised to explore the relationship of charge separation, geometry, molecular dipole moment (mu), polarizability (alpha), and hyperpolariz-abilities (beta, gamma) in conjugated organic molecules. We show that bond-length alternation (the average difference in length between single and double bonds in the molecule) is a key structurally observable parameter that can be correlated with hyperpolarizabilities and is thus relevant to the optimization of molecules and materials. By using this method, the relationship of bond-length alternation, mu, alpha, beta, and gamma for linear conjugated molecules is illustrated, and those molecules with maximized alpha, beta, and gamma are described. PMID:11607441

  17. The Laboratory Production of Complex Organic Molecules in Simulated Interstellar Ices

    NASA Technical Reports Server (NTRS)

    Dworkin, J. P.; Sandford, S. A.; Bernstein, M. P.; Allamandola, L. J.

    2002-01-01

    Much of the volatiles in interstellar dense clouds exist in ices surrounding dust grains. Their low temperatures preclude most chemical reactions, but ionizing radiation can drive reactions that produce a suite of new species, many of which are complex organics. The Astrochemistry Lab at NASA Ames studies the UV radiation processing of interstellar ice analogs to better identify the resulting products and establish links between interstellar chemistry, the organics in meteorites, and the origin of life on Earth. Once identified, the spectral properties of the products can be quantified to assist with the search for these species in space. Of particular interest are findings that UV irradiation of interstellar ice analogs produces molecules of importance in current living organisms, including quinones, amphiphiles, and amino acids.

  18. A Research Module for the Organic Chemistry Laboratory: Multistep Synthesis of a Fluorous Dye Molecule.

    PubMed

    Slade, Michael C; Raker, Jeffrey R; Kobilka, Brandon; Pohl, Nicola L B

    2014-01-14

    A multi-session research-like module has been developed for use in the undergraduate organic teaching laboratory curriculum. Students are tasked with planning and executing the synthesis of a novel fluorous dye molecule and using it to explore a fluorous affinity chromatography separation technique, which is the first implementation of this technique in a teaching laboratory. Key elements of the project include gradually introducing students to the use of the chemical literature to facilitate their searching, as well as deliberate constraints designed to force them to think critically about reaction design and optimization in organic chemistry. The project also introduces students to some advanced laboratory practices such as Schlenk techniques, degassing of reaction mixtures, affinity chromatography, and microwave-assisted chemistry. This provides students a teaching laboratory experience that closely mirrors authentic synthetic organic chemistry practice in laboratories throughout the world. PMID:24501431

  19. Adsorption of Organic Molecules on Kaolinite from the Exchange-Hole Dipole Moment Dispersion Model.

    PubMed

    Johnson, Erin R; Otero-de-la-Roza, Alberto

    2012-12-11

    Intermolecular interactions between organic molecules and clay minerals are important in a wide range of chemical applications, ranging from oil-sands petroleum extraction to environmental chemistry and catalysis. The binding energies between each of benzene, n-hexane, pyridine, 2-propanol, and water and the kaolinite surface are calculated using density functional theory with the exchange-hole dipole moment dispersion model. The dominant noncovalent interactions are found to be hydrogen bonding for pyridine, 2-propanol, and water, OH-π interactions for benzene, and CH-O interactions for n-hexane. All molecules considered are more strongly bound to the hydrophilic alumina face, rather than the hydrophobic siloxane face, of kaolinte. PMID:26593201

  20. Electronic excitations in solution-processed oligothiophene small-molecules for organic solar cells

    NASA Astrophysics Data System (ADS)

    Gala, F.; Mattiello, L.; Brunetti, F.; Zollo, G.

    2016-02-01

    First principles calculations based on density functional theory and many body perturbation theory have been employed to study the optical absorption properties of a newly synthesized oligo-thiophene molecule, with a quaterthiophene central unit, that has been designed for solution-processed bulk-heterojunction solar cells. To this aim we have employed the GW approach to obtain quasiparticle energies as a pre-requisite to solve the Bethe-Salpeter equation for the excitonic Hamiltonian. We show that the experimental absorption spectrum can be explained only by taking into account the inter-molecular transitions among the π-stacked poly-conjugated molecules that are typically obtained in solid-state organic samples.

  1. High-resolution electrohydrodynamic jet printing of small-molecule organic light-emitting diodes.

    PubMed

    Kim, Kukjoo; Kim, Gyeomuk; Lee, Bo Ram; Ji, Sangyoon; Kim, So-Yun; An, Byeong Wan; Song, Myoung Hoon; Park, Jang-Ung

    2015-08-28

    The development of alternative organic light-emitting diode (OLED) fabrication technologies for high-definition and low-cost displays is an important research topic as conventional fine metal mask-assisted vacuum evaporation has reached its limit to reduce pixel sizes and manufacturing costs. Here, we report an electrohydrodynamic jet (e-jet) printing method to fabricate small-molecule OLED pixels with high resolution (pixel width of 5 μm), which significantly exceeds the resolutions of conventional inkjet or commercial OLED display pixels. In addition, we print small-molecule emitting materials which provide a significant advantage in terms of device efficiency and lifetime compared to those with polymers. PMID:26214140

  2. Distribution and abundance of benthic organisms in the Sacramento River, California

    USGS Publications Warehouse

    Ferreira, Rodger F.; Green, D. Brady

    1977-01-01

    General comparisons were made between benthic organism samples collected in 1960-61 and 1972-73 from five sites in the Sacramento River between Red Bluff and Knights Landing, Calif. The composition of benthic organisms from both collection periods was similar. The 1972-73 data showed variable patterns in monthly changes at each site and downstream changes each month with number of organisms per square meter, number of taxa per square meter, and diversity index. Generally, the mean number of taxa per square meter and diversity index for all sampling periods were higher in the upper reach than the lower reach of the Sacramento River. (Woodard-USGS)

  3. Electron Transfer as a Probe of the Interfacial Quantum Dot-Organic Molecule Interaction

    NASA Astrophysics Data System (ADS)

    Peterson, Mark D.

    This dissertation describes a set of experimental and theoretical studies of the interaction between small organic molecules and the surfaces of semiconductor nanoparticles, also called quantum dots (QDs). Chapter 1 reviews the literature on the influence of ligands on exciton relaxation dynamics following photoexcitation of semiconductor QDs, and describes how ligands promote or inhibit processes such as emission, nonradiative relaxation, and charge transfer to redox active adsorbates. Chapter 2 investigates the specific interaction of alkylcarboxylated viologen derivatives with CdS QDs, and shows how a combination of steady-state photoluminescence (PL) and transient absorption (TA) experiments can be used to reveal the specific binding geometry of redox active organic molecules on QD surfaces. Chapter 3 expands on Chapter 2 by using PL and TA to provide information about the mechanisms through which methyl viologen (MV 2+) associates with CdS QDs to form a stable QD/MV2+ complex, suggesting two chemically distinct reactions. We use our understanding of the QD/molecule interaction to design a drug delivery system in Chapter 4, which employs PL and TA experiments to show that conformational changes in a redox active adsorbate may follow electron transfer, "activating" a biologically inert Schiff base to a protein inhibitor form. The protein inhibitor limits cell motility and may be used to prevent tumor metastasis in cancer patients. Chapter 5 discusses future applications of QD/molecule redox couples with an emphasis on efficient multiple charge-transfer reactions -- a process facilitated by the high degeneracy of band-edge states in QDs. These multiple charge-transfer reactions may potentially increase the thermodynamic efficiency of solar cells, and may also facilitate the splitting of water into fuel. Multiple exciton generation procedures, multi-electron transfer experiments, and future directions are discussed.

  4. Differences in leukocyte differentiation molecule abundances on domestic sheep (Ovis aries) and bighorn sheep (Ovis canadensis) neutrophils identified by flow cytometry.

    PubMed

    Highland, Margaret A; Schneider, David A; White, Stephen N; Madsen-Bouterse, Sally A; Knowles, Donald P; Davis, William C

    2016-06-01

    Although both domestic sheep (DS) and bighorn sheep (BHS) are affected by similar respiratory bacterial pathogens, experimental and field data indicate BHS are more susceptible to pneumonia. Cross-reactive monoclonal antibodies (mAbs) for use in flow cytometry (FC) are valuable reagents for interspecies comparative immune system analyses. This study describes cross-reactive mAbs that recognize leukocyte differentiation molecules (LDMs) and major histocompatibility complex antigens on DS and BHS leukocytes. Characterization of multichannel eosinophil autofluorescence in this study permitted cell-type specific gating of granulocytes for evaluating LDMs, specifically on neutrophils, by single-label FC. Evaluation of relative abundances of LDMs by flow cytometry revealed greater CD11a, CD11b, CD18 (β2 integrins) and CD 172a (SIRPα) on DS neutrophils and greater CD14 (lipopolysaccharide receptor) on BHS neutrophils. Greater CD25 (IL-2) was identified on BHS lymphocytes following Concavalin A stimulation. While DS and BHS have similar total peripheral blood leukocyte counts, BHS have proportionately more neutrophils. PMID:27260809

  5. Surface Enhanced Raman Spectroscopy of Volatile Organic molecules on the surface of Zinc Nanoparticles Produced by Laser Ablation

    NASA Astrophysics Data System (ADS)

    Singh, Subhash C.; Swarnkar, Raj K.; Ankit, Preyas; Chattopadhyaya, Mahesh C.; Gopal, R.

    2008-11-01

    Surface enhanced Raman spectroscopy have provided potential tool for the detection of organic/biological molecules within the cell of living organism. This technique is suitable for in vivo as well as in vitro detection upto single molecular level. In the present work we have studied SERS activity of zinc nanoparticles on CCl4 and CHCl3 molecules. Colloidal solution of zinc nanoparticles was found as a suitable substrate for Raman signal enhancement. The applied technique may be useful for the sensing of organic/biological molecules as a trace in solid as well as in liquid media.

  6. Remote detection and mapping of organic molecules in Titan's atmosphere using ALMA

    NASA Astrophysics Data System (ADS)

    Cordiner, Martin; Nixon, Conor A.; Charnley, Steven B.; Palmer, Maureen; Mumma, Michael J.; Molter, Edward; Teanby, Nicholas; Irwin, Patrick GJ; Kisiel, Zbigniew; Serigano, Joseph

    2016-06-01

    Titan is the largest moon of Saturn, with a thick (1.45 bar) atmosphere composed primarily of molecular nitrogen and methane. Atmospheric photochemistry results in the production of a wide range of complex organic molecules, including hydrocarbons, nitriles, aromatics and species of possible pre-biotic relevance. Studies of Titan's atmospheric chemistry thus provide a unique opportunity to explore the origin and evolution of complex organic matter in a primitive (terrestrial) planetary atmosphere. Underpinned by laboratory measurements, remote and in-situ observations of hydrocarbons, nitriles and oxygen-bearing species provide important new insights in this regard. The Atacama Large Millimeter/submillimeter Array (ALMA) is a powerful new facility, well suited to the study of molecular emission from Titan's upper and middle-atmosphere. This presentation will focus on results from our ongoing studies of Titan using ALMA during the period 2012-2014, including detection and mapping of rotational emission lines from molecules including HNC, CO, HC3N, CH3CN, C2H3CN and C2H5CN, as well minor isotopologues. Possible chemical formation pathways for these species will be discussed, and the the scope for improved understanding of non-aqueous organic chemistry through laboratory experiments and atmospheric/liquid-phase simulations under Titan-like conditions will be examined.

  7. Characterization of Highly Oxidized Molecules in Fresh and Aged Biogenic Secondary Organic Aerosol.

    PubMed

    Tu, Peijun; Hall, Wiley A; Johnston, Murray V

    2016-04-19

    In this work, highly oxidized multifunctional molecules (HOMs) in fresh and aged secondary organic aerosol (SOA) derived from biogenic precursors are characterized with high-resolution mass spectrometry. Fresh SOA was generated by mixing ozone with a biogenic precursor (β-pinene, limonene, α-pinene) in a flow tube reactor. Aging was performed by passing the fresh SOA through a photochemical reactor where it reacted with hydroxyl radicals. Although these aerosols were as a whole not highly oxidized, molecular analysis identified a significant number of HOMs embedded within it. HOMs in fresh SOA consisted mostly of monomers and dimers, which is consistent with condensation of extremely low-volatility organic compounds (ELVOCs) that have been detected in the gas phase in previous studies and linked to SOA particle formation. Aging caused an increase in the average number of carbon atoms per molecule of the HOMs, which is consistent with particle phase oxidation of (less oxidized) oligomers already existing in fresh SOA. HOMs having different combinations of oxygen-to-carbon ratio, hydrogen-to-carbon ratio and average carbon oxidation state are discussed and compared to low volatility oxygenated organic aerosol (LVOOA), which has been identified in ambient aerosol based on average elemental composition but not fully understood at a molecular level. For the biogenic precursors and experimental conditions studied, HOMs in fresh biogenic SOA have molecular formulas more closely resembling LVOOA than HOMs in aged SOA, suggesting that aging of biogenic SOA is not a good surrogate for ambient LVOOA. PMID:27000653

  8. Designing small molecule polyaromatic p- and n-type semiconductor materials for organic electronics

    NASA Astrophysics Data System (ADS)

    Collis, Gavin E.

    2015-12-01

    By combining computational aided design with synthetic chemistry, we are able to identify core 2D polyaromatic small molecule templates with the necessary optoelectronic properties for p- and n-type materials. By judicious selection of the functional groups, we can tune the physical properties of the material making them amenable to solution and vacuum deposition. In addition to solubility, we observe that the functional group can influence the thin film molecular packing. By developing structure-property relationships (SPRs) for these families of compounds we observe that some compounds are better suited for use in organic solar cells, while others, varying only slightly in structure, are favoured in organic field effect transistor devices. We also find that the processing conditions can have a dramatic impact on molecular packing (i.e. 1D vs 2D polymorphism) and charge mobility; this has implications for material and device long term stability. We have developed small molecule p- and n-type materials for organic solar cells with efficiencies exceeding 2%. Subtle variations in the functional groups of these materials produces p- and ntype materials with mobilities higher than 0.3 cm2/Vs. We are also interested in using our SPR approach to develop materials for sensor and bioelectronic applications.

  9. Diels-Alder attachment of a planar organic molecule to a dangling bond dimer on a hydrogenated semiconductor surface.

    PubMed

    Godlewski, Szymon; Kawai, Hiroyo; Engelund, Mads; Kolmer, Marek; Zuzak, Rafal; Garcia-Lekue, Aran; Novell-Leruth, Gerard; Echavarren, Antonio M; Sanchez-Portal, Daniel; Joachim, Christian; Saeys, Mark

    2016-06-22

    Construction of single-molecule electronic devices requires the controlled manipulation of organic molecules and their properties. This could be achieved by tuning the interaction between the molecule and individual atoms by local "on-surface" chemistry, i.e., the controlled formation of chemical bonds between the species. We demonstrate here the reversible attachment of a planar conjugated polyaromatic molecule to a pair of unpassivated dangling bonds on a hydrogenated Ge(001):H surface via a Diels-Alder [4+2] addition using the tip of a scanning tunneling microscope (STM). Due to the small stability difference between the covalently bonded and a nearly undistorted structure attached to the dangling bond dimer by long-range dispersive forces, we show that at cryogenic temperatures the molecule can be switched between both configurations. The reversibility of this covalent bond forming reaction may be applied in the construction of complex circuits containing organic molecules with tunable properties. PMID:27271337

  10. Pre-biotic organic molecules in hydrothermal quartz veins from the Archaean Yilgarn province, Australia

    NASA Astrophysics Data System (ADS)

    Mayer, Christian; Schreiber, Ulrich; Dyker, Gerald; Kirnbauer, Thomas; Mulder, Ines; Sattler, Tobias; Schöler, Heinfried; Tubbesing, Christoph

    2013-04-01

    According to a model recently published by Schreiber et al. (OLEB 2012), pre-biotic organic molecules as earliest markers for a chemical evolution have been formed in tectonic faults of the first Archaean cratons. These faults are often documented by quartz- and other hydrothermal vein mineralization. During the growth of these quartzes, small portions of hydrothermal fluids are enclosed which conserve the chemical composition of the given fluid medium. According to our model, the preconditions for the geochemical formation of organic molecules are a suitable carbon source (e.g. carbon dioxide), varying P/T conditions, and catalysts. This given, rising hydrothermal fluids such as mineral-rich water and supercritical carbon dioxide in deep faults with contacts to the upper earth mantle offer conditions which allow for reactions similar to the Fischer-Tropsch synthesis. So far, the inclusions which possibly have conserved the products of these reactions have not been analyzed for possible organic constituents. First analytical results of a Mesozoic hydrothermal quartz vein from central Germany (Taunus) reveal that several organic compounds are found in fluid inclusions. However, the true origin of these compounds is unclear due to possible contamination by adjacent Corg-rich metasediments. Therefore, we have extended the study to hydrothermal quartz veins from the Archaean Yilgarn craton, to impact-generated quartz veins of the Shoemaker-Crater as well as to hydrothermal quartz boulders from a 2.7 to 3 billion years old conglomerate near Murchison (Western Australia). In one of the samples from the conglomerate, a wide spectrum of organic compounds such as bromomethane, butane, isoprene, benzene, and toluene have been detected. The time interval between the quartz formation, its erosion and its sedimentation is unknown. Possibly, the analyzed quartz sample was formed in a hydrothermal vein long before any living cells have existed on earth. In this case, the given

  11. The effect of a thiol-containing organic molecule on molybdenum adsorption onto pyrite

    NASA Astrophysics Data System (ADS)

    Freund, Carla; Wishard, Anthony; Brenner, Ryan; Sobel, Marisa; Mizelle, Jack; Kim, Alex; Meyer, Drew A.; Morford, Jennifer L.

    2016-02-01

    The effect of a small thiol-containing organic molecule on the adsorption of Mo to pyrite was investigated through the use of equilibration experiments with molybdate (MoO42-), tetrathiomolybdate (MoS42-), and 2-mercaptopropionic acid (2MPA). MoO42-, MoS42-, and 2MPA individually adsorb to pyrite through the formation of specific interactions with the mineral surface. In select combination experiments, 2MPA effectively out-competes MoO42- for pyrite surface sites, which is indicative of the relatively weaker MoO42--pyrite interactions. Results suggest that the presence of 2MPA on the pyrite surface would inhibit MoO42- access to catalytic mineral surface sites for the transformation of MoO42- to MoS42-. In contrast, thiols are not expected to be an obstacle to Mo uptake once the "switch point", or the critical H2S concentration required for the formation of MoS42-, has been surpassed. This is due to the stronger adsorption of MoS42- to the pyrite surface. EXAFS results support weak specific interactions with little change to the MoO42- environment upon adsorption to pyrite. In contrast, larger changes to the Mo-S internuclear distances during MoS42- adsorption to pyrite support a more substantial structural change upon adsorption. MoS42- is able to bind to both the pyrite surface and a thiol-containing organic molecule to form a ternary structure on the pyrite surface, and may provide for a molecular-level connection between Mo and thiol-containing organic molecules. Mo(VI) is reduced to Mo(IV) during MoS42- adsorption to pyrite as a result of ligand-induced reduction, thereby confirming that the thiolated form of Mo is necessary for Mo reduction.

  12. Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells.

    PubMed

    Lee, Cheng-Kuang; Pao, Chun-Wei

    2016-08-17

    Solution-processed small-molecule organic solar cells are a promising renewable energy source because of their low production cost, mechanical flexibility, and light weight relative to their pure inorganic counterparts. In this work, we developed a coarse-grained (CG) Gay-Berne ellipsoid molecular simulation model based on atomistic trajectories from all-atom molecular dynamics simulations of smaller system sizes to systematically study the nanomorphology of the SMDPPEH/PCBM/solvent ternary blend during solution processing, including the blade-coating process by applying external shear to the solution. With the significantly reduced overall system degrees of freedom and computational acceleration from GPU, we were able to go well beyond the limitation of conventional all-atom molecular simulations with a system size on the order of hundreds of nanometers with mesoscale molecular detail. Our simulations indicate that, similar to polymer solar cells, the optimal blending ratio in small-molecule organic solar cells must provide the highest specific interfacial area for efficient exciton dissociation, while retaining balanced hole/electron transport pathway percolation. We also reveal that blade-coating processes have a significant impact on nanomorphology. For given donor/acceptor blending ratios, applying an external shear force can effectively promote donor/acceptor phase segregation and stacking in the SMDPPEH domains. The present study demonstrated the capability of an ellipsoid-based coarse-grained model for studying the nanomorphology evolution of small-molecule organic solar cells during solution processing/blade-coating and provided links between fabrication protocols and device nanomorphologies. PMID:27435212

  13. Mars Organic Molecule Analyzer : The Search For Biosignatures And Biohints On Mars

    NASA Astrophysics Data System (ADS)

    Buch, Arnaud; Freissinet, C.; Brault, A.; Sternberg, R.; Rodier, C.; Szopa, C.; Coll, P.; Pinnick, V.; MOMA Team

    2012-10-01

    The joint ESA-Roscosmos Exo-Mars-2018 rover mission seeks the signs of past or present life on Mars. The Mars Organic Molecule Analyzer (MOMA) aboard the ExoMars rover will be a key analytical tool in providing chemical (molecular) information from the solid samples, with particular focus on the characterization of organic content. One of the instruments aboard MOMA is a gas chromatography-mass spectrometry (GC-MS) which provides a unique ability to characterize a broad range of compounds allowing chemical analyses on volatile and non-volatile species. The key challenge with the analysis of refractory organic compounds contained in soil is their extraction and subsequent analysis by GC-MS. Since the extraction of organic matter is not possible by liquid solvent extraction, thermodesoprtion followed by derivatization has been developed. The goal of the thermodesorption is to quickly extract the organic matter before degradation. One of the main focus is to determine the chirality of amino acids. Indeed, on earth homochirality (especially the L-form) is an indicator for the presence of life. However, other refractory compounds can be analyzed: nucleobases, carbox-ylic acids, PAHs, etc. Thermodesorption occurs within a range of temperatures from 150 °C to 300 °C over a period of 30 s to 10 min, depending on the chemical compound. Under these conditions, we have shown that amino acids are not degraded and that their chirality is preserved. Once extracted, refractory molecules with labile hydrogens (e.g. amino acids, nucleobases, carboxylic acids, etc.) were derivatized. General and sensitive derivatization occurs with a sillylated compounds N,N-methyl-tert-butyl-dimethylsilyl-trifluoroacetamide (MTBSTFA). Derivative compounds were separated on an RTX-5 (Restek) column. If a chiral separation was targeted, then dimethylformamide dimethylacetale derivatization (DMF-DMA) was utilized. With DMF-DMA 11 of the 19 proteinic amino acids were separated on the Chirasil

  14. An Investigation of the Interrelationships Between Linear and NonLinear Polarizabilities and Bond Length Alternation on Connugated Organic Molecules

    NASA Technical Reports Server (NTRS)

    Gorman, C. B.; Marder, S. R.

    1993-01-01

    A computational method was devised to explore the relationship between charge separation, geometry, molecular dipole moment, polarizability, and hyperpolarizabilities in comjugated organic molecules. It is shown that bond length alternation (the average difference in length between single and double bonds in the molecule) is a key structurally observable parameter that can be correlated with hyperpolarizabilities and is thus relevant to the optimizaton of molecules and materials.

  15. A triply interpenetrated microporous metal-organic framework for selective sorption of gas molecules.

    PubMed

    Chen, Banglin; Ma, Shengqian; Hurtado, Eric J; Lobkovsky, Emil B; Zhou, Hong-Cai

    2007-10-15

    A microporous metal-organic framework Zn(ADC)(4,4'-Bpe)(0.5).xG [1; ADC = 4,4'-azobenzenedicarboxylate, 4,4'-Bpe = trans-bis(4-pyridyl)ethylene, G = guest molecules] with a triply interpenetrative primitive cubic net was synthesized and characterized. With pores of about 3.4 x 3.4 A, the activated 1a exhibits highly selective sorption behavior toward H(2)/N(2), H(2)/CO, and CO(2)/CH(4). PMID:17854181

  16. Rationally designed micropores within a metal-organic framework for selective sorption of gas molecules.

    PubMed

    Chen, Banglin; Ma, Shengqian; Zapata, Fatima; Fronczek, Frank R; Lobkovsky, Emil B; Zhou, Hong-Cai

    2007-02-19

    A microporous metal-organic framework, MOF, Cu(FMA)(4,4'-Bpe)0.5 (3a, FMA = fumarate; 4,4'-Bpe = 4,4'-Bpe = trans-bis(4-pyridyl)ethylene) was rationally designed from a primitive cubic net whose pores are tuned by double framework interpenetration. With pore cavities of about 3.6 A, which are interconnected by pore windows of 2.0 x 3.2 A, 3a shows highly selective sorption behaviors of gas molecules. PMID:17291116

  17. Modified spontaneous emission of organic molecules in-filled in inverse opals.

    PubMed

    Deng, Lier; Wang, Yongsheng; He, Dawei

    2011-11-01

    Inverse opals were prepared by replication of colloidal crystal templates made from silica spheres 298 nm in diameter. The air between the silica spheres was filled with the mixture of the monomer poly(methyl methacrylate) (PMMA) and the organic molecule Alq3 that can be subsequently polymerized. After removing the silica sphere templates, the photonic bandgap effect on the spontaneous emission of Alq3 were investigated. The dip in the fluorescence spectrum was interpreted in terms of redistribution of the photon density of states in the photonic crystal. PMID:22413286

  18. Surface-Mediated Stimuli Responsive Delivery of Organic Molecules from Porous Carriers to Adhered Cells.

    PubMed

    Ergün, Bahar; De Cola, Luisa; Galla, Hans-Joachim; Kehr, Nermin Seda

    2016-07-01

    The alternating layer-by-layer deposition of oppositely charged polyelectrolytes on fluorescence-dye-(Hst)-loaded zeolites L ((Hst) Zeo-PSS/PLL) is described. The arrays and nanocomposite (NC) hydrogels of (Hst) Zeo-PSS/PLL are prepared. The subsequent cell experiments show the potential application of arrays and NC hydrogels of (Hst) Zeo-PSS/PLL as alternative 2D- and 3D-surfaces, respectively, for 2D- and 3D-surface-mediated controlled organic molecules delivery applications. PMID:27114067

  19. A solvatochromic method for determining second-order polarizabilities of organic molecules

    SciTech Connect

    Paley, M.S.; Harris, J.M. ); Looser, H.; Baumert, J.C.; Bjorklund, G.C.; Jundt, D.; Twieg, R.J. )

    1989-08-04

    A simple experimental method for determining optical second-order polarizabilities of organic molecules for second harmonic generation (SHG) is developed by using a two-level quantum mechanical model. Required values of excited-state dipole moments are obtained from a solvatochromic method based on the theoretical treatment of McRae. Second-order polarizabilities obtained by this method for a series of compounds compare well with those obtained by the conventional EFISH technique. The solvatochromic method has the important advantage that measurements can be made rapidly with simple equipment available in most chemistry laboratories.

  20. Third order optical nonlinearities characteristics of Disperse Red1 organic dye molecules inside of polymeric nanocapsules

    NASA Astrophysics Data System (ADS)

    Sharifimehr, Mohammad Reza; Ayoubi, Kazem; Mohajerani, Ezeddin

    2015-11-01

    Measuring nonlinear optical response of a specific material in a mixture, not only leads to investigate the behavior of a particular component in various circumstances, but also can be a way to select suitable combination and optimum concentration of additives and therefore obtaining the maximum nonlinear optical signals. In this work, by using dual-arm Z-scan technique, the nonlinear refractive index of Disperse Red1 (DR1) organic dye molecules inside the core of prepared polymeric nanocapsules was measured among various materials which prepared nanocapsules were made of them. Then the measured value was compared with nonlinear refractive index of DR1 solved in dichloromethane.

  1. Separation of rare gases and chiral molecules by selective binding in porous organic cages

    SciTech Connect

    Chen, Linjiang; Reiss, Paul S.; Chong, Samantha Y.; Holden, Daniel; Jelfs, Kim E.; Hasell, Tom; Little, Marc A.; Kewley, Adam; Briggs, Michael E.; Stephenson, Andrew; Thomas, K. M.; Armstrong, Jayne A.; Bell, Jon; Busto, Jose; Noel, Raymond; Liu, Jian; Strachan, Denis M.; Thallapally, Praveen K.; Cooper, Andrew I.

    2014-10-31

    Abstract: The rare gases krypton, xenon, and radon pose both an economic opportunity and a potential environmental hazard. Xenon is used in commercial lighting, medical imaging, and anesthesia, and can sell for $5,000 per kilogram. Radon, by contrast, Is naturally radioactive and the second largest cause of lung cancer, and radioactive xenon, 133Xe, was a major pollutant released In the Fukushima Daiichi Nuclear Power Plant disaster. We describe an organic cage molecule that can capture xenon and radon with unprecedented selectivity, suggesting new technologies for environmental monitoring, removal of pollutants, or the recovery of rare, valuable elements from air.

  2. Standoff detection of large organic molecules using Rydberg fingerprint spectroscopy and microwave Rayleigh scattering

    SciTech Connect

    Rudakov, Fedor M; Zhang, Zhili

    2012-01-01

    We present a technique for nonintrusive and standoff detection of large organic molecules using coherent microwave Rayleigh scattering from plasma produced by structure sensitive photoionization through Rydberg states. We test the method on 1,4-diazobicyclooctane. Transitions between the 3s Rydberg state and higher lying Rydberg states are probed using two-color photoionization with 266?nm photons and photons in the range of 460-2400 nm. Photoionization is detected using microwave radiation, which is scattered by the unbounded electrons. Highly resolved Rydberg spectra are acquired in vacuum and in air.

  3. A Perspective on Designing Chiral Organic Magnetic Molecules with Unusual Behavior in Magnetic Exchange Coupling.

    PubMed

    Sarbadhikary, Prodipta; Shil, Suranjan; Panda, Anirban; Misra, Anirban

    2016-07-01

    A total of nine diradical-based organic chiral magnetic molecules with allene and cumulene couplers have been theoretically designed, and subsequently, their magnetic property has been studied by density functional theory. It is found that with an increase in length of the coupler, a remarkable increase in spin density within the coupler takes place. An increase in the length of the coupler reduces the energy of LUMO, and a smaller HOMO-LUMO gap facilitates stronger magnetic coupling and thereby a higher magnetic exchange coupling constant (J). This observation is supported by the occupation number of natural orbitals. PMID:27285309

  4. Approaches for optimizing the first electronic hyperpolarizability of conjugated organic molecules

    NASA Technical Reports Server (NTRS)

    Marder, S. R.; Beratan, D. N.; Cheng, L.-T.

    1991-01-01

    Conjugated organic molecules with electron-donating and -accepting moieties can exhibit large electronic second-order nonlinearities, or first hyperpolarizabilities, beta. The present two-state, four-orbital independent-electron analysis of beta leads to the prediction that its absolute value will be maximized at a combination of donor and acceptor strengths for a given conjugated bridge. Molecular design strategies for beta optimization are proposed which give attention to the energetic manipulations of the bridge states. Experimental results have been obtained which support the validity of this approach.

  5. Room temperature phosphorescence from a guest molecule confined in the restrictive space of an organic-inorganic supramolecular assembly.

    PubMed

    Ishida, Yohei; Shimada, Tetsuya; Ramasamy, Elamparuthi; Ramamurthy, Vaidhyanathan; Takagi, Shinsuke

    2016-08-01

    Stable room-temperature phosphorescence of guest aromatic molecules was achieved by the effective suppression of oxygen quenching. The organic capsule (first wall) suppressed static oxygen quenching by enclosing a guest molecule, and dynamic quenching via the capsule opening-closing process was well suppressed and manipulated by the intercalation of this capsule into the restrictive space between clay nanosheets (second wall). PMID:27411736

  6. Computational screening of large molecule adsorption by metal-organic frameworks.

    SciTech Connect

    Allendorf, Mark D.; Greathouse, Jeffery A.

    2010-04-01

    Grand canonical Monte Carlo simulations were performed to investigate trends in low-pressure adsorption of a broad range of organic molecules by a set of metal-organic frameworks (MOFs). The organic analytes considered here are relevant to applications in chemical detection: small aromatics (o-, m-, and p-xylene), polycyclic aromatic hydrocarbons (naphthalene, anthracene, phenanthrene), explosives (TNT and RDX), and chemical warfare agents (GA and VM). The framework materials included several Zn-MOFs (IRMOFs 1-3, 7, 8), a Cr-MOF (CrMIL-53lp), and a Cu-MOF (HKUST-1). Many of the larger organics were significantly adsorbed by the target MOFs at low pressure, which is consistent with the exceptionally high isosteric heats of adsorption (25 kcal/mol - 60 kcal/mol) for this range of analyte. At a higher loading pressure of 101 kPa, the Zn-MOFs show a much higher volumetric uptake than either CrMIL-53-lp or HKUST-1 for all types of analyte. Within the Zn-MOF series, analyte loading is proportional to free volume, and loading decreases with increasing analyte size due to molecular packing effects. CrMIL-53lp showed the highest adsorption energy for all analytes, suggesting that this material may be suitable for low-level detection of organics.

  7. Trapping and desorption of complex organic molecules in water at 20 K

    NASA Astrophysics Data System (ADS)

    Burke, Daren J.; Puletti, Fabrizio; Woods, Paul M.; Viti, Serena; Slater, Ben; Brown, Wendy A.

    2015-10-01

    The formation, chemical, and thermal processing of complex organic molecules (COMs) is currently a topic of much interest in interstellar chemistry. The isomers glycolaldehyde, methyl formate, and acetic acid are particularly important because of their role as pre-biotic species. It is becoming increasingly clear that many COMs are formed within interstellar ices which are dominated by water. Hence, the interaction of these species with water ice is crucially important in dictating their behaviour. Here, we present the first detailed comparative study of the adsorption and thermal processing of glycolaldehyde, methyl formate, and acetic acid adsorbed on and in water ices at astrophysically relevant temperatures (20 K). We show that the functional group of the isomer dictates the strength of interaction with water ice, and hence the resulting desorption and trapping behaviour. Furthermore, the strength of this interaction directly affects the crystallization of water, which in turn affects the desorption behaviour. Our detailed coverage and composition dependent data allow us to categorize the desorption behaviour of the three isomers on the basis of the strength of intermolecular and intramolecular interactions, as well as the natural sublimation temperature of the molecule. This categorization is extended to other C, H, and O containing molecules in order to predict and describe the desorption behaviour of COMs from interstellar ices.

  8. Effect of carbazole as a donor moiety on the second-order nonlinearity of organic molecules

    NASA Astrophysics Data System (ADS)

    Meshulam, Guilia; Berkovic, Garry; Kotler, Zvi; Ben-Asuly, Amos; Mazor, Royi; Shapiro, Lev; Khodorkovsky, Vladimir

    1999-10-01

    The second order nonlinearity of conjugated organic molecules involving, 1,3 indandione derivatives as an acceptor moiety has been studied. Varying the donor from dialkylamino to the chemically similar substituent, N- carbazolyl resulted in a drastic reduction of electric field induced second harmonic (beta) values. For some molecules, even a small negative value of (beta) was received. Quantum chemical calculations indicate that the decrease occurs as a result of two overlapping transitions, which contribute to (beta) with opposite signs. The charge transfer band gives a positive (beta) zzz along the molecular long axis, while a transition essentially within the carbazole moiety provides a negative (beta zzz contribution to (beta EFISH. Thus, these molecules must be described with a 2D model as opposed to the 'classical' model of 1D nonlinear optical chromophores. The prediction of the 2D model was verified experimentally by using a combination of two methods, EFISH and Hyper-Rayleigh Scattering, which probe different combination of the (beta) tensor elements.

  9. The vibrational energy flow transition in organic molecules: Theory meets experiment

    PubMed Central

    Bigwood, R.; Gruebele, M.; Leitner, D. M.; Wolynes, P. G.

    1998-01-01

    Most large dynamical systems are thought to have ergodic dynamics, whereas small systems may not have free interchange of energy between degrees of freedom. This assumption is made in many areas of chemistry and physics, ranging from nuclei to reacting molecules and on to quantum dots. We examine the transition to facile vibrational energy flow in a large set of organic molecules as molecular size is increased. Both analytical and computational results based on local random matrix models describe the transition to unrestricted vibrational energy flow in these molecules. In particular, the models connect the number of states participating in intramolecular energy flow to simple molecular properties such as the molecular size and the distribution of vibrational frequencies. The transition itself is governed by a local anharmonic coupling strength and a local state density. The theoretical results for the transition characteristics compare well with those implied by experimental measurements using IR fluorescence spectroscopy of dilution factors reported by Stewart and McDonald [Stewart, G. M. & McDonald, J. D. (1983) J. Chem. Phys. 78, 3907–3915]. PMID:9600899

  10. Investigating organic molecules responsible of auxin-like activity of humic acid fraction extracted from vermicompost.

    PubMed

    Scaglia, Barbara; Nunes, Ramom Rachide; Rezende, Maria Olímpia Oliveira; Tambone, Fulvia; Adani, Fabrizio

    2016-08-15

    This work studied the auxin-like activity of humic acids (HA) obtained from vermicomposts produced using leather wastes plus cattle dung at different maturation stages (fresh, stable and mature). Bioassays were performed by testing HA concentrations in the range of 100-6000mgcarbonL(-1). (13)C CPMAS-NMR and GC-MS instrumental methods were used to assess the effect of biological processes and starting organic mixtures on HA composition. Not all HAs showed IAA-like activity and in general, IAA-like activity increased with the length of the vermicomposting process. The presence of leather wastes was not necessary to produce the auxin-like activity of HA, since HA extracted from a mix of cattle manure and sawdust, where no leather waste was added, showed IAA-like activity as well. CPMAS (13)CNMR revealed that HAs were similar independently of the mix used and that the humification process involved the increasing concentration of pre-existing alkali soluble fractions in the biomass. GC/MS allowed the identification of the molecules involved in IAA-like effects: carboxylic acids and amino acids. The concentration of active molecules, rather than their simple presence in HA, determined the bio-stimulating effect, and a good linear regression between auxin-like activity and active stimulating molecules concentration was found (R(2)=-0.85; p<0.01, n=6). PMID:27100009

  11. Molecular design of non-linear optical properties and synthesis of organic molecules

    SciTech Connect

    Clark, R.D.; Tan, L.; Martinez, A.; Romero, E.; Ballard, J.; Penn, B.; Moore, C.; Cardelino, B.; Sanghadasa, M.

    1995-06-01

    Non-linear optical properties of organic molecules are of interest because of their possible use in telecommunications and optical computers. Prediction of these properties prior to synthesis is of importance in order to save synthesis time. The second-order polarizabilities of a series of compounds have been predicted based on a finite-field approach using a modified version of the MOPAC program together with the HYPER program developed by Cardelino and Moore. These predictions have then been compared with EFISH measurements made on selected compounds. The EFISH results were adjusted to account for dispersion and solvent effects. As expected, with nitroanilines, the amino group and the aromatic ring of the molecular must be coplanar in order to give a good correlation. The theoretical technique is currently being used to design and identify candidate molecules that should have high second-order polarizability values. Synthesis and measurements of selected candidate molecules are being undertaken; crystal growth and thin film work will follow as appropriate.

  12. Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

    SciTech Connect

    Kroeger, Ingo; Stadtmueller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian

    2011-12-21

    The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.

  13. Efficient Synthesis and Photosensitizer Performance of Nonplanar Organic Donor-Acceptor Molecules.

    PubMed

    Yuan, Yuping; Michinobu, Tsuyoshi; Satoh, Norifusa; Ashizawa, Minoru; Han, Liyuan

    2015-08-01

    Nonplanar organic donor-acceptor molecules bearing a carboxylic acid group were synthesized by the formal [2+2] cycloaddition-retroelectrocyclization reaction between aniline-substituted alkynes and tetracyanoethylene (TCNE) or 7,7,8,8-tetracyanoquinodimethane (TCNQ). This reaction offers an atom-economic one-step approach to donor-acceptor chromophores in satisfactory high yields. The resulting donor-acceptor molecules were characterized by conventional analytical techniques. In addition, the nonplanarity and intermolecular interactions were investigated by X-ray crystallography. The energy levels and intramolecular charge-transfer (CT), evaluated by UV-Vis-near IR spectroscopy and electrochemistry, suggested that there is a linear correlation between the optical and electrochemical band gaps. Based on these structural and electronic analyses, the photosensitizer performances of the donor-acceptor molecules in dye-sensitized solar cells (DSSCs) were initially investigated using TiO2 or SnO2 electrodes. Although the power conversion efficiencies were limited, the incident-photon-to-current-conversion efficiency (IPCE) spectra indicated a better photocurrent generation for the devices on SnO2 as compared to those on TiO2. PMID:26369162

  14. Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips.

    PubMed

    Hapala, Prokop; Temirov, Ruslan; Tautz, F Stefan; Jelínek, Pavel

    2014-11-28

    Recently, the family of high-resolution scanning probe imaging techniques using decorated tips has been complemented by a method based on inelastic electron tunneling spectroscopy (IETS). The new technique resolves the inner structure of organic molecules by mapping the vibrational energy of a single carbon monoxide (CO) molecule positioned at the apex of a scanning tunneling microscope (STM) tip. Here, we explain high-resolution IETS imaging by extending a model developed earlier for STM and atomic force microscopy (AFM) imaging with decorated tips. In particular, we show that the tip decorated with CO acts as a nanoscale sensor that changes the energy of its frustrated translation mode in response to changes of the local curvature of the surface potential. In addition, we show that high resolution AFM, STM, and IETS-STM images can deliver information about the charge distribution within molecules deposited on a surface. To demonstrate this, we extend our mechanical model by taking into account electrostatic forces acting on the decorated tip in the surface Hartree potential. PMID:25494078

  15. Enabling enhanced emission and low-threshold lasing of organic molecules using special Fano resonances of macroscopic photonic crystals

    PubMed Central

    Zhen, Bo; Chua, Song-Liang; Lee, Jeongwon; Rodriguez, Alejandro W.; Liang, Xiangdong; Johnson, Steven G.; Joannopoulos, John D.; Soljačić, Marin; Shapira, Ofer

    2013-01-01

    The nature of light interaction with matter can be dramatically altered in optical cavities, often inducing nonclassical behavior. In solid-state systems, excitons need to be spatially incorporated within nanostructured cavities to achieve such behavior. Although fascinating phenomena have been observed with inorganic nanostructures, the incorporation of organic molecules into the typically inorganic cavity is more challenging. Here, we present a unique optofluidic platform comprising organic molecules in solution suspended on a photonic crystal surface, which supports macroscopic Fano resonances and allows strong and tunable interactions with the molecules anywhere along the surface. We develop a theoretical framework of this system and present a rigorous comparison with experimental measurements, showing dramatic spectral and angular enhancement of emission. We then demonstrate that these enhancement mechanisms enable lasing of only a 100-nm thin layer of diluted solution of organic molecules with substantially reduced threshold intensity, which has important implications for organic light-emitting devices and molecular sensing. PMID:23918363

  16. Focused Role of an Organic Small-Molecule PBD on Performance of the Bistable Resistive Switching.

    PubMed

    Li, Lei; Sun, Yanmei; Ai, Chunpeng; Lu, Junguo; Wen, Dianzhong; Bai, Xuduo

    2015-12-01

    An undoped organic small-molecule 2-(4-tert-butylphenyl)-5-(4-biphenylyl)-1,3,4-oxadiazole (PBD) and a kind of nanocomposite blending poly(methyl methacrylate) (PMMA) into PBD are employed to implement bistable resistive switching. For the bistable resistive switching indium tin oxide (ITO)/PBD/Al, its ON/OFF current ratio can touch 6. What is more, the ON/OFF current ratio, approaching to 10(4), is available due to the storage layer PBD:PMMA with the chemical composition 1:1 in the bistable resistive switching ITO/PBD:PMMA/Al. The capacity, data retention of more than 1 year and endurance performance (>10(4) cycles) of ITO/PBD:PMMA(1:1)/Al, exhibits better stability and reliability of the samples, which underpins the technique and application of organic nonvolatile memory. PMID:26573933

  17. Focused Role of an Organic Small-Molecule PBD on Performance of the Bistable Resistive Switching

    NASA Astrophysics Data System (ADS)

    Li, Lei; Sun, Yanmei; Ai, Chunpeng; Lu, Junguo; Wen, Dianzhong; Bai, Xuduo

    2015-11-01

    An undoped organic small-molecule 2-(4-tert-butylphenyl)-5-(4-biphenylyl)-1,3,4-oxadiazole (PBD) and a kind of nanocomposite blending poly(methyl methacrylate) (PMMA) into PBD are employed to implement bistable resistive switching. For the bistable resistive switching indium tin oxide (ITO)/PBD/Al, its ON/OFF current ratio can touch 6. What is more, the ON/OFF current ratio, approaching to 104, is available due to the storage layer PBD:PMMA with the chemical composition 1:1 in the bistable resistive switching ITO/PBD:PMMA/Al. The capacity, data retention of more than 1 year and endurance performance (>104 cycles) of ITO/PBD:PMMA(1:1)/Al, exhibits better stability and reliability of the samples, which underpins the technique and application of organic nonvolatile memory.

  18. Human Heart Mitochondrial DNA Is Organized in Complex Catenated Networks Containing Abundant Four-way Junctions and Replication Forks*

    PubMed Central

    Pohjoismäki, Jaakko L. O.; Goffart, Steffi; Tyynismaa, Henna; Willcox, Smaranda; Ide, Tomomi; Kang, Dongchon; Suomalainen, Anu; Karhunen, Pekka J.; Griffith, Jack D.; Holt, Ian J.; Jacobs, Howard T.

    2009-01-01

    Analysis of human heart mitochondrial DNA (mtDNA) by electron microscopy and agarose gel electrophoresis revealed a complete absence of the θ-type replication intermediates seen abundantly in mtDNA from all other tissues. Instead only Y- and X-junctional forms were detected after restriction digestion. Uncut heart mtDNA was organized in tangled complexes of up to 20 or more genome equivalents, which could be resolved to genomic monomers, dimers, and linear fragments by treatment with the decatenating enzyme topoisomerase IV plus the cruciform-cutting T7 endonuclease I. Human and mouse brain also contained a population of such mtDNA forms, which were absent, however, from mouse, rabbit, or pig heart. Overexpression in transgenic mice of two proteins involved in mtDNA replication, namely human mitochondrial transcription factor A or the mouse Twinkle DNA helicase, generated abundant four-way junctions in mtDNA of heart, brain, and skeletal muscle. The organization of mtDNA of human heart as well as of mouse and human brain in complex junctional networks replicating via a presumed non-θ mechanism is unprecedented in mammals. PMID:19525233

  19. Stability of metal organic frameworks and interaction of small gas molecules in these materials

    NASA Astrophysics Data System (ADS)

    Tan, Kui

    The work in this dissertation combines spectroscopy ( in-situ infrared absorption and Raman), powder X-ray diffraction and DFT calculations to study the stability of metal organic frameworks materials (MOFs) in the presence of water vapor and other corrosive gases (e.g., SO 2, NO2 NO), and the interaction and competitive co-adsorption of several gases within MOFs by considering two types of prototypical MOFs: 1) a MOF with saturated metal centers based on paddlewheel secondary building units: M(bdc)(ted)0.5 [M=Cu, Zn, Ni, Co, bdc = 1,4-benzenedicarboxylate, ted = triethylenediamine], and 2) a MOF with unsaturated metal centers: M2(dobdc) [M=Mg2+, Zn2+, Ni2+, Co2+ and dobdc = 2,5-dihydroxybenzenedicarboxylate]. We find that the stability of MOFs to water vapor critically depends on their structure and the specific metal cation in the building units. For M(bdc)(ted)0.5, the metal-bdc bond is the most vulnerable for Cu(bdc)(ted)0.5, while the metal-ted bond is first attacked for the Zn and Co analogs. In contrast, Ni(bdc)(ted)0.5 remains stable under the same conditions. For M2(dobdc), or MOF-74, the weak link is the dobdc-metal bond. The water molecule is dissociatively adsorbed at the metal-oxygen group with OH adsorption directly on the metal center and H adsorption on the bridging O of the phenolate group in the dobdc linker. Other technologically important molecules besides water, such as NO, NO2, SO2, tend to poison M2(dobdc) through dissociative or molecular adsorption onto the open metal sites. A high uptake SO2 capacity was measured in M(bdc)(ted)0.5, attributed to multipoint interactions between the guest SO2 molecule and the MOF host. In the case of competitive co-adsorption between CO2 and other small molecules, we find that binding energy alone is not a good indicator of molecular site occupation within the MOF (i.e., it cannot successfully predict and evaluate the displacement of CO2 by other molecules). Instead, we show that the kinetic barrier for the

  20. Fullerene-free small molecule organic solar cells with a high open circuit voltage of 1.15 V.

    PubMed

    Ni, Wang; Li, Miaomiao; Kan, Bin; Liu, Feng; Wan, Xiangjian; Zhang, Qian; Zhang, Hongtao; Russell, Thomas P; Chen, Yongsheng

    2016-01-11

    A new small molecule named DTBTF with thiobarbituric acid as a terminal group was designed and synthesized as an acceptor for organic photovoltaic applications. DTBTF exhibits strong absorption in the visible region, and a relatively high lying LUMO energy level (-3.62 eV). All-small-molecule organic solar cells based on DR3TSBDT:DTBTF blend films show a considerable PCE of 3.84% with a high V(oc) of 1.15 V. PMID:26538446

  1. Describing the Conformational Landscape of Small Organic Molecules through Gaussian Mixtures in Dihedral Space.

    PubMed

    Pisani, Pasquale; Piro, Paolo; Decherchi, Sergio; Bottegoni, Giovanni; Sona, Diego; Murino, Vittorio; Rocchia, Walter; Cavalli, Andrea

    2014-06-10

    Due to the well-known structure-function paradigm, conformational equilibrium plays a major role in molecular recognition. Therefore, a deep understanding of the conformational profile of small organic molecules is an essential prerequisite to modern computer-assisted drug design. However, a thorough analysis and a meaningful representation of the conformational landscape of drug-like molecules remains a challenge. The thermodynamic equilibrium of conformational states can be described in terms of probability density function (PDF) defined in the space of the relevant degrees of freedom of the system. In principle, this PDF could be estimated by traditional histogram methods, which are, however, hampered by several limitations when the variables forming the space are more than two or three. Here, we present an unsupervised parametric fitting procedure based on cluster analysis, aimed at estimating the PDF in the conformational space of small drug-like molecules with low sensitivity to data dimensionality. Indeed, data are represented in the dihedral space of the molecule and clustered using a simple adaptation of the standard k-means algorithm for periodic data. In the final step of the analysis, the PDF is derived as a linear combination of multivariate circular Gaussian distributions. We show that exploiting the analytic properties of Gaussian distributions, the proposed approach makes it possible to analyze the conformational ensemble in higher dimensional spaces with several advantages over the histogram-based methods. The posterior analysis of the PDF also helps identify a minimal subset of variables able to provide a meaningful representation of the conformational space. We tested our approach on alanine dipeptide, alanine tetrapeptide, and rilpivirine with satisfactory results compared to standard histogram-based methods and to those based on chemical intuition. PMID:26580776

  2. First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

    PubMed

    Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

    2015-02-01

    Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications. PMID:25631921

  3. Temperature and composition-dependent density of states in organic small-molecule/polymer blend transistors

    NASA Astrophysics Data System (ADS)

    Hunter, Simon; Mottram, Alexander D.; Anthopoulos, Thomas D.

    2016-07-01

    The density of trap states (DOS) in organic p-type transistors based on the small-molecule 2,8-difluoro-5,11-bis(triethylsilylethynyl) anthradithiophene (diF-TES ADT), the polymer poly(triarylamine) and blends thereof are investigated. The DOS in these devices are measured as a function of semiconductor composition and operating temperature. We show that increasing operating temperature causes a broadening of the DOS below 250 K. Characteristic trap depths of ˜15 meV are measured at 100 K, increasing to between 20 and 50 meV at room-temperature, dependent on the semiconductor composition. Semiconductor films with high concentrations of diF-TES ADT exhibit both a greater density of trap states as well as broader DOS distributions when measured at room-temperature. These results shed light on the underlying charge transport mechanisms in organic blend semiconductors and the apparent freezing-out of hole conduction through the polymer and mixed polymer/small molecule phases at temperatures below 225 K.

  4. Synthesis of oxygen-free Titan tholins: implications in organic molecules product from hydrolysis

    NASA Astrophysics Data System (ADS)

    Brassé, C.; Raulin, F.; Coll, P.; Buch, A.

    2013-09-01

    Titan, the largest moon of Saturn, is known for its dense and nitrogen-rich atmosphere. The organic aerosols which are produced in Titan's atmosphere are objects of astrobiological interest. In this paper we focus on their potential chemical evolution when they reach the surface and interact with putative ammonia-water cryomagma[1]. In this context we have followed the evolution of alkaline pH hydrolysis (25wt% ammonia-water) of Titan tholins (produced by an experimental setup using a plasma DC discharge named PLASMA) at low temperature. Our group identified urea as the main product of tholins hydrolysis along with several amino acids (alanine, glycine and aspartic acid). However, those molecules have also been detected in non-hydrolyzed tholins meaning that oxygen gets in the PLASMA reactor during the tholins synthesis [2]. So the synthesis system has been improved by isolating the whole device in a specially designed glove box which protect the PLASMA experiment from the terrestrial atmosphere. After confirming the non-presence of oxygen in tholins produced with this new experimental setup, we performed alkaline pH hydrolysis of oxygen-free tholins in order to verify that organic molecules cited above are indeed in-situ produced. Those results will be exposed on the poster.

  5. First Detection of Non-Chlorinated Organic Molecules Indigenous to a Martian Sample

    NASA Technical Reports Server (NTRS)

    Freissinet, C.; Glavin, D. P.; Buch, A.; Szopa, C.; Summons, R. E.; Eigenbrode, J. L.; Archer, P. D., Jr.; Brinckerhoff, W. B.; Brunner, A. E.; Cabane, M.; Franz, H. B.; Kashyap, S.; Malespin, C. A.; Martin, M.; Millan, M.; Miller, K.; Navarro-González, R.; Prats, B. D.; Steele, A.; Teinturier, S.; Mahaffy, P. R.

    2016-01-01

    The Sample Analysis at Mars (SAM) instrument onboard Curiosity can perform pyrolysis of martian solid samples, and analyze the volatiles by direct mass spectrometry in evolved gas analysis (EGA) mode, or separate the components in the GCMS mode (coupling the gas chromatograph and the mass spectrometer instruments). In addition, SAM has a wet chemistry laboratory designed for the extraction and identification of complex and refractory organic molecules in the solid samples. The chemical derivatization agent used, N-methyl-N-tert-butyldimethylsilyl- trifluoroacetamide (MTBSTFA), was sealed inside seven Inconel metal cups present in SAM. Although none of these foil-capped derivatization cups have been punctured on Mars for a full wet chemistry experiment, an MTBSTFA leak was detected and the resultant MTBSTFA vapor inside the instrument has been used for a multi-sol MTBSTFA derivatization (MD) procedure instead of direct exposure to MTBSTFA liquid by dropping a solid sample directly into a punctured wet chemistry cup. Pyr-EGA, Pyr-GCMS and Der-GCMS experiments each led to the detection and identification of a variety of organic molecules in diverse formations of Gale Crater.

  6. Anisotropic charge transport in large single crystals of π-conjugated organic molecules.

    PubMed

    Hourani, Wael; Rahimi, Khosrow; Botiz, Ioan; Koch, Felix Peter Vinzenz; Reiter, Günter; Lienerth, Peter; Heiser, Thomas; Bubendorff, Jean-Luc; Simon, Laurent

    2014-05-01

    The electronic properties of organic semiconductors depend strongly on the nature of the molecules, their conjugation and conformation, their mutual distance and the orientation between adjacent molecules. Variations of intramolecular distances and conformation disturb the conjugation and perturb the delocalization of charges. As a result, the mobility considerably decreases compared to that of a covalently well-organized crystal. Here, we present electrical characterization of large single crystals made of the regioregular octamer of 3-hexyl-thiophene (3HT)8 using a conductive-atomic force microscope (C-AFM) in air. We find a large anisotropy in the conduction with charge mobility values depending on the crystallographic orientation of the single crystal. The smaller conduction is in the direction of π-π stacking (along the long axis of the single crystal) with a mobility value in the order of 10(-3) cm(2) V(-1) s(-1), and the larger one is along the molecular axis (in the direction normal to the single crystal surface) with a mobility value in the order of 0.5 cm(2) V(-1) s(-1). The measured current-voltage (I-V) curves showed that along the molecular axis, the current followed an exponential dependence corresponding to an injection mode. In the π-π stacking direction, the current exhibits a space charge limited current (SCLC) behavior, which allows us to estimate the charge carrier mobility. PMID:24658783

  7. The AstroBiology Explorer (ABE) MIDEX Mission Concept: Using Infrared Spectroscopy to Identify Organic Molecules in Space

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; Vincenzi, Donald (Technical Monitor)

    2002-01-01

    One of the principal means by which organic compounds are detected and identified in space is by infrared spectroscopy. Past IR studies (telescopic and laboratory) have demonstrated that much of the carbon in the interstellar medium (ISM) is in complex organic species of a variety of types, but the distribution, abundance, and evolutionary relationships of these materials are not well understood. The Astrobiology Explorer (ABE) is a MIDEAST mission concept designed to conduct IR spectroscopic observations to detect and identify these materials to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. Systematic studies include the observation of planetary nebulae and stellar outflows, protostellar objects, Solar System Objects, and galaxies, and multiple lines of sight through dense molecular clouds and the diffuse ISM. ABE will also search for evidence of D enrichment in complex molecules in all these environments. The mission is currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corp. ABE is a cryogenically-cooled 60 cm diameter space telescope equipped with 3 cryogenic cross-dispersed spectrographs that share a single common slit. The 3 spectrometers each measure single spectral octaves (2.5-5, 5-10, 10-20 microns) and together cover the entire 2.5 - 20 micron region simultaneously. The spectrometers use state-of-the-art 1024x1024 pixel detectors, with a single InSb array for the 2.5-5 micron region and two Si:As arrays for the 5-10 and 10-20 micron regions. The spectral resolution is wavelength dependent but is greater than 2000 across the entire spectral range. ABE would operate in a heliocentric, Earth drift-away orbit and is designed to take maximum advantage of this environment for cooling, thermal stability, and mission lifetime. ABE would have a core science mission lasting approximately 1.5 years.

  8. Abundance and diversity of total and nitrifying prokaryotes as influenced by biochemical quality of organic inputs combined with mineral nitrogen

    NASA Astrophysics Data System (ADS)

    Muema, Esther; Vanlauwe, Bernard; Röhl, Carolin; Cadisch, Georg; Rasche, Frank

    2014-05-01

    Ammonia-oxidizing bacteria and archaea (AOB, AOA) co-exist in soil, but they respond differently to distinct fertilization strategies in agricultural soils. Accordingly, effects of organic inputs and combination with mineral nitrogen (N) on AOB and AOA remain poorly understood. The aim of this study was to compare soil amendment with contrasting quality of organic inputs (i.e., high quality Tithonia diversifolia (TD; C/N ratio: 13, Lignin: 8.9 %; Polyphenols: 1.7 %), intermediate quality Calliandra calothyrsus (CC; 13; 13; 9.4) and low quality Zea mays (ZM; 59; 5.4; 1.2)), and combination with mineral N on the abundance (i.e., DNA-based gene quantification) and community structure (i.e., T-RFLP analysis) of total bacterial and archaea (16S rRNA gene), as well as AOB and AOA (targeting the amoA gene) communities in a Humic Nitisol. Soils (0-15 cm depth) were sampled prior to the onset of the rainy season in March 2012 in a 10 years old field experiment established in the central highlands of Kenya in 2002. Since the start of the experiment, organic inputs were applied annually at a rate of 4 Mg C ha-1 and mineral N twice a year as calcium ammonium nitrate (5Ca(NO3)2NH4NO3) at a rate of 120 kg N ha-1 growing season-1. Quality of organic inputs posed only a significant effect on the AOB community structure between TD versus ZM and CC versus ZM. Moreover, TD significantly increased the size of AOB over ZM input, while higher abundances for total bacteria, total archaea and AOA were measured in ZM and TD over CC. This was explained by high and available N in TD, but low lignin and polyphenol contents in TD and ZM as opposed to CC. AOB responded sensitively (i.e., complete community structure separation) to mineral N, specifically when combined with low quality ZM. Hence, AOB community was specifically responsive to quality of organic inputs and combination of low organic input with mineral N over AOA and total prokaryotic communities in the studied soil. The results

  9. Laboratory insights into the chemical and kinetic evolution of several organic molecules under simulated Mars surface UV radiation conditions

    NASA Astrophysics Data System (ADS)

    Poch, O.; Kaci, S.; Stalport, F.; Szopa, C.; Coll, P.

    2014-11-01

    The search for organic carbon at the surface of Mars, as clues of past habitability or remnants of life, is a major science goal of Mars' exploration. Understanding the chemical evolution of organic molecules under current martian environmental conditions is essential to support the analyses performed in situ. What molecule can be preserved? What is the timescale of organic evolution at the surface? This paper presents the results of laboratory investigations dedicated to monitor the evolution of organic molecules when submitted to simulated Mars surface ultraviolet radiation (190-400 nm), mean temperature (218 ± 2 K) and pressure (6 ± 1 mbar) conditions. Experiments are done with the MOMIE simulation setup (for Mars Organic Molecules Irradiation and Evolution) allowing both a qualitative and quantitative characterization of the evolution the tested molecules undergo (Poch, O. et al. [2013]. Planet. Space Sci. 85, 188-197). The chemical structures of the solid products and the kinetic parameters of the photoreaction (photolysis rate, half-life and quantum efficiency of photodecomposition) are determined for glycine, urea, adenine and chrysene. Mellitic trianhydride is also studied in order to complete a previous study done with mellitic acid (Stalport, F., Coll, P., Szopa, C., Raulin, F. [2009]. Astrobiology 9, 543-549), by studying the evolution of mellitic trianhydride. The results show that solid layers of the studied molecules have half-lives of 10-103 h at the surface of Mars, when exposed directly to martian UV radiation. However, organic layers having aromatic moieties and reactive chemical groups, as adenine and mellitic acid, lead to the formation of photoresistant solid residues, probably of macromolecular nature, which could exhibit a longer photostability. Such solid organic layers are found in micrometeorites or could have been formed endogenously on Mars. Finally, the quantum efficiencies of photodecomposition at wavelengths from 200 to 250 nm

  10. Raman scattering in organic semiconductors based on erbium biphthalocyanine molecules and chlorine-containing europium-lutetium triphthalocyanine molecules

    SciTech Connect

    Belogorokhov, I. A.; Mamichev, D. A.; Dronov, M. A.; Pushkarev, V. E.; Tomilova, L. G.; Khokhlov, D. R.

    2010-08-15

    The Raman spectra of semiconductor structures based on erbium biphthalocyanine molecules and chlorine-substituted europium-lutetium triphthalocyanine molecules are studied on excitation with Ar{sup +} laser radiation at the wavelength 514 nm. The data on the spectral position of Raman intensity peaks related to vibronic states of the basic molecular groups forming the semiconductor are obtained. Raman lines irrelevant to the known vibronic states of the basic phthalocyanine molecular groups are observed in the ranges 100-500 and 500-900 cm{sup -1}. It is shown that, in the spectra of triphthalocyanine, some lines are structurally complex and shifted with respect to the characteristic lines of molecular groups by several inverse centimeters.

  11. Search for organic molecules at the Mars surface: The “Martian Organic Material Irradiation and Evolution” (MOMIE) project

    NASA Astrophysics Data System (ADS)

    Stalport, F.; Coll, P.; Szopa, C.; Raulin, F.

    2008-12-01

    The life on Mars remains an open question because of the lack of proof of its past emergence and its current presence. The only indices of a potential Martian life were provided by the Viking Landers, and the study of the Martian meteorite ALH84001 discovered in the Antarctic. In the two case, the results of experiments could be explained either by the presence of life forms or by abiotic processes. The recent data of Mars Express orbiter and Mars Exploration Rovers show different proofs of a past environment favourable for life. Among the targets we seek, the organic molecules are primordial because they are necessary to the origin of life. A key question is to know if they are present, in which concentration and under which form. Within the framework of a search for organic, we are developing an experimental setup simulating as close as possible the environmental conditions of Mars surface in order to determine how organic species evolve. We present here the first step of the development of this experiment which focuses on the study of the impact of the solar UV radiations reaching the Mars surface on glycine. First results show that glycine does not resist if directly exposed to UV radiations.

  12. Self-Assembling Amphiphilic Molecules: A Possible Relationship Between Interstellar Chemistry and Meteoritic Organics

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; Dworkin, Jason P.; Deamer, David W.; Allamandola, Louis J.; DeVincenzi, Donald (Technical Monitor)

    2001-01-01

    Interstellar gas and dust comprise the primary material from which the solar system formed. Evidence that some of this material was organic in nature and survived incorporation into the protosolar nebula is provided by the presence of deuterium-enriched organics in meteorites and interplanetary dust particles. Once the inner planets had sufficiently cooled, late accretionary infall of meteoroids and cosmic dust must have seeded them with some of these complex organic compounds. Delivery of such extraterrestrial compounds may have contributed to the organic inventory necessary for the origin of life. Interstellar ices, the building blocks of comets, tie up a large fraction of the biogenic elements available in molecular clouds. In our efforts to understand their synthesis, chemical composition, and physical properties, we report here that a complex mixture of molecules is produced by ultraviolet (UV) photolysis of realistic, interstellar ice analogs, and that some of the components have properties relevant to the origin of life, including the ability to self-assemble into vesicular structures.

  13. Inorganics in Organics: Tracking down the Intrinsic Equilibriums between Organic Molecules and Trace Elements in Oceanic Waters

    NASA Astrophysics Data System (ADS)

    Lechtenfeld, O. J.; Koch, B. P.; Kattner, G.

    2010-12-01

    Recent developments in analytical instrumentation enable to describe biogeochemical processes in oceanic waters on a molecular level. This is the prerequisite to integrate biological and geochemical parameters and to develop chemical cycles on a global perspective. The state-of-the-art Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) applications for dissolved organic matter (DOM) focus mainly on carbon, hydrogen, oxygen and nitrogen isotopes. Implementation of sulfur and especially phosphorus in the molecular formula assignment has been questionable because of ambiguous calculated elemental formulas. On the other hand, many compounds bearing these elements are well known to occur in the dissolved state as part of the permanent recycling processes (e.g. phospholipids, phosphonates) but analytics of dissolved organic phosphorus (DOP) and sulfur (DOS) are often hampered by the large inorganic P and S pools. Even less is known about complexation characteristics of the DOM moieties. Although electrochemical methods provide some information about trace metal speciation, the high amount of organic molecules and its insufficient description as chemical functional classes prevent the assignment of trace metals to ligand classes. Nevertheless, it is undoubtful that a varying but extensive amount of transition metals is bond in form of organic complexes. Hyphenation of reversed phase high performance liquid chromatography (RP-HPLC) with high resolution inductively coupled plasma mass spectrometry (HR-ICP-MS) is a valuable tool to study these metal-organic interactions in a qualitative and quantitative approach. We established a desolvation method that allows direct transfer of high organic solvent loads into the plasma. Thus, in combination with internal standardization and external calibration, the investigation of a broad polarity scale was possible. This approach overcomes previous restrictions to non-organic solvent separation techniques like size

  14. Abundance and Characterization of Dissolved Organic Carbon in Suburban Streams of Baltimore, Maryland, USA

    NASA Astrophysics Data System (ADS)

    Mora, G.; Fazekas, M.

    2014-12-01

    The contribution of streams and rivers to the carbon cycle is significant, transporting to the oceans ~1.4 Pg C/yr, with dissolved carbon corresponding to as much as 0.7 Pg C/yr. Changes in land use have the potential effect of modifying this flux, particularly in urban areas where impervious areas are common. To investigate the effect of urbanization on riverine carbon transport, we studied four first-order streams in Towson, a suburb of Baltimore, Maryland, USA. The watersheds from the studied streams exhibit different levels of urbanization as measured by the percentage of impervious areas. Samples from these four streams were taken weekly, and several chemical constituents were measured either in the field or in the laboratory. These constituents included nitrate, dissolved organic nitrogen, pH, dissolved organic carbon (DOC), total carbon, dissolved inorganic carbon (DIC), phosphate, the carbon isotopic compositions of DOC and DIC, and fluorescence intensity of the DOC. Results show that DOC concentrations were consistently below 5 mg C/L regardless of the level of imperviousness of the watershed. Similarly, carbon isotope ratios were consistent across the studied streams, with values centered around -26.4 per mil, thus suggesting a significant influx of soil-derived organic carbon originated from C3 plants that are common in the watersheds. Confirming this interpretation, fluorescence spectroscopy data suggest a humic-like origin for the DOC of the streams, thus pointing to the heterotrophic nature of the streams. The combined results suggest that the studied streams exhibit similar DOC concentrations, carbon isotopic values, and fluorescence spectra, despite their level of impervious surfaces in their watersheds.

  15. Abundance of organic compounds photochemically produced in the atmospheres of the Outer Planets

    NASA Technical Reports Server (NTRS)

    Raulin, F.; Bossard, A.; Toupance, G.; Ponnamperuma, C.

    1979-01-01

    Organic photochemical syntheses in the Jovian atmosphere was simulated by irradiating, at 147 nm, gaseous mixtures of methane and ammonia with varying amounts of hydrogen. Some results relevant to the photochemistry of the Jupiter atmosphere at several tens of kilometers above the clouds were obtained: (1) a favorable effect of the pressure of high amounts of H2 on the yield of hydrocarbon synthesis when NH3 is mixed with CH4; (2) a very low yield of synthesis of unsaturated hydrocarbons in such conditions; and (3) the possibility of formation of detectable amounts of HCN and CH3CN.

  16. Evaluation of thermodynamic and photophysical properties of tricarbocyanine near-IR dyes in organized media using single-molecule monitoring

    NASA Astrophysics Data System (ADS)

    Soper, Steven A.; Legendre, Benjamin L., Jr.; Huang, Jiping

    1995-05-01

    Detection of single NIR fluorescent dye molecules in the organized media sodium dodecyl sulfate (SDS) and triton X-100 surfactnts above their critical micelle concentrations was used to determine partition coefficients and photophysical properties of dye molecules resident within the micelle aggregate. Inspection of the filtered data showed evidence of large amplitude photon bursts arising from single molecular events in these organized media. In pure H 2O containing dye, no bursts were observed. The results indicate that only molecules resident within the hydrophobic core of the micelle were detected. From the number of events observed and the number of events expected, partition coefficients ( Kp) for IR-132 in SDS and triton X-100 solutions were calculated. In addition, the photon yield per molecule associated with only those molecules resident within the hydrophobic cavity of the micelle was determined.

  17. Structural Design Principle of Small-Molecule Organic Semiconductors for Metal-Free, Visible-Light-Promoted Photocatalysis.

    PubMed

    Wang, Lei; Huang, Wei; Li, Run; Gehrig, Dominik; Blom, Paul W M; Landfester, Katharina; Zhang, Kai A I

    2016-08-01

    Herein, we report on the structural design principle of small-molecule organic semiconductors as metal-free, pure organic and visible light-active photocatalysts. Two series of electron-donor and acceptor-type organic semiconductor molecules were synthesized to meet crucial requirements, such as 1) absorption range in the visible region, 2) sufficient photoredox potential, and 3) long lifetime of photogenerated excitons. The photocatalytic activity was demonstrated in the intermolecular C-H functionalization of electron-rich heteroaromates with malonate derivatives. A mechanistic study of the light-induced electron transport between the organic photocatalyst, substrate, and the sacrificial agent are described. With their tunable absorption range and defined energy-band structure, the small-molecule organic semiconductors could offer a new class of metal-free and visible light-active photocatalysts for chemical reactions. PMID:27378555

  18. Extraction of Organic Molecules from Terrestrial Material: Quantitative Yields from Heat and Water Extractions

    NASA Technical Reports Server (NTRS)

    Beegle, L. W.; Abbey, W. A.; Tsapin, A. T.; Dragoi, D.; Kanik, I.

    2004-01-01

    best terrestrial analogs of Mars and they represent one of the absolute best case scenarios for finding organic molecules on the Martian surface.

  19. Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 2: 2D NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Deshmukh, Ashish P.; Pacheco, Carlos; Hay, Michael B.; Myneni, Satish C. B.

    2007-07-01

    Carboxyl groups are abundant in natural organic molecules (NOM) and play a major role in their reactivity. The structural environments of carboxyl groups in IHSS soil and river humic samples were investigated using 2D NMR (heteronuclear and homonuclear correlation) spectroscopy. Based on the 1H- 13C heteronuclear multiple-bond correlation (HMBC) spectroscopy results, the carboxyl environments in NOM were categorized as Type I (unsubstituted and alkyl-substituted aliphatic/alicyclic), Type II (functionalized carbon substituted), Type IIIa, b (heteroatom and olefin substituted), and Type IVa, b (5-membered heterocyclic aromatic and 6-membered aromatic). The most intense signal in the HMBC spectra comes from the Type I carboxyl groups, including the 2JCH and 3JCH couplings of unsubstituted aliphatic and alicyclic acids, though this spectral region also includes the 3JCH couplings of Type II and III structures. Type II and III carboxyls have small but detectable 2JCH correlations in all NOM samples except for the Suwannee River humic acid. Signals from carboxyls bonded to 5-membered aromatic heterocyclic fragments (Type IVa) are observed in the soil HA and Suwannee River FA, while correlations to 6-membered aromatics (Type IVb) are only observed in Suwannee River HA. In general, aromatic carboxylic acids may be present at concentrations lower than previously imagined in these samples. Vibrational spectroscopy results for these NOM samples, described in an accompanying paper [Hay M. B. and Myneni S. C. B. (2007) Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy. Geochim. Cosmochim. Acta (in press)], suggest that Type II and Type III carboxylic acids with α substituents (e.g., -OH, -OR, or -CO 2H) constitute the majority of carboxyl structures in all humic substances examined. Furoic and salicylic acid structures (Type IV) are also feasible fragments, albeit as minor constituents. The

  20. Metal-organic and supramolecular architectures based on mechanically interlocked molecules

    NASA Astrophysics Data System (ADS)

    Fernando, Isurika Rosini

    The focus of this work is on mechanically interlocked molecules (MIMs), which have unusual physicochemical and mechanical properties with potential applications in nano-scale/molecular devices and high strength materials. Rotaxanes, for example, consist of an axle-like molecule threaded through a wheel-like molecule, with bulky groups at the two ends of the axle preventing the wheel from dissociating. The position of the wheel along the axle can be switched in a controllable and reversible manner by applying external stimuli, a feature that might lead to the next generation of computers. Molecularly woven materials (MWMs), another example of molecules with mechanically interlocked features, are predicted to be unprecedentedly strong while being lightweight and flexible. With the ultimate goal of achieving control over the functioning of molecular devices in the solid state, a variety of pseudorotaxane building blocks were prepared and characterized, including a novel, rare blue-colored motif. The temperature-dependent assembly/disassembly of pseudorotaxanes was exploited for the construction of single-wavelength colorimetric temperature sensors over a 100 °C window. Pseudorotaxanes based on aromatic crown ether wheels and disubstituted 4,4'-bipyridinium axles were converted into rotaxanes upon binding to metal complexes (zinc, cadmium, mercury, copper, cobalt), and the formation of ordered crystalline arrays was studied in the solid state. The columnar organization of pseudorotaxanes by Hg2X6 2-- complexes (X = Cl, Br, I), leading to unprecedented dichroic (blue/red) rotaxane crystals, was demonstrated for the first time. From the crystal structures studied it became apparent that negatively charged metal complexes are needed for successful assembly with the positively charged pseudorotaxane units. To be able to use the more common, positively charged metal ions for rotaxane framework construction, neutral and negatively charged pseudorotaxanes were synthesized

  1. EVAPORATION: a new vapor pressure estimation method for organic molecules including non-additivity and intramolecular interactions

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Ceulemans, K.; Müller, J.-F.

    2011-04-01

    We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict vapour pressure p0 of organic molecules needing only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: carbonyls, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

  2. Determination of Natural 14C Abundances in Dissolved Organic Carbon in Organic-Rich Marine Sediment Porewaters by Thermal Sulfate Reduction

    NASA Astrophysics Data System (ADS)

    Johnson, L.; Komada, T.

    2010-12-01

    The abundances of natural 14C in dissolved organic carbon (DOC) in the marine environment hold clues regarding the processes that influence the biogeochemical cycling of this large carbon reservoir. At present, UV irradiation is the widely accepted method for oxidizing seawater DOC for determination of their 14C abundances. This technique yields precise and accurate values with low blanks, but it requires a dedicated vacuum line, and hence can be difficult to implement. As an alternative technique that can be conducted on a standard preparatory vacuum line, we modified and tested a thermal sulfate reduction method that was previously developed to determine δ13C values of marine DOC (Fry B. et al., 1996. Analysis of marine DOC using a dry combustion method. Mar. Chem., 54: 191-201.) to determine the 14C abundances of DOC in marine sediment porewaters. In this method, the sample is dried in a 100 ml round-bottom Pyrex flask in the presence of excess oxidant (K2SO4) and acid (H3PO4), and combusted at 550 deg.C. The combustion products are cryogenically processed to collect and quantify CO2 using standard procedures. Materials we have oxidized to date range from 6-24 ml in volume, and 95-1500 μgC in size. The oxidation efficiency of this method was tested by processing known amounts of reagent-grade dextrose and sucrose (as examples of labile organic matter), tannic acid and humic acid (as examples of complex natural organic matter), and porewater DOC extracted from organic-rich nearshore sediments. The carbon yields for all of these materials averaged 99±4% (n=18). The 14C abundances of standard materials IAEA C-6 and IAEA C-5 processed by this method using >1mgC aliquots were within error of certified values. The size and the isotopic value of the blank were determined by a standard dilution technique using IAEA C-6 and IAEA C-5 that ranged in size from 150 to 1500 μgC (n=4 and 2, respectively). This yielded a blank size of 6.7±0.7 μgC, and a blank isotopic

  3. Effect of flagellates on free-living bacterial abundance in an organically contaminated aquifer

    USGS Publications Warehouse

    Kinner, N.E.; Harvey, R.W.; Kazmierkiewicz-Tabaka, M.

    1997-01-01

    Little is known about the role of protists in the saturated subsurface. Porous media microcosms containing bacteria and protists, were used to determine whether flagellates from an organically contaminated aquifer could substantively affect the number of free- living bacteria (FLB). When flagellates were present, the 3-40% maximum breakthrough of fluorescent y labelled FLB injected into the microcosms was much lower than the 60-130% observed for killed controls Grazing and clearance rates (3-27 FLB flag-1 h-1 and 12-23 nI flag-1 h-1, respectively) calculated from the data were in the range reported for flagellates in other aqueous environments. The data provide evidence that flagellate bacterivory is an important control on groundwater FLB populations.

  4. Assessment of Hybrid Organic-Inorganic Antimony Sulfides for Earth-Abundant Photovoltaic Applications.

    PubMed

    Yang, Ruo Xi; Butler, Keith T; Walsh, Aron

    2015-12-17

    Hybrid organic-inorganic solar absorbers are currently the subject of intense interest; however, the highest-performing materials contain Pb. Here we assess the potential of three Sb-based semiconductors: (i) Sb2S3, (ii) Cs2Sb8S13, and (iii) (CH3NH3)2Sb8S13. While the crystal structure of Sb2S3 is composed of 1D chains, 2D layers are formed in the ternary cesium and hybrid methylammonium antimony sulfide compounds. In each case, a stereochemically active Sb 5s(2) lone pair is found, resulting in a distorted coordination environment for the Sb cations. The bandgap of the binary sulfide is found to increase, while the ionization potential also changes, upon transition to the more complex compounds. Based on the predicted electronic structure, device configurations are suggested to be suitable for photovoltaic applications. PMID:26624204

  5. Rock samples analysis with the pyrolysis system of the Mars Organic Molecule Analyzer (MOMA)

    NASA Astrophysics Data System (ADS)

    Steininger, H.; Goetz, W.; Goesmann, F.

    2012-12-01

    The Mars Organic Molecule Analyzer (MOMA) is a combined pyrolysis gas chromatograph mass spectrometer (GC-MS) and laser desorption mass spectrometer (LD-MS). It will be the key instrument of the ESA/Roscosmos ExoMars 2018 mission to search for extinct and extant life. Additionally the instrument will be able to detect the organic background which has possibly been delivered to Mars by meteorites. Several samples containing a wide range of organic molecules have been tested with a flight analog injection system. The results of the tests were compared to results obtained by a commercial pyrolysis system, the Pyrola pyrolysis unit. The first experimental setup (Pyrola unit) consists of a small quartz tube with an electrically heated platinum filament. A constant helium flow transports the volatilized compounds through an injection needle directly into the injector of the GC. The whole system is heated to 175°C. The second experimental setup (flight analog injection system) consists of a 6 mm diameter platinum oven connected to a microvalve plate to route the gas from the oven to the GC. The microvalves can be switched electrically. The volatiles are subsequently trapped in a cold trap consisting of a Tenax filed tube. Heating this tube releases the volatiles and injects them through an injection needle into the GC. A Varian 4000 GC-MS with RTX-5 column was used to separate and analyze the volatiles generated from both experimental setups. During the experiments several natural rock samples with a broad content of organic material have been analyzed. The sample material was crushed and ground. To obtain comparable results the same amount of sample was used in both setups. Lower temperatures were used in the flight analog injection system due to restrictions of the reusable oven. Lower temperatures normally lead to only a slight decrease in the very heavy and non-volatile compounds but do not change the overall appearance of the chromatogram. Significant differences in

  6. Organic molecules in the polar ice: from chemical analysis to environmental proxies

    NASA Astrophysics Data System (ADS)

    Barbante, Carlo; Zennaro, Piero; Giorio, Chiara; Kehrwald, Natalie; Benton, Alisa K.; Wolff, Eric W.; Kalberer, Markus; Kirchgeorg, Torben; Zangrando, Roberta; Barbaro, Elena; Gambaro, Andrea

    2015-04-01

    The molecular and isotopic compositions of organic matter buried in ice contains information that helps reconstruct past environmental conditions, evaluate histories of climate change, and assess impacts of humans on ecosystems. In recent years novel analytical techniques were developed to quantify molecular compounds in ice cores. As an example, biomass burning markers, including monosaccharide anhydrides, lightweight carboxylic acids, lignin and resin pyrolysis products, black carbon, and charcoal records help in reconstructing past fire activity across seasonal to millennial time scales. Terrestrial biomarkers, such as plant waxes (e.g. long-chain n-alkanes) are also a promising paleo vegetation proxy in ice core studies. Polycyclic aromatic hydrocarbons are ubiquitous pollutants recently detected in ice cores. These hydrocarbons primarily originate from incomplete combustion of organic matter and fossil fuels (e.g. diesel engines, domestic heating, industrial combustion) and therefore can be tracers of past combustion activities. In order to be suitable for paloeclimate purposes, organic molecular markers detected in ice cores should include the following important features. Markers have to be stable under oxidizing atmospheric conditions, and ideally should not react with hydroxyl radicals, during their transport to polar regions. Organic markers must be released in large amounts in order to be detected at remote distances from the sources. Proxies must be specific, in order to differentiate them from other markers with multiple sources. The extraction of glaciochemical information from ice cores is challenging due to the low concentrations of some impurities, thereby demanding rigorous control of external contamination sources and sensitive analytical techniques. Here, we review the analysis and use of organic molecules in ice as proxies of important environmental and climatic processes.

  7. Proton Donor/acceptor Propensities of Ammonia: Rotational Studies of its Molecular Complexes with Organic Molecules

    NASA Astrophysics Data System (ADS)

    Giuliano, Barbara M.; Maris, Assimo; Melandri, Sonia; Favero, Laura B.; Evangelisti, Luca; Caminati, Walther

    2009-06-01

    We studied the rotational spectra of the adducts of ammonia with several organic molecules, namely tert-butanol, glycidol, ethyl alcohol, anisol and 1,4-difluorobenzene. The adducts with glycidol and ethanol have been observed for both conformers of the substrate molecule. Based on the rotational and ^{14}N quadrupole coupling constants of the various complexes, we found a considerably different behaviour of ammonia, with respect to water, in its proton donor/acceptor double role. In the interaction with the three alcohol molecules, NH_{3} acts as a proton acceptor and the OH groups as a proton donor. However, in the case of glycidol-NH_{3}, a secundary N-H\\cdotsO interaction occurrs between ammonia and the ether oxygen. This interaction generates a sizable V_{3} barrier to the internal rotation of the NH_{3} moiety, while NH_{3} undergoes a free rotation in tert-butanol-NH_{3} and in ethanol-NH_{3}. As to the anisole-NH_{3} and 1,4-difluorobenzene-NH_{3} complexes, the NH_{3} group explicits its double proton donor/acceptor role, although through two weak (C_{Me}-H\\cdotsN and N-H\\cdotsπ) H-bonds. There is, however, an important difference between the two complexes, because in the first one NH_{3} lies out of the aromatic plane, while in the second one it is in the plane of the aromatic ring. B. M. Giuliano, M. C. Castrovilli, A. Maris, S. Melandri, W. Caminati and E. A. Cohen, Chem.Phys.Lett., 2008, 463, 330 B. M. Giuliano, S. Melandri, A. Maris, L. B. Favero and W. Caminati, Angew.Chem.Int.Ed., 2009, 48, 1102

  8. Near-Infrared Spectroscopy of Simple Organic Molecules in the GV Tau N Protoplanetary Disk

    NASA Astrophysics Data System (ADS)

    Gibb, Erika

    2014-06-01

    T Tauri stars are low mass young stars that may serve as analogs to the early solar system. Observations of organic molecules in the protoplanetary disks surrounding T Tauri stars are important for characterizing the chemical and physical processes that lead to planet formation. We used NIRSPEC on Keck 2 to perform a high resolution (λ/Δλ ˜ 25,000) L-band survey of T Tauri star GV Tau N, a nearly edge-on young star in the L1524 molecular cloud. The nearly edge-on orientation is rare but necessary to sample the disk in absorption, rather than the more common emission line measurements. GV Tau N is one of only two sources for which HCN and C_2H_2 have been reported in absorption (Gibb et al. 2007; Doppmann et al. 2008). More recently, we reported the first detection of methane, CH_4 (Gibb & Horne 2013). The rotational temperatures are relatively high, implying that HCN, C_2H_2, CH_4, and water originate in the warm molecular layer of the inner protoplanetary disk. Differences in rotational temperature for different molecules suggest that the absorbing column for each molecule samples a different radial distribution. Doppmann, G. W., Najita, K. R., & Carr, J. S. 2008, ApJ, 685, 298 Gibb, E. L., Van Brunt, K. A., Brittain, S. D., & Rettig, T. W. 2007, ApJ, 660, 1572 Gibb, E. L., Horne, D. 2013, ApJ, 776, L28 E.L.G. was supported by NSF Astronomy grant AST-0908230 and NASA Exobiology grant NNX07AK38G.

  9. Cooperative Chemisorption-Induced Physisorption of CO2 Molecules by Metal-Organic Chains.

    PubMed

    Feng, Min; Petek, Hrvoje; Shi, Yongliang; Sun, Hao; Zhao, Jin; Calaza, Florencia; Sterrer, Martin; Freund, Hans-Joachim

    2015-12-22

    Effective CO2 capture and reduction can be achieved through a molecular scale understanding of interaction of CO2 molecules with chemically active sites and the cooperative effects they induce in functional materials. Self-assembled arrays of parallel chains composed of Au adatoms connected by 1,4-phenylene diisocyanide (PDI) linkers decorating Au surfaces exhibit self-catalyzed CO2 capture leading to large scale surface restructuring at 77 K (ACS Nano 2014, 8, 8644-8652). We explore the cooperative interactions among CO2 molecules, Au-PDI chains and Au substrates that are responsible for the self-catalyzed capture by low temperature scanning tunneling microscopy (LT-STM), X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), temperature-programmed desorption (TPD), and dispersion corrected density functional theory (DFT). Decorating Au surfaces with Au-PDI chains gives the interfacial metal-organic polymer characteristics of both a homogeneous and heterogeneous catalyst. Au-PDI chains activate the normally inert Au surfaces by promoting CO2 chemisorption at the Au adatom sites even at <20 K. The CO2(δ-) species coordinating Au adatoms in-turn seed physisorption of CO2 molecules in highly ordered two-dimensional (2D) clusters, which grow with increasing dose to a full monolayer and, surprisingly, can be imaged with molecular resolution on Au crystal terraces. The dispersion interactions with the substrate force the monolayer to assume a rhombic structure similar to a high-pressure CO2 crystalline solid rather than the cubic dry ice phase. The Au surface supported Au-PDI chains provide a platform for investigating the physical and chemical interactions involved in CO2 capture and reduction. PMID:26548479

  10. Coupling between diffusion and orientation of pentacene molecules on an organic surface.

    PubMed

    Rotter, Paul; Lechner, Barbara A J; Morherr, Antonia; Chisnall, David M; Ward, David J; Jardine, Andrew P; Ellis, John; Allison, William; Eckhardt, Bruno; Witte, Gregor

    2016-04-01

    The realization of efficient organic electronic devices requires the controlled preparation of molecular thin films and heterostructures. As top-down structuring methods such as lithography cannot be applied to van der Waals bound materials, surface diffusion becomes a structure-determining factor that requires microscopic understanding. Scanning probe techniques provide atomic resolution, but are limited to observations of slow movements, and therefore constrained to low temperatures. In contrast, the helium-3 spin-echo (HeSE) technique achieves spatial and time resolution on the nm and ps scale, respectively, thus enabling measurements at elevated temperatures. Here we use HeSE to unveil the intricate motion of pentacene admolecules diffusing on a chemisorbed monolayer of pentacene on Cu(110) that serves as a stable, well-ordered organic model surface. We find that pentacene moves along rails parallel and perpendicular to the surface molecules. The experimental data are explained by admolecule rotation that enables a switching between diffusion directions, which extends our molecular level understanding of diffusion in complex organic systems. PMID:26901514

  11. Trap states in ZnPc:C60 small-molecule organic solar cells

    NASA Astrophysics Data System (ADS)

    Burtone, Lorenzo; Fischer, Janine; Leo, Karl; Riede, Moritz

    2013-01-01

    Trap states are known to be one of the key parameters limiting charge transport in organic semiconductors and hence the performance of organic solar cells. Here, small-molecule organic solar cells based on a bulk heterojunction between zinc-phtalocyanine (ZnPc) and the fullerene C60 are characterized according to their trapping nature by noninvasive methods and under ambient conditions. We show how impedance spectroscopy, applied to systematically varied device structures, reveals the trap localization as well as its occupation mechanisms. Further insight is given from investigations of different device working points and illumination intensities. Thus, we find the traps to be bulk states in the active layer with an electron-trapping nature. They can be described by a Gaussian energy distribution of 55 meV width, centered at 0.46 eV below the electron transport level and with a concentration of 3.5 × 1016 cm-3. Moreover, the trap states act as recombination centers in the presence of injected or photogenerated charge carriers. The results are confirmed by electrical simulations.

  12. Modifying the thermal conductivity of small molecule organic semiconductor thin films with metal nanoparticles

    PubMed Central

    Wang, Xinyu; Parrish, Kevin D.; Malen, Jonathan A.; Chan, Paddy K. L.

    2015-01-01

    Thermal properties of organic semiconductors play a significant role in the performance and lifetime of organic electronic devices, especially for scaled-up large area applications. Here we employ silver nanoparticles (Ag NPs) to modify the thermal conductivity of the small molecule organic semiconductor, dinaphtho[2,3-b:2’,3’-f]thieno[3,2-b]thiophene (DNTT). The differential 3-ω method was used to measure the thermal conductivity of Ag-DNTT hybrid thin films. We find that the thermal conductivity of pure DNTT thin films do not vary with the deposition temperature over a range spanning 24 °C to 80 °C. The thermal conductivity of the Ag-DNTT hybrid thin film initially decreases and then increases when the Ag volume fraction increases from 0% to 32%. By applying the effective medium approximation to fit the experimental results of thermal conductivity, the extracted thermal boundary resistance of the Ag-DNTT interface is 1.14 ± 0.98 × 10−7 m2-K/W. Finite element simulations of thermal conductivity for realistic film morphologies show good agreement with experimental results and effective medium approximations. PMID:26531766

  13. Formaldehyde and organic molecule production in astrophysical ices at cryogenic temperatures

    NASA Technical Reports Server (NTRS)

    Schutte, W. A.; Allamandola, L. J.; Sandford, S. A.

    1993-01-01

    Thermally promoted formaldehyde (H2CO) reactions in cryogenic ices have been studied to test their importance as a source of organic molecules in comets and interstellar ices. Ices containing H2CO, H2O, CH3OH, CO, and NH3 were investigated by using infrared spectroscopy. Small traces of NH3 (NH3/H2CO equal to or greater than 0.005) are sufficient to convert significant fractions (40 percent or greater) of the H2CO into more complex organics. However, H2CO reactions do not proceed without NH3. Spectral evidence for reaction onset appeared between 40 and 80 K, depending on the ice. Five distinct products were formed. These principally consist of polyoxymethylene and related derivatives. Polyoxymethylene itself was not made in significant amounts in cometary analogs. These products differ from those produced by ultraviolet and particle irradiation. The nature and relative amounts of the products depend on the initial composition, making these materials excellent tracers of a comet's history. About 3 percent of the organics in p-Halley's coma could have been produced by thermal H2CO reactions.

  14. Photochemistry of organic molecules in the Solar System : Experiments in Terrestrial orbit and laboratory simulations

    NASA Astrophysics Data System (ADS)

    Cottin, Hervé; Guan, Yuan Yong; Coll, Patrice; Coscia, David; Fray, Nicolas; Macari, Frederique; Raulin, Francois; Stalport, Fabien; Szopa, Cyril; Chaput, Didier; Viso, Michel; Bertrand, Marylene; Chabin, Annie; Thirkell, Laurent; Westall, Frances; Maurel, Marie-Christine; Vergne, Jacques; Brack, André

    Photochemistry is leading the chemical evolution in the Solar System. The VUV photolysis of organic compounds is easy to study in the laboratory, with monochromatic sources, but it is difficult to simulate the whole range of wavelengths corresponding to the most energetic part of the Solar radiation (<190nm). This is why the results obtained in laboratory are difficult to extrapolate to the extraterrestrial environments. Space is the only laboratory allowing the exposure of samples to all the space parameters simultaneously. We present the preparation and follow-up of experiments with exobiological interest, in Terrestrial orbit, (AMINO, PRO- CESS, and UV-olution) organized by the European Space Agency (ESA). The experiments are carried out on a FOTON capsule, using the BIOPAN facility (UVolution Sept.2007), and on the International Space Station, using the EXPOSE facilities on the COLUMBUS European module (PROCESS - beginning Feb 2008) and the Russian module ZARYA (AMINO) (beginning expected by the end of 2008). In this project, organic molecules related to the study of the chemistry of Mars, Titan, meteorites or Comets are exposed in space between 10 days and 18 months (according to the experiment). The evolution of the samples can be studied when the samples are returned to Earth, and compared to the results of ground experiments. Preliminary results of the Uvolution experiment will be presented.

  15. Coupling between diffusion and orientation of pentacene molecules on an organic surface

    NASA Astrophysics Data System (ADS)

    Rotter, Paul; Lechner, Barbara A. J.; Morherr, Antonia; Chisnall, David M.; Ward, David J.; Jardine, Andrew P.; Ellis, John; Allison, William; Eckhardt, Bruno; Witte, Gregor

    2016-04-01

    The realization of efficient organic electronic devices requires the controlled preparation of molecular thin films and heterostructures. As top-down structuring methods such as lithography cannot be applied to van der Waals bound materials, surface diffusion becomes a structure-determining factor that requires microscopic understanding. Scanning probe techniques provide atomic resolution, but are limited to observations of slow movements, and therefore constrained to low temperatures. In contrast, the helium-3 spin-echo (HeSE) technique achieves spatial and time resolution on the nm and ps scale, respectively, thus enabling measurements at elevated temperatures. Here we use HeSE to unveil the intricate motion of pentacene admolecules diffusing on a chemisorbed monolayer of pentacene on Cu(110) that serves as a stable, well-ordered organic model surface. We find that pentacene moves along rails parallel and perpendicular to the surface molecules. The experimental data are explained by admolecule rotation that enables a switching between diffusion directions, which extends our molecular level understanding of diffusion in complex organic systems.

  16. Activation of diatomic and triatomic molecules for the synthesis of organic compounds: Metal catalysis at the subseafloor biosphere

    NASA Astrophysics Data System (ADS)

    Luther, George W., III

    Chemical synthesis of organic molecules from simple diatomic and triatomic molecules is enhanced by transition metal catalysis. The actual forms of the catalysts that were available in prebiotic times to initiate the first formation of simple organic compounds are not known. However, the petroleum industry has made an enormous research effort to make organic materials from small molecules using various transition metal compounds as catalysts, and we can make estimates regarding the functional forms of catalysts. Recent work has speculated on the formation of small organic molecules that are the building blocks for life at hydrothermal vents and the subsurface seafloor, but the kinetics and proposed reaction intermediates as catalysts in these studies are not obvious. Metals, which are the center of these catalysts and which are present in the subseafloor biosphere, are typically in low oxidation states (e.g.; 0, +1) and have a rich chemistry that permits ease of ligand substitution and electron transfer reactions as well as insertion reactions, which are necessary chemical pathways for organic and biochemical synthesis. In addition, the metals overcome some of the poor electron acceptor properties of small molecules (e.g., N2) via these pathways. This paper describes in detail possible kinetic pathways and gives examples of organic chemical syntheses/transformations that are used in abiotic and biotic processes. These reactions are kinetically controlled and the catalysts are regenerated during synthesis.

  17. Higher Molecular Mass Organic Matter Molecules Compete with Orthophosphate for Adsorption to Iron (Oxy)hydroxide.

    PubMed

    Chassé, Alexander W; Ohno, Tsutomu

    2016-07-19

    The competition between orthophosphate and water-extractable organic matter (WEOM) for adsorption to iron (oxy)hydroxide mineral surfaces is an important factor in determining the plant bioavailability of P in soils. Chemical force spectroscopy was used to determine the binding force between orthophosphate and iron (oxy)hydroxide that was coated onto atomic force microscopy (AFM) tips and adsorbed with WEOM. The force measurements were conducted at pH 4.65 and 0.02 M ionic strength which are representative of typical acid soil solutions. The chemical composition of the WEOM was determined by ultrahigh resolution electrospray ionization Fourier transform ion cyclotron mass spectrometry. The results indicate a correlation between aromatic WEOM molecules that are greater than 600 Da and the reduced binding force of orthophosphate to WEOM-adsorbed iron (oxy)hydroxide AFM tips suggesting that the molecular mass of aromatic WEOM molecules plays a critical role in regulating the WEOM-P interactions with surface functional groups of minerals. Based on the results of this study, we show the importance of obtaining a detailed, molecular-scale understanding of soil processes that can help develop better management strategies to reduce waste of limited P resources and adverse environmental impacts. Specifically, soil amendments with greater content of high molecular mass aromatic components may positively affect dissolved P use efficiency in soils by maintaining P in soil solution. PMID:27362894

  18. A modular molecular framework for utility in small-molecule solution-processed organic photovoltaic devices

    SciTech Connect

    Welch, Gregory C.; Perez, Louis A.; Hoven, Corey V.; Zhang, Yuan; Dang, Xuan-Dung; Sharenko, Alexander; Toney, Michael F.; Kramer, Edward J.; Nguyen, Thuc-Quyen; Bazan, Guillermo C.

    2011-07-22

    We report on the design, synthesis and characterization of light harvesting small molecules for use in solution-processed small molecule bulk heterojunction (SM-BHJ) solar cell devices. These molecular materials are based upon an acceptor/donor/acceptor (A/D/A) core with donor endcapping units. Utilization of a dithieno(3,2-b;2',3'-d)silole (DTS) donor and pyridal[2,1,3]thiadiazole (PT) acceptor leads to strong charge transfer characteristics, resulting in broad optical absorption spectra extending well beyond 700 nm. SM-BHJ solar cell devices fabricated with the specific example 5,5'-bis{7-(4-(5-hexylthiophen-2-yl)thiophen-2-yl)-[1,2,5]thiadiazolo[3,4-c]pyridine}-3,3'-di-2-ethylhexylsilylene-2,2'-bithiophene (6) as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor component showed short circuit currents above -10 mA cm-2 and power conversion efficiencies (PCEs) over 3%. Thermal processing is a critical factor in obtaining favorable active layer morphologies and high PCE values. A combination of UV-visible spectroscopy, conductive and photo-conductive atomic force microscopies, dynamic secondary mass ion spectrometry (DSIMS), and grazing incident wide angle X-ray scattering (GIWAXS) experiments were carried out to characterize how thermal treatment influences the active layer structure and organization.

  19. Sequential photochemical and microbial degradation of organic molecules bound to humic acid

    SciTech Connect

    Amador, J.A.; Zika, R.G. ); Alexander, M. )

    1989-11-01

    We studied the effects of photochemical processes on the mineralization by soil microorganisms of (2-{sup 14}C)glycine bound to soil humic acid. Microbial mineralization of these complexes in the dark increased inversely with the molecular weight of the complex molecules. Sunlight irradiation of glycine-humic acid complexes resulted in loss of absorbance in the UV range and an increase in the amount of {sup 14}C-labeled low-molecular-weight photoproducts and the rate and extent of mineralization. More than half of the radioactivity in the low-molecular-weight photoproducts appears to be associated with carboxylic acids. Microbial mineralization of the organic carbon increased with solar flux and was proportional to the loss of A{sub 330}. Mineralization was proportional to the percentage of the original complex that was converted to low-molecular-weight photoproducts. Only light at wavelengths below 380 nm had an effect on the molecular weight distribution of the products formed from the glycine-humic acid complexes and on the subsequent microbial mineralization. Our results indicate that photochemical processes generate low-molecular-weight, readily biodegradable molecules from high-molecular-weight complexes of glycine with humic acid.

  20. Theoretical study of Contact Effects in Current through an Organic Molecule

    NASA Astrophysics Data System (ADS)

    Nara, Jun; Kino, Hiori; Kobayashi, Nobuhiko; Tsukada, Masaru; Ohno, Takahisa

    2003-03-01

    Recently, the transport properties of single-organic molecules have attracted much attention. In analyzing their transport properties theoretically, it is important to include the realistic atomic configurations of the contact between molecules and metal electrodes. We calculated the conductance of a benzene-(1,4)-dithiolate sandwiched with two gold electrodes by means of ab initio method, and examined the effect of the contact structures on it. It is found that the conductance depends significantly on the bonding site of the S atom on Au(111) surface such that a current through the ontop site is much smaller than that through the hollow site or the bridge site. These results suggest that the contact structure is essential to determine the conductance properties of molecular devices. The present calculations were carried out using the Numerical Materials Simulator in National Institute for Materials Science. This research is partially supported by ACT-JST and Special Coordination Funds of the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government.

  1. Understanding Small-Molecule Interactions in Metal-Organic Frameworks: Coupling Experiment with Theory.

    PubMed

    Lee, Jason S; Vlaisavljevich, Bess; Britt, David K; Brown, Craig M; Haranczyk, Maciej; Neaton, Jeffrey B; Smit, Berend; Long, Jeffrey R; Queen, Wendy L

    2015-10-14

    Metal-organic frameworks (MOFs) have gained much attention as next-generation porous media for various applications, especially gas separation/storage, and catalysis. New MOFs are regularly reported; however, to develop better materials in a timely manner for specific applications, the interactions between guest molecules and the internal surface of the framework must first be understood. A combined experimental and theoretical approach is presented, which proves essential for the elucidation of small-molecule interactions in a model MOF system known as M2 (dobdc) (dobdc(4-) = 2,5-dioxido-1,4-benzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Cu, or Zn), a material whose adsorption properties can be readily tuned via chemical substitution. It is additionally shown that the study of extensive families like this one can provide a platform to test the efficacy and accuracy of developing computational methodologies in slightly varying chemical environments, a task that is necessary for their evolution into viable, robust tools for screening large numbers of materials. PMID:26033176

  2. Impact of an atmospheric argon plasma jet on a dielectric surface and desorption of organic molecules

    NASA Astrophysics Data System (ADS)

    Damany, Xavier; Pasquiers, Stéphane; Blin-Simiand, Nicole; Bauville, Gérard; Bournonville, Blandine; Fleury, Michel; Jeanney, Pascal; Santos Sousa, João

    2016-08-01

    The propagation of a DC-pulsed argon plasma jet through the surrounding ambient air, and its interaction with an ungrounded glass plate placed on the jet trajectory, was studied by means of fast imaging. The surface plays an important role in the spatio-temporal characteristics of the plasma. Indeed, for an argon jet propagating perpendicularly to the surface, the plasma jet structure changes from filamentary to diffuse when the distance between the nozzle of the capillary tube and the surface is short (≤10 mm). Changing the angle between the capillary tube and the glass plate, and varying the gas flow rate strongly affects the spatial extension of the plasma that develops on the surface. This surface plasma propagates while the plasma in the argon jet is maintained with the same luminous intensity. Finally, this plasma jet shows interesting characteristics for desorption of low volatile organic molecules such as bibenzyl. A maximum removal of bibenzyl is located at the intersection area between the jet axis and the glass surface, and some of the initially deposited molecules are found intact in gas phase. Contribution to the topical issue "6th Central European Symposium on Plasma Chemistry (CESPC-6)", edited by Nicolas Gherardi, Ester Marotta and Cristina Paradisi

  3. First-principles Hubbard U approach for small molecule binding in metal-organic frameworks.

    PubMed

    Mann, Gregory W; Lee, Kyuho; Cococcioni, Matteo; Smit, Berend; Neaton, Jeffrey B

    2016-05-01

    We apply first-principles approaches with Hubbard U corrections for calculation of small molecule binding energetics to open-shell transition metal atoms in metal-organic frameworks (MOFs). Using density functional theory with van der Waals dispersion-corrected functionals, we determine Hubbard U values ab initio through an established linear response procedure for M-MOF-74, for a number of different metal centers (M = Ti, V, Cr, Mn, Fe, Co, Ni, and Cu). While our ab initio U values differ from those used in previous work, we show that they result in lattice parameters and electronic contributions to CO2-MOF binding energies that lead to excellent agreement with experiments and previous results, yielding lattice parameters within 3%. In addition, U-dependent calculations for an example system, Co-MOF-74, suggest that the CO2 binding energy grows monotonically with the value of Hubbard U, with the binding energy shifting 4 kJ/mol (or 0.041 eV) over the range of U = 0-5.4 eV. These results provide insight into an approximate but computationally efficient means for calculation of small molecule binding energies to open-shell transition metal atoms in MOFs and suggest that the approach can be predictive with good accuracy, independent of the cations used and the availability of experimental data. PMID:27155622

  4. A flexible metal–organic framework: Guest molecules controlled dynamic gas adsorption

    DOE PAGESBeta

    Mahurin, Shannon Mark; Li, Man -Rong; Wang, Hailong; Lu, Zhengliang; Chen, Banglin; Dai, Sheng; Yue, Yanfeng; Rabone, Jeremy A.; Liu, Hongjun; Wang, Jihang; et al

    2015-04-13

    A flexible metal–organic framework (MOF) of [Zn3(btca)2(OH)2]·(guest)n (H2btca = 1,2,3-benzotriazole-5-carboxylic acid) that exhibits guest molecule-controlled dynamic gas adsorption is reported in which carbon dioxide molecules rather than N2, He, and Ar induce a structural transition with a corresponding appearance of additional steps in the isotherms. Physical insights into the dynamic adsorption behaviors of flexible compound 1 were detected by gas adsorption at different temperatures and different pressures and confirmed by Fourier transform infrared spectroscopy and molecular simulations. Interestingly, by taking advantage of the flexible nature inherent to the framework, this MOF material enables highly selective adsorption of CO2/N2, CO2/Ar, andmore » CO2/He of 36.3, 32.6, and 35.9, respectively, at 298 K. Furthermore, this class of flexible MOFs has potential applications for controlled release, molecular sensing, noble gas separation, smart membranes, and nanotechnological devices.« less

  5. A flexible metal–organic framework: Guest molecules controlled dynamic gas adsorption

    SciTech Connect

    Mahurin, Shannon Mark; Li, Man -Rong; Wang, Hailong; Lu, Zhengliang; Chen, Banglin; Dai, Sheng; Yue, Yanfeng; Rabone, Jeremy A.; Liu, Hongjun; Wang, Jihang; Fang, Youxing

    2015-04-13

    A flexible metal–organic framework (MOF) of [Zn3(btca)2(OH)2]·(guest)n (H2btca = 1,2,3-benzotriazole-5-carboxylic acid) that exhibits guest molecule-controlled dynamic gas adsorption is reported in which carbon dioxide molecules rather than N2, He, and Ar induce a structural transition with a corresponding appearance of additional steps in the isotherms. Physical insights into the dynamic adsorption behaviors of flexible compound 1 were detected by gas adsorption at different temperatures and different pressures and confirmed by Fourier transform infrared spectroscopy and molecular simulations. Interestingly, by taking advantage of the flexible nature inherent to the framework, this MOF material enables highly selective adsorption of CO2/N2, CO2/Ar, and CO2/He of 36.3, 32.6, and 35.9, respectively, at 298 K. Furthermore, this class of flexible MOFs has potential applications for controlled release, molecular sensing, noble gas separation, smart membranes, and nanotechnological devices.

  6. Extended π-conjugated molecules derived from naphthalene diimides toward organic emissive and semiconducting materials.

    PubMed

    Li, Yonghai; Zhang, Guanxin; Yang, Ge; Guo, Yunlong; Di, Chong'an; Chen, Xin; Liu, Zitong; Liu, Huiying; Xu, Zhenzhen; Xu, Wei; Fu, Hongbing; Zhang, Deqing

    2013-04-01

    In this paper, a new synthetic way to modify naphthalene diimide (NDI) at "shoulder" positions is reported. The key step of the transformation is the intramolecular cyclization involving ethynyl and imidecarbonyl groups. The structure of the intermediate pyrylium cation was confirmed by X-ray crystal structural analysis. New conjugated molecules 1a-g were successfully synthesized in acceptable yields. Their absorption and fluorescence spectra were measured. Among them 1c-f are strongly emissive in solutions. Furthermore, 1b-f are also fluorescent in their solid states; in particular, 1b exhibits a typical aggregation-induced enhanced emission feature. Yellow-emissive microfibrils of 1d show potential optical waveguide behavior. HOMO/LUMO energies of 1a-f were determined based on their cyclic voltammograms. The results also reveal that HOMO/LUMO energies of these new conjugated molecules are influenced by the two flanking moieties. Notably, the thin film of 1c that is emissive shows p-type semiconducting behavior with hole mobility up to 0.0063 cm(2) V(-1) s(-1) based on the transfer and output characteristics of the OFET (organic field effect transistor). PMID:23461275

  7. Sequential photochemical and microbial degradation of organic molecules bound to humic Acid.

    PubMed

    Amador, J A; Alexander, M; Zika, R G

    1989-11-01

    We studied the effects of photochemical processes on the mineralization by soil microorganisms of [2-C]glycine bound to soil humic acid. Microbial mineralization of these complexes in the dark increased inversely with the molecular weight of the complex molecules. Sunlight irradiation of glycine-humic acid complexes resulted in loss of absorbance in the UV range and an increase in the amount of C-labeled low-molecular-weight photoproducts and the rate and extent of mineralization. More than half of the radioactivity in the low-molecular-weight photoproducts appears to be associated with carboxylic acids. Microbial mineralization of the organic carbon increased with solar flux and was proportional to the loss of A(330). Mineralization was proportional to the percentage of the original complex that was converted to low-molecular-weight photoproducts. Only light at wavelengths below 380 nm had an effect on the molecular weight distribution of the products formed from the glycine-humic acid complexes and on the subsequent microbial mineralization. Our results indicate that photochemical processes generate low-molecular-weight, readily biodegradable molecules from high-molecular-weight complexes of glycine with humic acid. PMID:16348046

  8. Sequential Photochemical and Microbial Degradation of Organic Molecules Bound to Humic Acid

    PubMed Central

    Amador, José A.; Alexander, Martin; Zika, Rod G.

    1989-01-01

    We studied the effects of photochemical processes on the mineralization by soil microorganisms of [2-14C]glycine bound to soil humic acid. Microbial mineralization of these complexes in the dark increased inversely with the molecular weight of the complex molecules. Sunlight irradiation of glycine-humic acid complexes resulted in loss of absorbance in the UV range and an increase in the amount of 14C-labeled low-molecular-weight photoproducts and the rate and extent of mineralization. More than half of the radioactivity in the low-molecular-weight photoproducts appears to be associated with carboxylic acids. Microbial mineralization of the organic carbon increased with solar flux and was proportional to the loss of A330. Mineralization was proportional to the percentage of the original complex that was converted to low-molecular-weight photoproducts. Only light at wavelengths below 380 nm had an effect on the molecular weight distribution of the products formed from the glycine-humic acid complexes and on the subsequent microbial mineralization. Our results indicate that photochemical processes generate low-molecular-weight, readily biodegradable molecules from high-molecular-weight complexes of glycine with humic acid. PMID:16348046

  9. First-principles Hubbard U approach for small molecule binding in metal-organic frameworks

    NASA Astrophysics Data System (ADS)

    Mann, Gregory W.; Lee, Kyuho; Cococcioni, Matteo; Smit, Berend; Neaton, Jeffrey B.

    2016-05-01

    We apply first-principles approaches with Hubbard U corrections for calculation of small molecule binding energetics to open-shell transition metal atoms in metal-organic frameworks (MOFs). Using density functional theory with van der Waals dispersion-corrected functionals, we determine Hubbard U values ab initio through an established linear response procedure for M-MOF-74, for a number of different metal centers (M = Ti, V, Cr, Mn, Fe, Co, Ni, and Cu). While our ab initio U values differ from those used in previous work, we show that they result in lattice parameters and electronic contributions to CO2-MOF binding energies that lead to excellent agreement with experiments and previous results, yielding lattice parameters within 3%. In addition, U-dependent calculations for an example system, Co-MOF-74, suggest that the CO2 binding energy grows monotonically with the value of Hubbard U, with the binding energy shifting 4 kJ/mol (or 0.041 eV) over the range of U = 0-5.4 eV. These results provide insight into an approximate but computationally efficient means for calculation of small molecule binding energies to open-shell transition metal atoms in MOFs and suggest that the approach can be predictive with good accuracy, independent of the cations used and the availability of experimental data.

  10. Transport properties of simple organic molecules in a transmembrane cyclic peptide nanotube.

    PubMed

    Xu, Jian; Fan, Jian Fen; Zhang, Ming Ming; Weng, Pei Pei; Lin, Hui Fang

    2016-05-01

    Multiple molecular dynamics simulations have been performed to explore the transport properties of single methane, methanol, and ethanol molecules through the water-filled transmembrane cyclic peptide nanotube (CPNT) of 8 × (WL)₄-POPE, as well as the potential application of this CPNT in the separation of an alcohol/water mixture. Molecular size and hydrophilicity/hydrophobicity were found to significantly influence molecular diffusion behavior in the channel. Methane and ethanol display more explicit distributions in midplane regions, while methanol mainly occurs in α-plane zones. Methane and ethanol drift faster near an α-plane zone, whereas methanol diffuses uniformly throughout the whole transmembrane region. The dipole orientation of channel methanol is significantly affected by the bare carbonyl groups at the tube mouths and flips mainly in gap 4, whereas the rotation of ethanol is blocked. Ball-shaped hydrophobic methane experiences more flips in gap 4. The PMF (potential of mean force) profiles of the three organic molecules disclose their different diffusion behaviors in the CPNT. Amphiphilic alcohols are able to form direct H-bonds with channel water and the tube. Both single and double water bridges with the tube were observed in the methanol and ethanol systems. The different adsorption behaviors of the alcohols and water in the dehydrated CPNT may lead to the potential application of the CPNT as a means of separating alcohols from water. PMID:27083567

  11. "Molecules-in-Medicine": Peer-Evaluated Presentations in a Fast-Paced Organic Chemistry Course for Medical Students

    ERIC Educational Resources Information Center

    Kadnikova, Ekaterina N.

    2013-01-01

    To accentuate the importance of organic chemistry in development of contemporary pharmaceuticals, a three-week unit entitled "Molecules-in-Medicine" was included in the curriculum of a comprehensive one-semester four-credit organic chemistry course. After a lecture on medicinal chemistry concepts and pharmaceutical practices, students…

  12. Diels-Alder Trapping of Photochemically Generated o-Xylenols: Application in the Synthesis of Novel Organic Molecules and Polymers

    NASA Technical Reports Server (NTRS)

    Meador, Michael A.

    2003-01-01

    Bis(o-xylenol) equivalents are useful synthetic intermediates in the construction of polymers and hydroxyl substituted organic molecules which can organize by hydrogen bonded self-assembly into unique supramolecular structures. These polymers and supramolecular materials have potential use as coatings and thin films in aerospace, electronic and biomedical applications.

  13. Modeling Stretching Modes of Common Organic Molecules with the Quantum Mechanical Harmonic Oscillator: An Undergraduate Vibrational Spectroscopy Laboratory Exercise

    ERIC Educational Resources Information Center

    Parnis, J. Mark; Thompson, Matthew G. K.

    2004-01-01

    An introductory undergraduate physical organic chemistry exercise that introduces the harmonic oscillator's use in vibrational spectroscopy is developed. The analysis and modeling exercise begins with the students calculating the stretching modes of common organic molecules with the help of the quantum mechanical harmonic oscillator (QMHO) model.

  14. Novel Flourescent Sensors for the Detection of Organic Molecules in Extraterrestrial Samples

    NASA Astrophysics Data System (ADS)

    Adkin, Roy C.; Bruce, James I.; Pearson, Victoria K.

    2015-04-01

    Organic compounds in extraterrestrial samples have mostly been elucidated by destructive analytical techniques therefore information regarding spatial relationships between minerals and organic species is lost. Minerals form under specific chemical and physical conditions so organic compounds associated with these minerals are likely to have formed under the same conditions. It is therefore possible to infer in which cosmological provinces their chemical evolution took place. We will describe progress towards developing fluorescent sensors that may resolve spatial discrimination. Lanthanide elements such as europium and terbium produce well defined line-like, high intensity and long lived fluorescent emissions. Interactions with organic molecules may alter the luminescent emission characteristics. The lanthanide atom needs to be rendered chemically inert but must remain susceptible to these organic molecule interactions. An organic ligand must be employed to attain this. DOTA (1,4,7,10-tetraazacyclododecanetetracetic acid) was chosen as a plausible organic ligand because its structure, a tetra-substituted cyclen ring, and ability to chelate are well characterized. It is also commercially available. Fluorescent lanthanide-DOTA complexes are used in many biological and analytical imaging applications so it is logical to investigate their applicability to fluorimetric analysis of extraterrestrial organics. Lanthanide-DOTA complexes are very stable because the lanthanide metal atom is enveloped within the DOTA structure. Experimental procedures were designed to investigate lanthanide/analyte interactions and their effect upon fluorescent emissions. A range of compounds were chosen giving a good representation of the organics identified in extraterrestrial samples and whether they may to interact with the lanthanide metal ion. An Europium-DOTA baseline fluorescent spectrum was obtained and compared against Europium-DOTA/analyte mixtures of a range of concentrations

  15. Directed self-organization of single DNA molecules in a nanoslit via embedded nanopit arrays

    PubMed Central

    Reisner, Walter; Larsen, Niels B.; Flyvbjerg, Henrik; Tegenfeldt, Jonas O.; Kristensen, Anders

    2009-01-01

    We show that arrays of nanopit structures etched in a nanoslit can control the positioning and conformation of single DNA molecules in nanofluidic devices. By adjusting the spacing, organization and placement of the nanopits it is possible to immobilize DNA at predetermined regions of a device without additional chemical modification and achieve a high degree of control over local DNA conformation. DNA can be extended between two nanopits and in closely spaced arrays will self-assemble into “connect-the-dots” conformations consisting of locally pinned segments joined by fluctuating linkers. These results have broad implications for nanotechnology fields that require methods for the nanoscale positioning and manipulation of DNA. PMID:19122138

  16. Studying the organization of DNA repair by single-cell and single-molecule imaging

    PubMed Central

    Uphoff, Stephan; Kapanidis, Achillefs N.

    2014-01-01

    DNA repair safeguards the genome against a diversity of DNA damaging agents. Although the mechanisms of many repair proteins have been examined separately in vitro, far less is known about the coordinated function of the whole repair machinery in vivo. Furthermore, single-cell studies indicate that DNA damage responses generate substantial variation in repair activities across cells. This review focuses on fluorescence imaging methods that offer a quantitative description of DNA repair in single cells by measuring protein concentrations, diffusion characteristics, localizations, interactions, and enzymatic rates. Emerging single-molecule and super-resolution microscopy methods now permit direct visualization of individual proteins and DNA repair events in vivo. We expect much can be learned about the organization of DNA repair by linking cell heterogeneity to mechanistic observations at the molecular level. PMID:24629485

  17. Gold nanoparticles for the colorimetric and fluorescent detection of ions and small organic molecules

    NASA Astrophysics Data System (ADS)

    Liu, Dingbin; Wang, Zhuo; Jiang, Xingyu

    2011-04-01

    In recent years, gold nanoparticles (AuNPs) have drawn considerable research attention in the fields of catalysis, drug delivery, imaging, diagnostics, therapy and biosensors due to their unique optical and electronic properties. In this review, we summarized recent advances in the development of AuNP-based colorimetric and fluorescent assays for ions including cations (such as Hg2+, Cu2+, Pb2+, As3+, Ca2+, Al3+, etc) and anions (such as NO2-, CN-, PF6-, F-, I-, oxoanions), and small organic molecules (such as cysteine, homocysteine, trinitrotoluene, melamine and cocaine, ATP, glucose, dopamine and so forth). Many of these species adversely affect human health and the environment. Moreover, we paid particular attention to AuNP-based colorimetric and fluorescent assays in practical applications.

  18. Facile Preparation of Bright-Fluorescent Soft Materials from Small Organic Molecules.

    PubMed

    Wang, Hang-Xing; Yang, Ze; Liu, Zhong-Guo; Wan, Jia-Yun; Xiao, Juan; Zhang, Hao-Li

    2016-06-01

    Highly fluorescent and biocompatible soft materials are desirable for many potential applications, but their synthetic processes are somehow complicated. Herein, we have explored the feasibility of synthesis of unconventional fluorescence soft materials from small organic molecules under mild conditions. A new blue-fluorescent soft material with high quantum yield (89.6 %) and eutectic feature prepared by simple heat treatment of citric acid (CA) and cysteine (Cys) aqueous mixtures below 100 °C in air was reported. The as-prepared fluorescent material has the features of facile preparation, low cost, scalable production and easy to process, making it suitable for applications like fluorescent labeling and light-emitting devices. This new finding opens a new venue for the preparation of fluorescent soft materials. PMID:27194639

  19. Organics and other molecules in the surfaces of Callisto and Ganymede

    USGS Publications Warehouse

    McCord, T.B.; Carlson, R.W.; Smythe, W.D.; Hansen, G.B.; Clark, R.N.; Hibbitts, C.A.; Fanale, F.P.; Granahan, J.C.; Segura, M.; Matson, D.L.; Johnson, T.V.; Martin, P.D.

    1997-01-01

    Five absorption features are reported at wavelengths of 3.4, 3.88, 4.05, 4.25, and 4.57 micrometers in the surface materials of the Galilean satellites Callisto and Ganymede from analysis of reflectance spectra returned by the Galileo mission near-infrared mapping spectrometer. Candidate materials include CO2, organic materials (such as tholins containing C???N and C-H), SO2, and compounds containing an SH-functional group; CO2, SO2, and perhaps cyanogen [(CN)2] may be present within the surface material itself as collections of a few molecules each. The spectra indicate that the primary surface constituents are water ice and hydrated minerals.

  20. From Molecules to Cells to Organisms: Understanding Health and Disease with Multidimensional Single-Cell Methods

    NASA Astrophysics Data System (ADS)

    Candia, Julián

    2013-03-01

    The multidimensional nature of many single-cell measurements (e.g. multiple markers measured simultaneously using Fluorescence-Activated Cell Sorting (FACS) technologies) offers unprecedented opportunities to unravel emergent phenomena that are governed by the cooperative action of multiple elements across different scales, from molecules and proteins to cells and organisms. We will discuss an integrated analysis framework to investigate multicolor FACS data from different perspectives: Singular Value Decomposition to achieve an effective dimensional reduction in the data representation, machine learning techniques to separate different patient classes and improve diagnosis, as well as a novel cell-similarity network analysis method to identify cell subpopulations in an unbiased manner. Besides FACS data, this framework is versatile: in this vein, we will demonstrate an application to the multidimensional single-cell shape analysis of healthy and prematurely aged cells.

  1. Persistent Photoconductivity in Monolayer MoS2 on Organic-molecule-functionalized Substrates

    NASA Astrophysics Data System (ADS)

    Wang, Wei-Hua; Wu, Yueh-Chun; Chen, Shao-Yu; Liu, Cheng-Hua; Ho, Po-Hsun; Chen, Chun-Wei; Liang, Chi-Te

    2014-03-01

    We demonstrate a giant persistent photoconductivity (PPC) effect in monolayer MoS2 in which the photocurrent robustly persists after illumination has ceased. This PPC effect in monolayer MoS2 on organic-molecule-functionalized substrates sustains up to room temperature and can be highly suppressed by applying source-drain/back-gate voltages to the transistors. Based on this persistency and controllability of the PPC effect, we achieve a room-temperature conductance bistability by utilizing optical and electrical pulses. The observed giant PPC effect in MoS2 can be attributed to a large electron-capture barrier of trap states, which is estimated to be as high as 390 meV.

  2. Nuclear magnetic resonance of laser-polarized noble gases in molecules, materials and organisms

    SciTech Connect

    Goodson, Boyd M.

    1999-12-01

    Conventional nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) are fundamentally challenged by the insensitivity that stems from the ordinarily low spin polarization achievable in even the strongest NMR magnets. However, by transferring angular momentum from laser light to electronic and nuclear spins, optical pumping methods can increase the nuclear spin polarization of noble gases by several orders of magnitude, thereby greatly enhancing their NMR sensitivity. This dissertation is primarily concerned with the principles and practice of optically pumped nuclear magnetic resonance (OPNMR). The enormous sensitivity enhancement afforded by optical pumping noble gases can be exploited to permit a variety of novel NMR experiments across many disciplines. Many such experiments are reviewed, including the void-space imaging of organisms and materials, NMR and MRI of living tissues, probing structure and dynamics of molecules in solution and on surfaces, and zero-field NMR and MRI.

  3. Benchmarking Density Functionals on Structural Parameters of Small-/Medium-Sized Organic Molecules.

    PubMed

    Brémond, Éric; Savarese, Marika; Su, Neil Qiang; Pérez-Jiménez, Ángel José; Xu, Xin; Sancho-García, Juan Carlos; Adamo, Carlo

    2016-02-01

    In this Letter we report the error analysis of 59 exchange-correlation functionals in evaluating the structural parameters of small- and medium-sized organic molecules. From this analysis, recently developed double hybrids, such as xDH-PBE0, emerge as the most reliable methods, while global hybrids confirm their robustness in reproducing molecular structures. Notably the M06-L density functional is the only semilocal method reaching an accuracy comparable to hybrids'. A comparison with errors obtained on energetic databases (including thermochemistry, reaction barriers, and interaction energies) indicate that most of the functionals have a coherent behavior, showing low (or high) deviations on both energy and structure data sets. Only a few of them are more prone toward one of these two properties. PMID:26730741

  4. Organic molecules on silicon surface: A way to tune metal dependent Schottky barrier

    NASA Astrophysics Data System (ADS)

    Rabinal, M. K.

    2016-09-01

    Effect of covalently bonded organic molecules on p-type Si surfaces, in controlling the performance of metal-silicon Schottky junctions, is studied. Monolayers of 1-dodecyne were formed on hydrated surfaces of p-type Si ((100) orientation) using weak Lewis acid. The chemical modification results in highly homogeneous surfaces. Gold-Si and Aluminum-Si junctions were prepared, both, on modified and unmodified Si surfaces, and I-V characteristics were studied. The results have been interpreted in terms of energy band diagrams. It is demonstrated that the molecular monolayer of 1-dodecyne is effective in controlling the surface states leading to unpinning of the Fermi level and junction responding to the work function of the metal, as expected from theoretical considerations. The simple method presented provides a unique technique to tune the electrical properties of devices with metal-semiconductor interfaces.

  5. Stable metal-organic frameworks containing single-molecule traps for enzyme encapsulation

    NASA Astrophysics Data System (ADS)

    Feng, Dawei; Liu, Tian-Fu; Su, Jie; Bosch, Mathieu; Wei, Zhangwen; Wan, Wei; Yuan, Daqiang; Chen, Ying-Pin; Wang, Xuan; Wang, Kecheng; Lian, Xizhen; Gu, Zhi-Yuan; Park, Jihye; Zou, Xiaodong; Zhou, Hong-Cai

    2015-01-01

    Enzymatic catalytic processes possess great potential in chemical manufacturing, including pharmaceuticals, fuel production and food processing. However, the engineering of enzymes is severely hampered due to their low operational stability and difficulty of reuse. Here, we develop a series of stable metal-organic frameworks with rationally designed ultra-large mesoporous cages as single-molecule traps (SMTs) for enzyme encapsulation. With a high concentration of mesoporous cages as SMTs, PCN-333(Al) encapsulates three enzymes with record-high loadings and recyclability. Immobilized enzymes that most likely undergo single-enzyme encapsulation (SEE) show smaller Km than free enzymes while maintaining comparable catalytic efficiency. Under harsh conditions, the enzyme in SEE exhibits better performance than free enzyme, showing the effectiveness of SEE in preventing enzyme aggregation or denaturation. With extraordinarily large pore size and excellent chemical stability, PCN-333 may be of interest not only for enzyme encapsulation, but also for entrapment of other nanoscaled functional moieties.

  6. Equilibrium 2H/1H fractionation in organic molecules: III. Cyclic ketones and hydrocarbons

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Sessions, Alex L.; Nielsen, Robert J.; Goddard, William A.

    2013-04-01

    Quantitative interpretation of stable hydrogen isotope ratios (2H/1H) in organic compounds is greatly aided by knowledge of the relevant equilibrium fractionation factors (ɛeq). Previous efforts have combined experimental measurements and hybrid Density Functional Theory (DFT) calculations to accurately predict equilibrium fractionations in linear (acyclic) organic molecules (Wang et al., 2009a,b), but the calibration produced by that study is not applicable to cyclic compounds. Here we report experimental measurements of equilibrium 2H/1H fractionation in six cyclic ketones, and use those data to evaluate DFT calculations of fractionation in diverse monocyclic and polycyclic compounds commonly found in sedimentary organic matter and petroleum. At 25, 50, and 75 °C, the experimentally measured ɛeq values for secondary and tertiary Hα in isotopic equilibrium with water are in the ranges of -130‰ to -150‰ and +10‰ to -40‰ respectively. Measured data are similar to DFT calculations of ɛeq for axial Hα but not equatorial Hα. In tertiary Cα positions with methyl substituents, this can be understood as a result of the methyl group forcing Hα atoms into a dominantly axial position. For secondary Cα positions containing both axial and equatorial Hα atoms, we propose that axial Hα exchanges with water significantly faster than the equatorial Hα does, due to the hyperconjugation-stabilized transition state. Interconversion of axial and equatorial positions via ring flipping is much faster than isotopic exchange at either position, and as a result the steady-state isotopic composition of both H's is strongly weighted toward that of axial Hα. Based on comparison with measured ɛeq values, a total uncertainty of 10-30‰ remains for theoretical ɛeq values. Using DFT, we systematically estimated the ɛeq values for individual H positions in various cyclic structures. By summing over all individual H positions, the molecular equilibrium fractionation was

  7. Linear Ion Traps in Space: The Mars Organic Molecule Analyzer (MOMA) Instrument and Beyond

    NASA Astrophysics Data System (ADS)

    Arevalo, Ricardo; Brinckerhoff, William; Mahaffy, Paul; van Amerom, Friso; Danell, Ryan; Pinnick, Veronica; Li, Xiang; Hovmand, Lars; Getty, Stephanie; Grubisic, Andrej; Goesmann, Fred; Cottin, Hervé

    2015-11-01

    Historically, quadrupole mass spectrometer (QMS) instruments have been used to explore a wide survey of planetary targets in our solar system, from Venus (Pioneer Venus) to Saturn (Cassini-Huygens). However, linear ion trap (LIT) mass spectrometers have found a niche as smaller, versatile alternatives to traditional quadrupole analyzers.The core astrobiological experiment of ESA’s ExoMars Program is the Mars Organic Molecule Analyzer (MOMA) onboard the ExoMars 2018 rover. The MOMA instrument is centered on a linear (or 2-D) ion trap mass spectrometer. As opposed to 3-D traps, LIT-based instruments accommodate two symmetrical ion injection pathways, enabling two complementary ion sources to be used. In the case of MOMA, these two analytical approaches are laser desorption mass spectrometry (LDMS) at Mars ambient pressures, and traditional gas chromatography mass spectrometry (GCMS). The LIT analyzer employed by MOMA also offers: higher ion capacity compared to a 3-D trap of the same volume; redundant detection subassemblies for extended lifetime; and, a link to heritage QMS designs and assembly logistics. The MOMA engineering test unit (ETU) has demonstrated the detection of organics in the presence of wt.%-levels of perchlorate, effective ion enhancement via stored waveform inverse Fourier transform (SWIFT), and derivation of structural information through tandem mass spectrometry (MS/MS).A more progressive linear ion trap mass spectrometer (LITMS), funded by the NASA ROSES MatISSE Program, is being developed at NASA GSFC and promises to augment the capabilities of the MOMA instrument by way of: an expanded mass range (i.e., 20 - 2000 Da); detection of both positive and negative ions; spatially resolved (<1 mm) characterization of individual rock core layers; and, evolved gas analysis and GCMS with pyrolysis up to 1300° C (enabling breakdown of refractory phases). The Advanced Resolution Organic Molecule Analyzer (AROMA) instrument, being developed through NASA

  8. The Rotational Spectrum of Complex Organic Molecules: 2(N)-METHYLAMINOETHANOL

    NASA Astrophysics Data System (ADS)

    Melandri, S.; Maris, A.; Calabrese, C.

    2013-06-01

    The detection of molecules in space, is based on their spectroscopic features and high resolution spectral data is needed to allow an unambiguous identification of them. Many of the molecules detected in space are complex organic molecules containing chains of carbon atoms and which therefore show a high degree of molecular flexibility. The high number of low energy conformations and the presence of large amplitude motions on shallow potential energy surfaces are peculiar to this kind of systems. The presence of a high number of stable conformers - often interconverting through small energy barriers - usually gives rise to very complex spectra, which represent a challenge for spectroscopic and computational methods. We report the rotational study of methylaminoethanol (MAE) performed by Free Jet Absorption Microwave Spectrocopy (FJAMW). For this species it has proved essential to compute the complete potential energy surfaces related to the low amplitude modes. This has been calculated at the B3LYP/6-311++G** level of theory while the stable geometries have been characterized MP2/6-311++G**. The interest in the conformational properties of MAE is twofold: in the first place, aminoethanol and thus also MAE can be considered precursors of aminoacids in the interstellar medium and secondly, the MAE side chain is present in important biological molecules such as adrenaline. The conformational preferences of MAE are dominated by the intramolecular hydrogen bond between the OH and NH2 groups and its flexibility and asymmetry generate a very high number of conformers. 24 stable conformations have been predicted and two conformers were observed by FJAMW spectroscopy with our 60-72 GHz spectrometer. With respect to a previous study we have extended the observed frequency range, partly reassigned the rotational spectrum of one of the conformers and determined the nuclear quadrupole constants. The search for higher energy conformers has also been undertaken. S. Charnley, in

  9. Abundance of Cosmogenic Noble Gases as a Marker of the Organic Degradation by Cosmic Rays in the Surface Martian Rocks. Implications to MSL and Mars 2020

    NASA Astrophysics Data System (ADS)

    Pavlov, A. A.; Vasilyev, G. I.; Ostryakov, V. M.; Pavlov, A. K.; Mahaffy, P.

    2014-07-01

    We conducted a modeling study which links the rates of cosmogenic isotopes production with the radiation accumulation rates on Mars. We calculated the degradation level of the organic molecules at Cumberland based on the observed cosmogenic isotopes.

  10. Laboratory simulation of interstellar grain chemistry and the production of complex organic molecules

    NASA Technical Reports Server (NTRS)

    Allamandola, L. J.; Sandford, S. A.; Valero, G. J.

    1990-01-01

    During the past 15 years considerable progress in observational techniques has been achieved in the middle infrared (5000 to 500 cm(-1), 2 to 20 microns m), the spectral region most diagnostic of molecular vibrations. Spectra of many different astronomical infrared sources, some deeply embedded in dark molecular clouds, are now available. These spectra provide a powerful probe, not only for the identification of interstellar molecules in both the gas solid phases, but also of the physical and chemical conditions which prevail in these two very different domains. By comparing these astronomical spectra with the spectra of laboratory ices one can determine the composition and abundance of the icy materials frozen on the cold (10K) dust grains present in the interior of molecular clouds. These grains and their ice mantles may well be the building blocks from which comets are made. As an illustration of the processes which can take place as an ice is irradiated and subsequently warmed, researchers present the infrared spectra of the mixture H2O:CH3OH:CO:NH3:C6H14 (100:50:10:10:10). Apart from the last species, the ratio of these compounds is representative of the simplest ices found in interstellar clouds. The last component was incorporated into this particular experiment as a tracer of the behavior of a non-aromatic hydrocarbon. The change in the composition that results from ultraviolet photolysis of this ice mixture using a UV lamp to simulate the interstellar radiation field is shown. Photolysis produces CO, CO2, CH4, HCO, H2CO, as well as a family of moderately volatile hydrocarbons. Less volatile carbonaceous materials are also produced. The evolution of the infrared spectrum of the ice as the sample is warmed up to room temperature is illustrated. Researchers believe that the changes are similar to those which occur as ice is ejected from a comet and warmed up by solar radiation. The warm-up sequence shows that the nitrile or iso-nitrile bearing compound

  11. Reducing dynamic disorder in small-molecule organic semiconductors by suppressing large-amplitude thermal motions

    NASA Astrophysics Data System (ADS)

    Illig, Steffen; Eggeman, Alexander S.; Troisi, Alessandro; Jiang, Lang; Warwick, Chris; Nikolka, Mark; Schweicher, Guillaume; Yeates, Stephen G.; Henri Geerts, Yves; Anthony, John E.; Sirringhaus, Henning

    2016-02-01

    Thermal vibrations and the dynamic disorder they create can detrimentally affect the transport properties of van der Waals bonded molecular semiconductors. The low-energy nature of these vibrations makes it difficult to access them experimentally, which is why we still lack clear molecular design rules to control and reduce dynamic disorder. In this study we discuss the promising organic semiconductors rubrene, 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothio-phene and 2,9-di-decyl-dinaphtho-[2,3-b:20,30-f]-thieno-[3,2-b]-thiophene in terms of an exceptionally low degree of dynamic disorder. In particular, we analyse diffuse scattering in transmission electron microscopy, to show that small molecules that have their side chains attached along the long axis of their conjugated core are better encapsulated in their crystal structure, which helps reduce large-amplitude thermal motions. Our work provides a general strategy for the design of new classes of very high mobility organic semiconductors with a low degree of dynamic disorder.

  12. Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

    NASA Astrophysics Data System (ADS)

    Ruggeri, Giulia; Takahama, Satoshi

    2016-04-01

    Functional groups (FGs) can be used as a reduced representation of organic aerosol composition in both ambient and controlled chamber studies, as they retain a certain chemical specificity. Furthermore, FG composition has been informative for source apportionment, and various models based on a group contribution framework have been developed to calculate physicochemical properties of organic compounds. In this work, we provide a set of validated chemoinformatic patterns that correspond to (1) a complete set of functional groups that can entirely describe the molecules comprised in the α-pinene and 1,3,5-trimethylbenzene MCMv3.2 oxidation schemes, (2) FGs that are measurable by Fourier transform infrared spectroscopy (FTIR), (3) groups incorporated in the SIMPOL.1 vapor pressure estimation model, and (4) bonds necessary for the calculation of carbon oxidation state. We also provide example applications for this set of patterns. We compare available aerosol composition reported by chemical speciation measurements and FTIR for different emission sources, and calculate the FG contribution to the O : C ratio of simulated gas-phase composition generated from α-pinene photooxidation (using the MCMv3.2 oxidation scheme).

  13. Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

    NASA Astrophysics Data System (ADS)

    Ruggeri, G.; Takahama, S.

    2015-11-01

    Functional groups (FGs) can be used as a reduced representation of organic aerosol composition in both ambient and environmental controlled chamber studies, as they retain a certain chemical specificity. Furthermore, FG composition has been informative for source apportionment, and various models based on a group contribution framework have been developed to calculate physicochemical properties of organic compounds. In this work, we provide a set of validated chemoinformatic patterns that correspond to: (1) groups incorporated in the SIMPOL.1 vapor pressure estimation model, (2) FGs that are measurable by Fourier transform infrared spectroscopy (FTIR), (3) a complete set of functional groups that can entirely describe the molecules comprised in the α-pinene and 1,3,5-trimethylbenzene MCMv3.2 oxidation schemes, and (4) bonds necessary for the calculation of carbon oxidation state. We also provide example applications for this set of patterns. We compare available aerosol composition reported by chemical speciation measurements and FTIR for different emission sources, and calculate the FG contribution to the O : C ratio of simulated gas phase composition generated from α-pinene photooxidation (using MCMv3.2 oxidation scheme).

  14. Microstructural control of calcite via incorporation of intracrystalline organic molecules in shells

    NASA Astrophysics Data System (ADS)

    Okumura, Taiga; Suzuki, Michio; Nagasawa, Hiromichi; Kogure, Toshihiro

    2013-10-01

    It is widely accepted that organic substances regulate or influence the structure of biominerals, but its direct evidences are not plenty. Here we show that the crystallographic microstructures in biotic calcites arise from incorporated intracrystalline organic molecules (IOMs), through a comparison between biotic calcites in shells and synthetic ones with the IOMs extracted from the shells. Although the prismatic layers of a pearl oyster (Pinctada fucata) and a pen shell (Atrina pectinata) morphologically resemble each other, the crystallographic features of constituent calcites are considerably different; in Pinctada, the IOMs are distributed inhomogeneously to form small-angle grain boundaries and associated crystal defects, whereas in Atrina, the IOMs are distributed almost homogeneously and defects are rare in the calcite crystals. We conducted in vitro calcite syntheses in the presence of the IOMs in EDTA-soluble extracts from the prisms. The IOMs in the extracts from Pinctada and Atrina were incorporated into synthetic calcites in a different manner, exhibiting defect-rich/free features as observed in the natural shells. With regard to amino acid compositions of the IOMs, the extract from Atrina has a higher proportion of acidic amino acids than that from Pinctada, implying that acidic proteins do not correlate directly to their affinity for calcium carbonate crystals.

  15. Reducing dynamic disorder in small-molecule organic semiconductors by suppressing large-amplitude thermal motions.

    PubMed

    Illig, Steffen; Eggeman, Alexander S; Troisi, Alessandro; Jiang, Lang; Warwick, Chris; Nikolka, Mark; Schweicher, Guillaume; Yeates, Stephen G; Henri Geerts, Yves; Anthony, John E; Sirringhaus, Henning

    2016-01-01

    Thermal vibrations and the dynamic disorder they create can detrimentally affect the transport properties of van der Waals bonded molecular semiconductors. The low-energy nature of these vibrations makes it difficult to access them experimentally, which is why we still lack clear molecular design rules to control and reduce dynamic disorder. In this study we discuss the promising organic semiconductors rubrene, 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothio-phene and 2,9-di-decyl-dinaphtho-[2,3-b:20,30-f]-thieno-[3,2-b]-thiophene in terms of an exceptionally low degree of dynamic disorder. In particular, we analyse diffuse scattering in transmission electron microscopy, to show that small molecules that have their side chains attached along the long axis of their conjugated core are better encapsulated in their crystal structure, which helps reduce large-amplitude thermal motions. Our work provides a general strategy for the design of new classes of very high mobility organic semiconductors with a low degree of dynamic disorder. PMID:26898754

  16. Reducing dynamic disorder in small-molecule organic semiconductors by suppressing large-amplitude thermal motions

    PubMed Central

    Illig, Steffen; Eggeman, Alexander S.; Troisi, Alessandro; Jiang, Lang; Warwick, Chris; Nikolka, Mark; Schweicher, Guillaume; Yeates, Stephen G.; Henri Geerts, Yves; Anthony, John E.; Sirringhaus, Henning

    2016-01-01

    Thermal vibrations and the dynamic disorder they create can detrimentally affect the transport properties of van der Waals bonded molecular semiconductors. The low-energy nature of these vibrations makes it difficult to access them experimentally, which is why we still lack clear molecular design rules to control and reduce dynamic disorder. In this study we discuss the promising organic semiconductors rubrene, 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothio-phene and 2,9-di-decyl-dinaphtho-[2,3-b:20,30-f]-thieno-[3,2-b]-thiophene in terms of an exceptionally low degree of dynamic disorder. In particular, we analyse diffuse scattering in transmission electron microscopy, to show that small molecules that have their side chains attached along the long axis of their conjugated core are better encapsulated in their crystal structure, which helps reduce large-amplitude thermal motions. Our work provides a general strategy for the design of new classes of very high mobility organic semiconductors with a low degree of dynamic disorder. PMID:26898754

  17. Electroluminescence from Spontaneously Generated Single-Vesicle Aggregates Using Solution-Processed Small Organic Molecules.

    PubMed

    Tsai, Yu-Tang; Tseng, Kuo-Pi; Chen, Yan-Fang; Wu, Chung-Chih; Fan, Gang-Lun; Wong, Ken-Tsung; Wantz, Guillaume; Hirsch, Lionel; Raffy, Guillaume; Del Guerzo, Andre; Bassani, Dario M

    2016-01-26

    Self-assembled aggregates offer great potential for tuning the morphology of organic semiconductors, thereby controlling their size and shape. This is particularly interesting for applications in electroluminescent (EL) devices, but there has been, to date, no reports of a functional EL device in which the size and color of the emissive domains could be controlled using self-assembly. We now report a series of molecules that spontaneously self-organize into small EL domains of sub-micrometer dimensions. By tailoring the emissive chromophores in solution, spherical aggregates that have an average size of 300 nm in diameter and emit any one color, including CIE D65 white, are spontaneously formed in solution. We show that the individual aggregates can be used in EL devices built either using small patterned electrodes or using a sandwich architecture to produce devices emitting in the blue, green, red, and white. Furthermore, sequential deposition of the three primary colors yields an RGB device in which single aggregates of each color are present in close proximity. PMID:26730851

  18. Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules

    SciTech Connect

    Nikiforov, Alexander; Gamez, Jose A.; Thiel, Walter; Huix-Rotllant, Miquel; Filatov, Michael

    2014-09-28

    Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 Å or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems.

  19. Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules

    NASA Astrophysics Data System (ADS)

    Nikiforov, Alexander; Gamez, Jose A.; Thiel, Walter; Huix-Rotllant, Miquel; Filatov, Michael

    2014-09-01

    Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 Å or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems.

  20. Results of the First Mars Organic Molecule Analyzer (MOMA) GC-MS Coupling

    NASA Astrophysics Data System (ADS)

    Buch, Arnaud; Pinnick, Veronica; Szopa, Cyril; Danell, Ryan; Grand, Noel; Van Amerom, Friso; Glavin, Daniel; Freissinet, Caroline; Humeau, Olivier; Coll, Patrice; Arevalo, Ricardo; Stalport, Fabien; Brinckerhoff, William; Steininger, Harald; Goesmann, Fred; Mahaffy, Paul; Raulin, Francois

    2014-11-01

    The Mars Organic Molecule Analyzer (MOMA) aboard the ExoMars rover will be a key analytical tool in providing chemical (molecular) information from the solid samples collected by the rover, with a particular focus on the char-acterization of the organic content. The core of the MOMA instrument is a gas chromatograph coupled with a mass spectrometer (GC-MS) which provides the unique capability to characterize a broad range of compounds, including both of volatile and non-volatile species. Samples will be crushed and deposited into sample cups seated in a rotating carousel. Soil samples will be analyzed either by UV laser desorption / ionization (LDI) or pyrolysis gas chromatography ion trap mass spectrometry (pyr-GC-ITMS).The French GC brassboard was coupled to the US ion trap mass spectrometer brassboard in a flight-like con-figuration for several coupling campains. The MOMA GC setup is based on the SAM heritage design with a He reservoir and 4 separate analytical modules including traps, columns and Thermal Conductivity Detectors. Solid samples are sealed and heated in this setup using a manual tapping station, designed and built at MPS in Germany, for GC-MS analysis. The gaseous species eluting from the GC are then ionized by an electron impact ionization source in the MS chamber and analyzed by the linear ion trap mass spectrometer. Volatile and non-volatile compounds were injected in the MOMA instrumental suite. Both of these compounds classes were detected by the TCD and by the MS. MS signal (total ion current) and single mass spectra by comparison with the NIST library, gave us an unambiguous confirmation of these identifications. The mass spectra arise from an average of 10 mass spectra averaged around a given time point in the total ion chromatogram.Based on commercial instrument, the MOMA requirement for sensitivity in the GC-MS mode for organic molecules is 1 pmol. In this test, sensitivity was determined for the GC TCD and MS response to a dilution

  1. Resolving the influence of nitrogen abundances on sediment organic matter in macrophyte-dominated lakes, using fluorescence spectroscopy.

    PubMed

    Yao, Xin; Wang, Shengrui; Jiao, Lixin; Yan, Caihong; Jin, Xiangcan

    2015-01-01

    A controlled experiment was designed to resolve the influence of nitrogen abundance on sediment organic matters in macrophyte-dominated lakes using fluorescence analysis. Macrophyte biomass showed coincident growth trends with time, but different variation rates with nitrogen treatment. All plant growth indexes with nitrogen addition (N, NH4Cl 100, 200, 400mg/kg, respectively) were lower than those of the control group. Four humic-like components, two autochthonous tryptophan-like components, and one autochthonous tyrosine-like component were identified using the parallel factor analysis model. The results suggested that the relative component changes of fluorescence in the colonized sediments were in direct relation to the change of root biomass with time. In the experiment, the root formation parameters of the plants studied were significantly affected by adding N in sediments, which may be related to the reason that the root growth was affected by N addition. Adding a low concentration of N to sediments can play a part in supplying nutrients to the plants. However, the intensive uptake of NH4(+) may result in an increase in the intracellular concentration of ammonia, which is highly toxic to the plant cells. Hence, our experiment results manifested that organic matter cycling in the macrophyte-dominated sediment was influenced by nitrogen enrichment through influencing vegetation and relevant microbial activity. PMID:25597678

  2. Self-organization of surfactant molecules on solid surface: an STM study of sodium alkyl sulfonates [rapid communication

    NASA Astrophysics Data System (ADS)

    Yin, Xiu-Li; Wan, Li-Jun; Yang, Zheng-Yu; Yu, Jia-Yong

    2005-02-01

    Adsorption and self-organization of sodium alkyl sulfonates (STS and SHS) on HOPG have been studied by using in situ scanning tunneling microscopy (STM). Both SHS and STS molecules adsorb on HOPG surface and form long-range well-ordered monolayers. The molecular rows and the axes of alkyl chain of the molecules cross each other at angles of 60° and 90° in the STS and SHS layers, respectively. Molecular details such as sulfonate functional group (head) and alkyl chain are clearly imaged. The neighboring molecules in different rows form a "head to head" configuration. Structural models for the molecular arrangement of the two adlayers are proposed.

  3. A "roller-wheel" Pt-containing small molecule that outperforms its polymer analogs in organic solar cells

    DOE PAGESBeta

    He, Wenhan; Wu, Qin; Livshits, Maksim Y.; Dickie, Diane A.; Yang, Jianzhong; Quinnett, Rachel; Rack, Jeffrey R.; Qin, Yang

    2016-05-23

    A novel Pt-bisacetylide small molecule (Pt-SM) featuring “roller-wheel” geometry was synthesized and characterized. When compared with conventional Pt-containing polymers and small molecules having “dumbbell” shaped structures, Pt-SM displays enhanced crystallinity and intermolecular π–π interactions, as well as favorable panchromatic absorption behaviors. Furthermore, organic solar cells (OSCs) employing Pt-SM achieve power conversion efficiencies (PCEs) up to 5.9%, the highest reported so far for Pt-containing polymers and small molecules.

  4. In situ patterning of organic molecules in aqueous solutions using an inverted electron-beam lithography system

    NASA Astrophysics Data System (ADS)

    Miyazako, Hiroki; Ishihara, Kazuhiko; Mabuchi, Kunihiko; Hoshino, Takayuki

    2016-06-01

    A method for in situ controlling the detachment and deposition of organic molecules such as sugars and biocompatible polymers in aqueous solutions by electron-beam (EB) scan is proposed and evaluated. It was demonstrated that EB irradiation could detach 2-methacryloyloxyethyl phosphorylcholine (MPC) polymers from a silicon nitride membrane. Moreover, organic molecules such as cationic polymers and sugars could be deposited on the membrane by EB irradiation. Spatial distributions of scattered electrons were numerically simulated, and acceleration voltage dependences of the detachment and deposition phenomena were experimentally measured. The simulations and experimental results suggest that the detachment of MPC polymers is mainly due to electrical effects of primary electrons, and that the deposition of organic molecules is mainly due to chemical reactions induced by primary electrons. In view of these findings, the proposed method can be applied to in situ and nanoscale patterning such as the fabrication of cell scaffolds.

  5. Chronic hypoxia and VEGF differentially modulate abundance and organization of myosin heavy chain isoforms in fetal and adult ovine arteries.

    PubMed

    Hubbell, Margaret C; Semotiuk, Andrew J; Thorpe, Richard B; Adeoye, Olayemi O; Butler, Stacy M; Williams, James M; Khorram, Omid; Pearce, William J

    2012-11-15

    Chronic hypoxia increases vascular endothelial growth factor (VEGF) and thereby promotes angiogenesis. The present study explores the hypothesis that hypoxic increases in VEGF also remodel artery wall structure and contractility through phenotypic transformation of smooth muscle. Pregnant and nonpregnant ewes were maintained at sea level (normoxia) or 3,820 m (hypoxia) for the final 110 days of gestation. Common carotid arteries harvested from term fetal lambs and nonpregnant adults were denuded of endothelium and studied in vitro. Stretch-dependent contractile stresses were 32 and 77% of normoxic values in hypoxic fetal and adult arteries. Hypoxic hypocontractility was coupled with increased abundance of nonmuscle myosin heavy chain (NM-MHC) in fetal (+37%) and adult (+119%) arteries. Conversely, hypoxia decreased smooth muscle MHC (SM-MHC) abundance by 40% in fetal arteries but increased it 123% in adult arteries. Hypoxia decreased colocalization of NM-MHC with smooth muscle α-actin (SM-αA) in fetal arteries and decreased colocalization of SM-MHC with SM-αA in adult arteries. Organ culture with physiological concentrations (3 ng/ml) of VEGF-A(165) similarly depressed stretch-dependent stresses to 37 and 49% of control fetal and adult values. The VEGF receptor antagonist vatalanib ablated VEGF's effects in adult but not fetal arteries, suggesting age-dependent VEGF receptor signaling. VEGF replicated hypoxic decreases in colocalization of NM-MHC with SM-αA in fetal arteries and decreases in colocalization of SM-MHC with SM-αA in adult arteries. These results suggest that hypoxic increases in VEGF not only promote angiogenesis but may also help mediate hypoxic arterial remodeling through age-dependent changes in smooth muscle phenotype and contractility. PMID:22992677

  6. Universal tight binding model for chemical reactions in solution and at surfaces. I. Organic molecules

    SciTech Connect

    Sheppard, T. J.; Lozovoi, A. Y.; Kohanoff, J. J.; Pashov, D. L.; Paxton, A. T.

    2014-07-28

    As is now well established, a first order expansion of the Hohenberg–Kohn total energy density functional about a trial input density, namely, the Harris–Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

  7. Universal tight binding model for chemical reactions in solution and at surfaces. I. Organic molecules

    NASA Astrophysics Data System (ADS)

    Sheppard, T. J.; Lozovoi, A. Y.; Pashov, D. L.; Kohanoff, J. J.; Paxton, A. T.

    2014-07-01

    As is now well established, a first order expansion of the Hohenberg-Kohn total energy density functional about a trial input density, namely, the Harris-Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

  8. Nanolithographic control of the spatial organization of cellular adhesion receptors at the single-molecule level

    PubMed Central

    Schvartzman, Mark; Palma, Matteo; Sable, Julia; Abramson, Justin; Hu, Xian; Sheetz, Michael P.; Wind, Shalom J.

    2011-01-01

    The ability to control the placement of individual molecules promises to enable a wide range of applications and is a key challenge in nanoscience and nanotechnology. Many biological interactions, in particular, are sensitive to the precise geometric arrangement of proteins. We have developed a technique which combines molecular-scale nanolithography with site-selective biochemistry to create biomimetic arrays of individual protein binding sites. The binding sites can be arranged in heterogeneous patterns of virtually any possible geometry with a nearly unlimited number of degrees of freedom. We have used these arrays to explore how the geometric organization of the extracellular matrix (ECM) binding ligand RGD (Arg-Gly-Asp) affects cell adhesion and spreading. Systematic variation of spacing, density and cluster size of individual integrin binding sites was used to elicit different cell behavior. Cell spreading assays on arrays of different geometric arrangements revealed a dramatic increase in spreading efficiency when at least 4 liganded sites were spaced within 60 nm or less, with no dependence on global density. This points to the existence of a minimal matrix adhesion unit for fibronectin defined in space and stoichiometry. Developing an understanding of the ECM geometries that activate specific cellular functional complexes is a critical step toward controlling cell behavior. Potential practical applications range from new therapeutic treatments to the rational design of tissue scaffolds that can optimize healing without scarring. More broadly, spatial control at the single-molecule level can elucidate factors controlling individual molecular interactions and can enable synthesis of new systems based on molecular-scale architectures. PMID:21319842

  9. Enantiomeric derivatization on the Mars Organic Molecule Analyzer (MOMA) experiment aboard ExoMars 2018: how to unravel martian chirality

    NASA Astrophysics Data System (ADS)

    Freissinet, C.; Buch, A.; Szopa, C.; Morisson, M.; Grand, N.; Raulin, F.; Brinckerhoff, W.

    2015-10-01

    The origin of homochirality in life on Earth remains unknown. The answer to this question lies in the study of chirality elsewhere in the Solar System. The Sample Analysis at Mars (SAM) experiment aboard Curiosity established the presence of organic molecules indigenous to a clay-rich sample on Mars [1]. However, SAM does not have the ability to separate between the enantiomers of potential medium- or high- molecular weight organic molecules. One of the wet chemistry experiments to be used in the MOMA instrument of the Exomars mission is designed for the extraction and identification of refractory organic chemical components in solid samples using gas chromatography-mass spectrometry (GCMS), while keeping the chiral center of the molecules intact [2]. This derivatization technique, using dimethylformamide dimethylacetal (DMF-DMA) as a reagent, will allow MOMA to separate the enantiomers of molecules of interest for astrobiology, such as amino acids, sugars or carboxylic acids. We present here the results of laboratory experiments which display the feasability and limitations of the detection of an enantiomeric excess of complex organic molecules in various analog samples, depending on the mineralogy of the Mars analog solid sample.

  10. Proazaphosphatranes: Versatile molecules with applications in fuel cell technology, biodiesel production and important organic transformations

    NASA Astrophysics Data System (ADS)

    Wadhwa, Kuldeep

    In recent years proazaphosphatranes of type P(RNCH2CH 2)3N have proven their synthetic utility as catalysts and as stoichiometric bases in a variety of organic transformations. Several reports from our group appeared in which the use of proazaphosphatranes for the activation of the silicon to synthesize useful organic intermediates. Herein we report the use of proazaphosphatranes to synthesize various useful small organic molecules by the activation of Si-O and Si-C bonds, along with efforts to gain evidence for silicon group activation. We previously demonstrated that a phosphatranium cation for which the counter anion is nitrate, is an excellent catalyst for aza- and thia-Michael reactions. Evidence was presented that such a nitrate salt in which the cation was bound to a solid support was superior to a commercially available nitrate anion exchange resin. These results prompted us to chemically bind phosphatranium salts to NafionRTM membrane supports to function as nitrate and hydroxide ion conducting membranes for fuel cell applications. Here we report the synthesis of a novel anion exchange fuel cell membrane by chemically attaching proazaphosphatranium and phosphatranium cations under microwave conditions to the sulfonic groups of Nafion-F RTM and the use of solid-state NMR techniques to determine the structure and composition of this anion exchange membrane. A thermally and air stable derivative of a proazaphosphatrane i.e., a benzyl azidoproazaphosphatrane, was discovered in our laboratory which was shown to be an excellent catalyst for biodiesel synthesis via the transesterification of soybean oil and for other Lewis base- catalyzed important organic transformations. However, the heterogeneous analog i.e., a Merrifield resin-bound azidoproazaphosphatrane, was found to be deactivated after 11 cycles for the transesterification of soybean oil. We report here an attempted synthesis of a TeflonRTM - and NafionRTM-bound azidoproazaphosphatrane. Such a solid

  11. Label-free detection of protein molecules secreted from an organ-on-a-chip model for drug toxicity assays

    NASA Astrophysics Data System (ADS)

    Morales, Andres W.; Zhang, Yu S.; Aleman, Julio; Alerasool, Parissa; Dokmeci, Mehmet R.; Khademhosseini, Ali; Ye, Jing Yong

    2016-03-01

    Clinical attrition is about 30% from failure of drug candidates due to toxic side effects, increasing the drug development costs significantly and slowing down the drug discovery process. This partly originates from the fact that the animal models do not accurately represent human physiology. Hence there is a clear unmet need for developing drug toxicity assays using human-based models that are complementary to traditional animal models before starting expensive clinical trials. Organ-on-a-chip techniques developed in recent years have generated a variety of human organ models mimicking different human physiological conditions. However, it is extremely challenging to monitor the transient and long-term response of the organ models to drug treatments during drug toxicity tests. First, when an organ-on-a-chip model interacts with drugs, a certain amount of protein molecules may be released into the medium due to certain drug effects, but the amount of the protein molecules is limited, since the organ tissue grown inside microfluidic bioreactors have minimum volume. Second, traditional fluorescence techniques cannot be utilized for real-time monitoring of the concentration of the protein molecules, because the protein molecules are continuously secreted from the tissue and it is practically impossible to achieve fluorescence labeling in the dynamically changing environment. Therefore, direct measurements of the secreted protein molecules with a label-free approach is strongly desired for organs-on-a-chip applications. In this paper, we report the development of a photonic crystal-based biosensor for label-free assays of secreted protein molecules from a liver-on-a-chip model. Ultrahigh detection sensitivity and specificity have been demonstrated.

  12. On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes

    SciTech Connect

    Moreira, Rodrigo A.; Melo, Celso P. de

    2014-09-28

    Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

  13. Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Hay, Michael B.; Myneni, Satish C. B.

    2007-07-01

    Carboxyls play an important role in the chemistry of natural organic molecules (NOM) in the environment, and their behavior is dependent on local structural environment within the macromolecule. We studied the structural environments of carboxyl groups in dissolved NOM from the Pine Barrens (New Jersey, USA), and IHSS NOM isolates from soils and river waters using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. It is well established that the energies of the asymmetric stretching vibrations of the carboxylate anion (COO -) are sensitive to the structural environment of the carboxyl group. These energies were compiled from previous infrared studies on small organic acids for a wide variety of carboxyl structural environments and compared with the carboxyl spectral features of the NOM samples. We found that the asymmetric stretching peaks for all NOM samples occur within a narrow range centered at 1578 cm -1, suggesting that all NOM samples examined primarily contain very similar carboxyl structures, independent of sample source and isolation techniques employed. The small aliphatic acids containing hydroxyl (e.g., D-lactate, gluconate), ether/ester (methoxyacetate, acetoxyacetate), and carboxylate (malonate) substitutions on the α-carbon, and the aromatic acids salicylate ( ortho-OH) and furancarboxylate ( O-heterocycle), exhibit strong overlap with the NOM range, indicating that similar structures may be common in NOM. The width of the asymmetric peak suggests that the structural heterogeneity among the predominant carboxyl configurations in NOM is small. Changes in peak area with pH at energies distant from the peak at 1578 cm -1, however, may be indicative of a small fraction of other aromatic carboxyls and aliphatic structures lacking α-substitution. This information is important in understanding NOM-metal and mineral-surface complexation, and in building appropriate structural and mechanistic models of humic materials.

  14. Small-molecule organic solar cells with multiple-layer donor

    NASA Astrophysics Data System (ADS)

    Arisawa, Kenta; Harafuji, Kenji

    2015-09-01

    Small-molecule organic solar cells (OSCs) with a multifunction three-layer donor are experimentally investigated to achieve higher power conversion efficiency. The proposed OSC has an indium tin oxide (ITO, anode)/three-layer donor/fullerene (C60, acceptor, 40 nm)/bathocuproine (BCP, cathode buffer, 10 nm)/Ag (cathode, 100 nm) structure. The three-layer donor is composed of 3-nm-thick pentacene/20-nm-thick copper phthalocyanine (CuPc)/5-nm-thick aluminum phthalocyanine chloride (ClAlPc). The OSC achieves a power conversion efficiency of 1.79%, which is 1.7 times as large as that for an OSC with a single-layer donor of 20-nm-thick CuPc. Atomic force microscopy observation is carried out to clarify in detail the surface morphology at typical organic layers. The acceptor C60 is in contact not only with ClAlPc but also with CuPc due to the vertical and wall-like growth of the ClAlPc layer. The open-circuit voltage for the OSC with the ClAlPc/C60 contact is 0.56 V, compared with 0.47 V for the OSC with the CuPc/C60 contact. The thin pentacene layer is uniformly grown on the ITO and serves to achieve a high short-circuit current density Jsc by lowering the barrier height for hole transport between ITO and CuPc. Jsc for the OSC with the thin pentacene layer is 5.60 mA/cm2, compared with 4.32 mA/cm2 for the OSC without the thin pentacene layer.

  15. Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.

    PubMed

    Gladich, Ivan; Rodriguez, Alex; Hong Enriquez, Rolando P; Guida, Filomena; Berti, Federico; Laio, Alessandro

    2015-10-15

    Short peptides offer a cheap alternative to antibodies for developing sensing units in devices for concentration measurement. We here describe a computational procedure that allows designing peptides capable of binding with high affinity a target organic molecule in aqueous or nonstandard solvent environments. The algorithm is based on a stochastic search in the space of the possible sequences of the peptide, and exploits finite temperature molecular dynamics simulations in explicit solvent to check if a proposed mutation improves the binding affinity or not. The procedure automatically produces peptides which form thermally stable complexes with the target. The estimated binding free energy reaches the 13 kcal/mol for Irinotecan anticancer drug, the target considered in this work. These peptides are by construction solvent specific; namely, they recognize the target only in the solvent in which they have been designed. This feature of the algorithm calls for applications in devices in which the peptide-based sensor is required to work in denaturants or under extreme conditions of pressure and temperature. PMID:26398715

  16. Small Organic Molecules in Pre-Cometary Ices: The Origins of Genetic Material

    NASA Astrophysics Data System (ADS)

    Bredehöft, J. H.; Meierhenrich, U. J.; Thiemann, W.; Rosenbauer, H.; Nuevo, M.; Muñoz Caro, G. M.; D'Hendecourt, L.

    Speaking of genetic material, one thinks of DNA first. An understanding of its fairly complex structure, composed of the sugar deoxyribose, phosphorous acid, and the purine- and pyrimidine-bases, adenine, guanine, cytosine, and thymine has led to the abandonment of theories of its spontaneous creation. In recent times, a number of theories regarding the evolutionary precursors of DNA have been presented. Namely these are the theories of the `RNA-world' (1) and a theory about the precursors of RNA, the so called `PNA-world' (2). In laboratory simulations of inter- and circumstellar pre-cometary ice analogues a number of organic molecules have been identified that corroborate these theories about the evolution of genetic material. Namely these are specific amino acids, which form the necessary material of the backbone of PNA, and a number of purine- and pyrimidine-bases which may have formed the elements of the code itself (3). The delivery of these constituents to earth via impact scenarios of mainly carbonaceous chondrites has also been confirmed in the case of the Murchinson meteorite (4, 5). (1) Gilbert, W., Nature 319, 618 (1986) (2) Egholm, M., Burchardt, O. et al., Nature 365, 566 (1993) (3) Bredehoeft, J.H., diploma, Univ. of Bremen, Germany, 2004. (4) Van der Welden, W. & Schwartz, A.W. , Geochim. cosmochim. Acta 41, 961-968 (1977) (5) Stoks, P.G. & Schwartz A.W., Nature 282, 709-710 (1979)

  17. Electrochemical reduction of carbon dioxide on pyrite as a pathway for abiogenic formation of organic molecules.

    PubMed

    Vladimirov, M G; Ryzhkov, Y F; Alekseev, V A; Bogdanovskaya, V A; Otroshchenko, V A; Kritsky, M S

    2004-08-01

    A wide spectrum of electrode potentials of minerals that compose sulfide ores enables the latter, when in contact with hydrothermal solutions, to form galvanic pairs with cathode potentials sufficient for electrochemical reduction of CO2. The experiments performed demonstrated the increase of cathode current on the rotating pyrite disc electrode in a range of potentials more negative than -800 mV in presence of CO2. In high-pressure experiments performed in a specially designed electrochemical cell equipped with a pyrite cathode and placed into autoclave, accumulation of formate was demonstrated after 24 hr passing of CO2 (50 atm, room temperature) through electrolyte solution. The formation of this product started on increasing the cathode potential to -800 mV (with respect to saturated silver chloride electrode). The yield grew exponentially upon cathode potential increase up to -1200 mV. The maximum current efficiency (0.12%) was registered at cathode potentials of about -1000 mV. No formate production was registered under normal atmospheric pressure and in the absence of imposed cathode potential. Neither in experiments, nor in control was formaldehyde found. It is proposed that the electrochemical reduction of CO2 takes part in the formation of organic molecules in hydrothermal solutions accompanying sulfide ore deposits and in 'black smokers' on the ocean floor. PMID:15279170

  18. The Synthesis of Organic Molecules of Intrinsic Microporosity Designed to Frustrate Efficient Molecular Packing

    PubMed Central

    Taylor, Rupert G. D.; Bezzu, C. Grazia; Carta, Mariolino; Msayib, Kadhum J.; Walker, Jonathan; Short, Rhys; Kariuki, Benson M.

    2016-01-01

    Abstract Efficient reactions between fluorine‐functionalised biphenyl and terphenyl derivatives with catechol‐functionalised terminal groups provide a route to large, discrete organic molecules of intrinsic microporosity (OMIMs) that provide porous solids solely by their inefficient packing. By altering the size and substituent bulk of the terminal groups, a number of soluble compounds with apparent BET surface areas in excess of 600 m2 g−1 are produced. The efficiency of OMIM structural units for generating microporosity is in the order: propellane>triptycene>hexaphenylbenzene>spirobifluorene>naphthyl=phenyl. The introduction of bulky hydrocarbon substituents significantly enhances microporosity by further reducing packing efficiency. These results are consistent with findings from previously reported packing simulation studies. The introduction of methyl groups at the bridgehead position of triptycene units reduces intrinsic microporosity. This is presumably due to their internal position within the OMIM structure so that they occupy space, but unlike peripheral substituents they do not contribute to the generation of free volume by inefficient packing. PMID:26751824

  19. Electron-molecule chemistry and charging processes on organic ices and Titan's icy aerosol surrogates

    NASA Astrophysics Data System (ADS)

    Pirim, C.; Gann, R. D.; McLain, J. L.; Orlando, T. M.

    2015-09-01

    Electron-induced polymerization processes and charging events that can occur within Titan's atmosphere or on its surface were simulated using electron irradiation and dissociative electron attachment (DEA) studies of nitrogen-containing organic condensates. The DEA studies probe the desorption of H- from hydrogen cyanide (HCN), acetonitrile (CH3CN), and aminoacetonitrile (NH2CH2CN) ices, as well as from synthesized tholin materials condensed or deposited onto a graphite substrate maintained at low temperature (90-130 K). The peak cross sections for H- desorption during low-energy (3-15 eV) electron irradiation were measured and range from 3 × 10-21 to 2 × 10-18 cm2. Chemical and structural transformations of HCN ice upon 2 keV electron irradiation were investigated using X-ray photoelectron and Fourier-transform infrared spectroscopy techniques. The electron-beam processed materials displayed optical properties very similar to tholins produced by conventional discharge methods. Electron and negative ion trapping lead to 1011 charges cm-2 on a flat surface which, assuming a radius of 0.05 μm for Titan aerosols, is ∼628 charges/radius (in μm). The facile charge trapping indicates that electron interactions with nitriles and complex tholin-like molecules could affect the conductivity of Titan's atmosphere due to the formation of large negative ion complexes. These negatively charged complexes can also precipitate onto Titan's surface and possibly contribute to surface reactions and the formation of dunes.

  20. Interface dipoles of organic molecules on Ag(111) in hybrid density-functional theory

    NASA Astrophysics Data System (ADS)

    Hofmann, Oliver T.; Atalla, Viktor; Moll, Nikolaj; Rinke, Patrick; Scheffler, Matthias

    2013-12-01

    We investigate the molecular acceptors 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA), 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) and 4,5,9,10-pyrenetetraone (PYTON) on Ag(111) using density-functional theory (DFT). For two groups of the Heyd-Scuseria-Ernzerhof (HSE(α, ω)) family of exchange-correlation functionals (ω = 0 and 0.2 Å) we study the isolated components as well as the combined systems as a function of the amount of exact-exchange (α). We find that hybrid functionals favour electron transfer to the adsorbate. Comparing with experimental work function data, for α ≈ 0.25 we report a notable but small improvement over (semi) local functionals for the interface dipole. Although Kohn-Sham eigenvalues are only approximate representations of ionization energies, incidentally, at this value also the density of states agrees well with the photoelectron spectra. However, increasing α to values for which the energy of the lowest unoccupied molecular orbital matches the experimental electron affinity in the gas phase worsens both the interface dipole and the density of states. Our results imply that semi-local DFT calculations may often be adequate for conjugated organic molecules on metal surfaces and that the much more computationally demanding hybrid functionals yield only small improvements.

  1. Rational design of charge transport molecules for blue organic light emitting devices

    NASA Astrophysics Data System (ADS)

    Padmaperuma, Asanga; Cosimbescu, Lelia; Koech, Phillip; Polikarpov, Evgueni; Swensen, James; Gaspar, Daniel

    2012-02-01

    The efficiency and stability of blue OLEDs continue to be the primary roadblock to developing organic solid-state white lighting as well as power efficient displays. It is generally accepted that such high quantum efficiency can be achieved with the use of organometallic phosphor doped OLEDs. The transport layers can be designed to increase the carrier density as a way to reduce the drive voltage. We have developed a comprehensive library of charge transporting molecules using combination of theoretical modeling and experimental evidence. Our work focuses on using chemical structure design and computational methods to develop host, transport, emitter, and blocking materials for high efficiency blue OLEDs, along with device architectures to take advantage of these new materials. Through chemical modification of materials we are able to influence both the charge balance and emission efficiency of OLEDs, and understand the influence of the location of photon emission in OLEDs as a function of minor chemical modifications of host and electron transport materials. Design rules, structure-property relationships and results from state of the art OLEDs will be presented.

  2. Molecules in Focus: Collagen XII: Protecting bone and muscle integrity by organizing collagen fibrils

    PubMed Central

    Chiquet, Matthias; Birk, David E.; Bönnemann, Carsten G.; Koch, Manuel

    2014-01-01

    Collagen XII, largest member of the fibril-associated collagens with interrupted triple helix (FACIT) family, assembles from three identical α-chains encoded by the COL12A1 gene. The molecule consists of three threadlike N-terminal noncollagenous NC3 domains, joined by disulfide bonds and a short interrupted collagen triple helix towards the C-terminus. Splice variants differ considerably in size and properties: "small" collagen XIIB (220 kDa subunit) is similar to collagen XIV, whereas collagen XIIA (350 kDa) has a much larger NC3 domain carrying glycosaminoglycan chains. Collagen XII binds to collagen I-containing fibrils via its collagenous domain, whereas its large noncollagenous arms interact with other matrix proteins such as tenascin-X. In dense connective tissues and bone, collagen XII is thought to regulate organization and mechanical properties of collagen fibril bundles. Accordingly, recent findings show that collagen XII mutations cause Ehlers-Danlos/myopathy overlap syndrome associated with skeletal abnormalities and muscle weakness in mice and humans. PMID:24801612

  3. Growing Ultra-flat Organic Films on Graphene with a Face-on Stacking via Moderate Molecule-Substrate Interaction

    PubMed Central

    Wang, Ti; Kafle, Tika R.; Kattel, Bhupal; Liu, Qingfeng; Wu, Judy; Chan, Wai-Lun

    2016-01-01

    The electronic properties of small molecule organic crystals depend heavily on the molecular orientation. For multi-layer organic photovoltaics, it is desirable for the molecules to have a face-on orientation in order to enhance the out-of-plane transport properties. However, it is challenging to grow well-ordered and smooth films with a face-on stacking on conventional substrates such as metals and oxides. In this work, metal-phthalocyanine molecules is used as a model system to demonstrate that two-dimensional crystals such as graphene can serve as a template for growing high quality, ultra-flat organic films with a face-on orientation. Furthermore, the molecule-substrate interaction is varied systematically from strong to weak interaction regime with the interaction strength characterized by ultrafast electron transfer measurements. We find that in order to achieve the optimum orientation and morphology, the molecule-substrate interaction needs to be strong enough to ensure a face-on stacking while it needs to be weak enough to avoid film roughening. PMID:27356623

  4. Growing Ultra-flat Organic Films on Graphene with a Face-on Stacking via Moderate Molecule-Substrate Interaction

    NASA Astrophysics Data System (ADS)

    Wang, Ti; Kafle, Tika R.; Kattel, Bhupal; Liu, Qingfeng; Wu, Judy; Chan, Wai-Lun

    2016-06-01

    The electronic properties of small molecule organic crystals depend heavily on the molecular orientation. For multi-layer organic photovoltaics, it is desirable for the molecules to have a face-on orientation in order to enhance the out-of-plane transport properties. However, it is challenging to grow well-ordered and smooth films with a face-on stacking on conventional substrates such as metals and oxides. In this work, metal-phthalocyanine molecules is used as a model system to demonstrate that two-dimensional crystals such as graphene can serve as a template for growing high quality, ultra-flat organic films with a face-on orientation. Furthermore, the molecule-substrate interaction is varied systematically from strong to weak interaction regime with the interaction strength characterized by ultrafast electron transfer measurements. We find that in order to achieve the optimum orientation and morphology, the molecule-substrate interaction needs to be strong enough to ensure a face-on stacking while it needs to be weak enough to avoid film roughening.

  5. Growing Ultra-flat Organic Films on Graphene with a Face-on Stacking via Moderate Molecule-Substrate Interaction.

    PubMed

    Wang, Ti; Kafle, Tika R; Kattel, Bhupal; Liu, Qingfeng; Wu, Judy; Chan, Wai-Lun

    2016-01-01

    The electronic properties of small molecule organic crystals depend heavily on the molecular orientation. For multi-layer organic photovoltaics, it is desirable for the molecules to have a face-on orientation in order to enhance the out-of-plane transport properties. However, it is challenging to grow well-ordered and smooth films with a face-on stacking on conventional substrates such as metals and oxides. In this work, metal-phthalocyanine molecules is used as a model system to demonstrate that two-dimensional crystals such as graphene can serve as a template for growing high quality, ultra-flat organic films with a face-on orientation. Furthermore, the molecule-substrate interaction is varied systematically from strong to weak interaction regime with the interaction strength characterized by ultrafast electron transfer measurements. We find that in order to achieve the optimum orientation and morphology, the molecule-substrate interaction needs to be strong enough to ensure a face-on stacking while it needs to be weak enough to avoid film roughening. PMID:27356623

  6. Spatial variability in the abundance, composition, and age of organic matter in surficial sediments of the East China Sea

    NASA Astrophysics Data System (ADS)

    Wu, Ying; Eglinton, Timothy; Yang, Liyang; Deng, Bing; Montluçon, Daniel; Zhang, Jing

    2013-12-01

    the sources and fate of organic matter (OM) sequestered in continental margin sediments is of importance because the mode and efficiency of OM burial impact the carbon cycle and the regulation of atmospheric CO2 over long time scales. We carried out molecular (lignin-derived phenols from CuO oxidation), elemental, isotopic (δ13C, Δ14C), and sedimentological (grain size and mineral surface area) analyses in order to examine spatial variability in the abundance, source, age of surface sediments of the East China Sea. Higher terrigenous organic matter values were found in the main accumulating areas of fluvial sediments, including the Changjiang (Yangtze) Estuary and Zhejiang-Fujian coastal zone. Isotopic and biomarker data suggest that the sedimentary OM in the inner shelf region was dominated by aged (Δ14C = -423 ± 42‰) but relatively lignin-rich OM (Λ = 0.94 ± 0.57 mg/100 mg OC) associated with fine-grained sediments, suggesting important contributions from soils. In contrast, samples from the outer shelf, while of similar age (Δ14 C = -450 ± 99‰), are lignin poor (Λ = 0.25 ± 0.14 mg/100 mg OC) and associated with coarse-grained material. Regional variation of lignin phenols and OM ages indicates that OM content is fundamentally controlled by hydrodynamic sorting (especially, sediment redistribution and winnowing) and in situ primary production. Selective sorption of acid to aldehyde in clay fraction also modified the ratios of lignin phenols. The burial of lignin in East China Sea is estimated to be relatively efficient, possibly as a consequence of terrigenous OM recalcitrance and/or relatively high sedimentation rates in the Changjiang Estuary and the adjacent Zhejing-Fujian mud belt.

  7. "Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants.

    PubMed

    Albertsen, Mads; McIlroy, Simon J; Stokholm-Bjerregaard, Mikkel; Karst, Søren M; Nielsen, Per H

    2016-01-01

    Enhanced biological phosphorus removal (EBPR) is widely used to remove phosphorus from wastewater. The process relies on polyphosphate accumulating organisms (PAOs) that are able to take up phosphorus in excess of what is needed for growth, whereby phosphorus can be removed from the wastewater by wasting the biomass. However, glycogen accumulating organisms (GAOs) may reduce the EBPR efficiency as they compete for substrates with PAOs, but do not store excessive amounts of polyphosphate. PAOs and GAOs are thought to be phylogenetically unrelated, with the model PAO being the betaproteobacterial "Candidatus Accumulibacter phosphatis" (Accumulibacter) and the model GAO being the gammaproteobacterial "Candidatus Competibacter phosphatis". Here, we report the discovery of a GAO from the genus Propionivibrio, which is closely related to Accumulibacter. Propionivibrio sp. are targeted by the canonical fluorescence in situ hybridization probes used to target Accumulibacter (PAOmix), but do not store excessive amounts of polyphosphate in situ. A laboratory scale reactor, operated to enrich for PAOs, surprisingly contained co-dominant populations of Propionivibrio and Accumulibacter. Metagenomic sequencing of multiple time-points enabled recovery of near complete population genomes from both genera. Annotation of the Propionivibrio genome confirmed their potential for the GAO phenotype and a basic metabolic model is proposed for their metabolism in the EBPR environment. Using newly designed fluorescence in situ hybridization (FISH) probes, analyses of full-scale EBPR plants revealed that Propionivibrio is a common member of the community, constituting up to 3% of the biovolume. To avoid overestimation of Accumulibacter abundance in situ, we recommend the use of the FISH probe PAO651 instead of the commonly applied PAOmix probe set. PMID:27458436

  8. “Candidatus Propionivibrio aalborgensis”: A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants

    PubMed Central

    Albertsen, Mads; McIlroy, Simon J.; Stokholm-Bjerregaard, Mikkel; Karst, Søren M.; Nielsen, Per H.

    2016-01-01

    Enhanced biological phosphorus removal (EBPR) is widely used to remove phosphorus from wastewater. The process relies on polyphosphate accumulating organisms (PAOs) that are able to take up phosphorus in excess of what is needed for growth, whereby phosphorus can be removed from the wastewater by wasting the biomass. However, glycogen accumulating organisms (GAOs) may reduce the EBPR efficiency as they compete for substrates with PAOs, but do not store excessive amounts of polyphosphate. PAOs and GAOs are thought to be phylogenetically unrelated, with the model PAO being the betaproteobacterial “Candidatus Accumulibacter phosphatis” (Accumulibacter) and the model GAO being the gammaproteobacterial “Candidatus Competibacter phosphatis”. Here, we report the discovery of a GAO from the genus Propionivibrio, which is closely related to Accumulibacter. Propionivibrio sp. are targeted by the canonical fluorescence in situ hybridization probes used to target Accumulibacter (PAOmix), but do not store excessive amounts of polyphosphate in situ. A laboratory scale reactor, operated to enrich for PAOs, surprisingly contained co-dominant populations of Propionivibrio and Accumulibacter. Metagenomic sequencing of multiple time-points enabled recovery of near complete population genomes from both genera. Annotation of the Propionivibrio genome confirmed their potential for the GAO phenotype and a basic metabolic model is proposed for their metabolism in the EBPR environment. Using newly designed fluorescence in situ hybridization (FISH) probes, analyses of full-scale EBPR plants revealed that Propionivibrio is a common member of the community, constituting up to 3% of the biovolume. To avoid overestimation of Accumulibacter abundance in situ, we recommend the use of the FISH probe PAO651 instead of the commonly applied PAOmix probe set. PMID:27458436

  9. Variability in the bulk composition and abundance of dissolved organic matter in the lower Mississippi and Pearl rivers

    NASA Astrophysics Data System (ADS)

    Duan, Shuiwang; Bianchi, Thomas S.; Shiller, Alan M.; Dria, Karl; Hatcher, Patrick G.; Carman, Kevin R.

    2007-06-01

    In this study, we examined the temporal and spatial variability of dissolved organic matter (DOM) abundance and composition in the lower Mississippi and Pearl rivers and effects of human and natural influences. In particular, we looked at bulk C/N ratio, stable isotopes (δ15N and δ13C) and 13C nuclear magnetic resonance (NMR) spectrometry of high molecular weight (HMW; 0.2 μm to 1 kDa) DOM. Monthly water samples were collected at one station in each river from August 2001 to 2003. Surveys of spatial variability of total dissolved organic carbon (DOC) and nitrogen (DON) were also conducted in June 2003, from 390 km downstream in the Mississippi River and from Jackson to Stennis Space Center in the Pearl River. Higher DOC (336-1170 μM), C/N ratio,% aromaticity, and more depleted δ15N (0.76-2.1‰) were observed in the Pearl than in the lower Mississippi River (223-380 μM, 4.7-11.5‰, respectively). DOC, C/N ratio, δ13C, δ15N, and % aromaticity of Pearl River HMW DOM were correlated with water discharge, which indicated a coupling between local soil inputs and regional precipitation events. Conversely, seasonal variability in the lower Mississippi River was more controlled by spatial variability of a larger integrative signal from the watershed as well as in situ DOM processing. Spatially, very little change occurred in total DOC in the downstream survey of the lower Mississippi River, compared to a decrease of 24% in the Pearl River. Differences in DOM between these two rivers were reflective of the Mississippi River having more extensive river processing of terrestrial DOM, more phytoplankton inputs, and greater anthropogenic perturbation than the Pearl River.

  10. The analysis of surface-adsorbed organic molecules by alkali-assisted MIES combined with UPS(He I)

    NASA Astrophysics Data System (ADS)

    Günster, J.; Ochs, D.; Dieckhoff, S.; Kempter, V.

    1996-12-01

    Metastable impact electron spectroscopy (MIES) in combination with UPS(He I) is applied to the study of s-triazine and triethoxytriazine molecules adsorbed on Si(100) either alone or in combination with cesium atoms. It is demonstrated that the presence of the Cs atoms facilitates the identification of the adsorbed species considerably. It is concluded that (i) non-dissociative adsorption of the studied organic molecules occurs whereby the basal rings of the molecules lie flat on the silicon surface, in accordance with previous studies by Bu and Lin, (ii) the binding of the molecules to the surface is mainly via the lone pair orbitals of the nitrogen in the ring, and (iii) s-triazine reacts strongly with oxygen which bonds to the carbon atoms of the triazine ring.

  11. Spin-polarization inversion at small organic molecule/Fe{sub 4}N interfaces: A first-principles study

    SciTech Connect

    Zhang, Qian; Mi, Wenbo

    2015-09-21

    We report the first-principles calculations on the electronic structure and simulation of the spin-polarized scan tunneling microscopy graphic of the small organic molecules (benzene, thiophene, and cyclopentadienyl)/Fe{sub 4}N interfaces. It is found that the plane of benzene and thiophene keeps parallel to Fe{sub 4}N surface, while that of cyclopentadienyl does not. For all the systems, the organic molecules bind strongly with Fe{sub 4}N. Due to the hybridization between molecule p{sub z} orbitals and d orbitals of Fe, i.e., Zener interaction, all the three systems realize the spin-polarization inversion, whereas the spatial spin-polarization inversion distribution shows different intensities influenced by the competition between the spin polarization of C p{sub z} and Fe d states.

  12. Very low temperature formaldehyde reactions and the build-up of organic molecules in comets and interstellar ices

    NASA Technical Reports Server (NTRS)

    Schutte, W. A.; Allamandola, L. J.; Sandford, S. A.

    1995-01-01

    We have investigated thermally promoted reactions of formaldehyde (H2CO) in very low temperature ices. No such reactions occurred in ices of pure formaldehyde. However, addition of trace amounts of ammonia (NH3) were sufficient to catalyze reactions at temperatures as low as 40 K. Similar reactions could take place in interstellar ices and in Comets and produce considerable amounts of organic molecules.

  13. A metal-organic framework constructed using a flexible tripodal ligand and tetranuclear copper cluster for sensing small molecules.

    PubMed

    Hou, Chaoyi; Bai, Yue-Ling; Bao, XiaoLi; Xu, Liangzhen; Lin, Rong-Guang; Zhu, Shourong; Fang, Jianhui; Xu, Jiaqiang

    2015-05-01

    A new porous metal-organic framework (MOF) {[Cu4(OH)2(tci)2(bpy)2]·11H2O} (1) based on a tetranuclear copper cluster with intracluster antiferromagnetic interactions was synthesized. Quartz crystal microbalance (QCM) sensor studies reveal sensitive and selective sensing for small molecules. PMID:25857286

  14. Introducing Bond-Line Organic Structures in High School Biology: An Activity that Incorporates Pleasant-Smelling Molecules

    ERIC Educational Resources Information Center

    Rios, Andro C.; French, Gerald

    2011-01-01

    Chemical education occurs in settings other than just the chemistry classroom. High school biology courses are frequently where students are introduced to organic molecules and their importance to cellular chemistry. However, structural representations are often intimidating because students have not been introduced to the language. As part of a…

  15. Impact of local compressive stress on the optical transitions of single organic dye molecules

    NASA Astrophysics Data System (ADS)

    Stöttinger, Sven; Hinze, Gerald; Diezemann, Gregor; Oesterling, Ingo; Müllen, Klaus; Basché, Thomas

    2014-03-01

    The ability to mechanically control the optical properties of individual molecules is a grand challenge in nanoscience and could enable the manipulation of chemical reactivity at the single-molecule level. In the past, light has been used to alter the emission wavelength of individual molecules or modulate the energy transfer quantum yield between them. Furthermore, tensile stress has been applied to study the force dependence of protein folding/unfolding and of the chemistry and photochemistry of single molecules, although in these mechanical experiments the strength of the weakest bond limits the amount of applicable force. Here, we show that compressive stress modifies the photophysical properties of individual dye molecules. We use an atomic force microscope tip to prod individual molecules adsorbed on a surface and follow the effect of the applied force on the electronic states of the molecule by fluorescence spectroscopy. Applying a localized compressive force on an isolated molecule induces a stress that is redistributed throughout the structure. Accordingly, we observe reversible spectral shifts and even shifts that persist after retracting the microscope tip, which we attribute to transitions to metastable states. Using quantum-mechanical calculations, we show that these photophysical changes can be associated with transitions among the different possible conformers of the adsorbed molecule.

  16. CO2 and C2H2 in cold nanodroplets of oxygenated organic molecules and water.

    PubMed

    Devlin, J Paul; Balcı, F Mine; Maşlakcı, Zafer; Uras-Aytemiz, Nevin

    2014-11-14

    Recent demonstrations of subsecond and microsecond timescales for formation of clathrate hydrate nanocrystals hint at future methods of control of environmental and industrial gases such as CO2 and methane. Combined results from cold-chamber and supersonic-nozzle [A. S. Bhabhe, "Experimental study of condensation and freezing in a supersonic nozzle," Ph.D. thesis (Ohio State University, 2012), Chap. 7] experiments indicate extremely rapid encagement of components of all-vapor pre-mixtures. The extreme rates are derived from (a) the all-vapor premixing of the gas-hydrate components and (b) catalytic activity of certain oxygenated organic large-cage guests. Premixing presents no obvious barrier to large-scale conditions of formation. Further, from sequential efforts of the groups of Trout and Buch, a credible defect-based model of the catalysis mechanism exists for guidance. Since the catalyst-generated defects are both mobile and abundant, it is often unnecessary for a high percentage of the cages to be occupied by a molecular catalyst. Droplets represent the liquid phase that bridges the premixed vapor and clathrate hydrate phases but few data exist for the droplets themselves. Here we describe a focused computational and FTIR spectroscopic effort to characterize the aerosol droplets of the all-vapor cold-chamber methodology. Computational data for CO2 and C2H2, hetero-dimerized with each of the organic catalysts and water, closely match spectroscopic redshift patterns in both magnitude and direction. Though vibrational frequency shifts are an order of magnitude greater for the acetylene stretch mode, both CO2 and C2H2 experience redshift values that increase from that for an 80% water-methanol solvent through the solvent series to approximately doubled values for tetrahydrofuran and trimethylene oxide (TMO) droplets. The TMO solvent properties extend to a 50 mol.% solution of CO2, more than an order of magnitude greater than for the water-methanol solvent mixture

  17. CO2 and C2H2 in cold nanodroplets of oxygenated organic molecules and water

    NASA Astrophysics Data System (ADS)

    Devlin, J. Paul; Balcı, F. Mine; Maşlakcı, Zafer; Uras-Aytemiz, Nevin

    2014-11-01

    Recent demonstrations of subsecond and microsecond timescales for formation of clathrate hydrate nanocrystals hint at future methods of control of environmental and industrial gases such as CO2 and methane. Combined results from cold-chamber and supersonic-nozzle [A. S. Bhabhe, "Experimental study of condensation and freezing in a supersonic nozzle," Ph.D. thesis (Ohio State University, 2012), Chap. 7] experiments indicate extremely rapid encagement of components of all-vapor pre-mixtures. The extreme rates are derived from (a) the all-vapor premixing of the gas-hydrate components and (b) catalytic activity of certain oxygenated organic large-cage guests. Premixing presents no obvious barrier to large-scale conditions of formation. Further, from sequential efforts of the groups of Trout and Buch, a credible defect-based model of the catalysis mechanism exists for guidance. Since the catalyst-generated defects are both mobile and abundant, it is often unnecessary for a high percentage of the cages to be occupied by a molecular catalyst. Droplets represent the liquid phase that bridges the premixed vapor and clathrate hydrate phases but few data exist for the droplets themselves. Here we describe a focused computational and FTIR spectroscopic effort to characterize the aerosol droplets of the all-vapor cold-chamber methodology. Computational data for CO2 and C2H2, hetero-dimerized with each of the organic catalysts and water, closely match spectroscopic redshift patterns in both magnitude and direction. Though vibrational frequency shifts are an order of magnitude greater for the acetylene stretch mode, both CO2 and C2H2 experience redshift values that increase from that for an 80% water-methanol solvent through the solvent series to approximately doubled values for tetrahydrofuran and trimethylene oxide (TMO) droplets. The TMO solvent properties extend to a 50 mol.% solution of CO2, more than an order of magnitude greater than for the water-methanol solvent mixture

  18. Differences in leukocyte differentiation molecule abundances on domestic sheep (Ovis aries) and bighorn sheep (Ovis canadensis) neutrophils identified by flow cytometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Abundance was assessed by utilizing a panel of cross-reactive monoclonal antibodies (mAbs) tested in this study. Characterization of multichannel autofluorescence of eosinophils permitted cell-type specific gating of granulocytes for quantification of LDMs on neutrophils and eosinophils by indirect,...

  19. Comprehensive approach to intrinsic charge carrier mobility in conjugated organic molecules, macromolecules, and supramolecular architectures.

    PubMed

    Saeki, Akinori; Koizumi, Yoshiko; Aida, Takuzo; Seki, Shu

    2012-08-21

    (-1) s(-1), based on a combination of flash-photolysis TRMC and transient absorption spectroscopy (TAS) measurements. Single-crystal rubrene showed an ambipolarity with anisotropic charge carrier transport along each crystal axis on the nanometer scale. Finally, we describe the charge carrier mobility of a self-assembled nanotube consisting of a large π-plane of hexabenzocoronene (HBC) partially appended with an electron acceptor. The local (intratubular) charge carrier mobility reached 3 cm(2) V(-1) s(-1) for the nanotubes that possessed well-ordered π-stacking, but it dropped to 0.7 cm(2) V(-1) s(-1) in regions that contained greater amounts of the electron acceptor because those molecules reduced the structural integrity of π-stacked HBC arrays. Interestingly, the long-range (intertubular) charge carrier mobility was on the order of 10(-4) cm(2) V(-1) s(-1) and monotonically decreased when the acceptor content was increased. These results suggest the importance of investigating charge carrier mobilities by frequency-dependent charge carrier motion for the development of more efficient organic electronic devices. PMID:22676381

  20. Unusual cocrystals made of a Schiff base metal complex and an organic molecule - Close-packing vs. hydrogen bond interactions

    NASA Astrophysics Data System (ADS)

    Buvaylo, Elena A.; Kokozay, Vladimir N.; Rubini, Katia; Vassilyeva, Olga Yu.; Skelton, Brian W.

    2014-08-01

    The mononuclear complexes [ML2]0 (M = Co, Ni, Zn; HL - Schiff base ligand formed in situ from 2-pyridinecarbaldehyde and anthranilic acid, AA) can efficiently interact with unreacted AA molecules to produce CoL2·AA·H2O (1), NiL2·AA·H2O (2) and ZnL2·AA·0.25CH3OH·0.5H2O (3) cocrystals. Compounds 1-3 have been obtained as single crystals and characterized by elemental analysis, IR spectroscopy, thermal analysis, and single-crystal X-ray diffraction techniques. The compounds crystallize in the triclinic space group P1‾, with 1 and 2 being isomorphous. Neutral ML2 molecules in 1-3 show no crystallographically imposed symmetry with the metal atoms octahedrally surrounded by two anionic ligands in a mer configuration. Of the two crystallographically distinct AA molecules, one molecule only is engaged in H-bonding N/Osbnd H⋯O interactions with ML2 units. The solid-state organization of the cocrystals is described as an insertion of the organic molecules between the layers of ML2 complexes as they occur in the reported native NiL2·H2O structure.

  1. Diamondoid Structure in a Metal-Organic Framework of Fe4 Single-Molecule Magnets.

    PubMed

    Rigamonti, Luca; Cotton, Carri; Nava, Andrea; Lang, Heinrich; Rüffer, Tobias; Perfetti, Mauro; Sorace, Lorenzo; Barra, Anne-Laure; Lan, Yanhua; Wernsdorfer, Wolfgang; Sessoli, Roberta; Cornia, Andrea

    2016-09-12

    A 3D metal-organic framework (MOF) having single-molecule magnet (SMM) linkers was prepared in crystalline form by using a tetrairon(III) complex functionalised with two divergent pyridyl groups, namely [Fe4 (pPy)2 (dpm)6 ] (1; H3 pPy=2-(hydroxymethyl)-2-(pyridin-4-yl)propane-1,3-diol, Hdpm=dipivaloylmethane). Reaction of 1 with silver(I) perchlorate afforded {[Fe4 (pPy)2 (dpm)6 ]2 Ag}ClO4 (2), which crystallises in a cubic face-centred lattice and exhibits two interlocked diamondoid networks. In 2, the SMMs act as linear ditopic synthons, and silver(I) ions as tetrahedral nodes coordinated by four pyridyl nitrogen atoms. The magnetic properties of 1 (S=5 and D≈-0.4 cm(-1) in the ground spin state) are largely preserved in 2, which shows slow magnetic relaxation with an anisotropy barrier of Ueff /kB =11.46(10) K in zero field and 14.25(8) K in an applied field of 1 kOe. However, crystal symmetry triggers highly noncollinear magnetic anisotropy contributions oriented at 109.47° from each other along the threefold axes of AgN4 tetrahedra, a unique scenario fully confirmed by a single-crystal cantilever torque magnetometry investigation. Magnetisation curves down to 0.03 K demonstrated the occurrence of a wide hysteresis loop when the magnetic field was swept along one of the four Ag-N bonds. By symmetry, the crystalline compound can then be persistently magnetised parallel or antiparallel to the four main diagonals of the unit cell, although the crystals have no overall second-order anisotropy. PMID:27356278

  2. Two-photon Photoemission of Organic Semiconductor Molecules on Ag(111)

    SciTech Connect

    Yang, Aram

    2008-05-01

    Angle- and time-resolved two-photon photoemission (2PPE) was used to study systems of organic semiconductors on Ag(111). The 2PPE studies focused on electronic behavior specific to interfaces and ultrathin films. Electron time dynamics and band dispersions were characterized for ultrathin films of a prototypical n-type planar aromatic hydrocarbon, PTCDA, and representatives from a family of p-type oligothiophenes.In PTCDA, electronic behavior was correlated with film morphology and growth modes. Within a fewmonolayers of the interface, image potential states and a LUMO+1 state were detected. The degree to which the LUMO+1 state exhibited a band mass less than a free electron mass depended on the crystallinity of the layer. Similarly, image potential states were measured to have free electron-like effective masses on ordered surfaces, and the effective masses increased with disorder within the thin film. Electron lifetimes were correlated with film growth modes, such that the lifetimes of electrons excited into systems created by layer-by-layer, amorphous film growth increased by orders of magnitude by only a few monolayers from the surface. Conversely, the decay dynamics of electrons in Stranski-Krastanov systems were limited by interaction with the exposed wetting layer, which limited the barrier to decay back into the metal.Oligothiophenes including monothiophene, quaterthiophene, and sexithiophene were deposited on Ag(111), and their electronic energy levels and effective masses were studied as a function of oligothiophene length. The energy gap between HOMO and LUMO decreased with increasing chain length, but effective mass was found to depend on domains from high- or low-temperature growth conditions rather than chain length. In addition, the geometry of the molecule on the surface, e.g., tilted or planar, substantially affected the electronic structure.

  3. Activation of carbon-hydrogen bonds in alkanes and other organic molecules using organotransition metal complexes

    SciTech Connect

    Bergman, R.G.

    1991-10-01

    We have recently begun to investigate the interaction of C-H activating iridium and rhodium complexes with functionalized organic molecules, to determine the effect of functional groups on the process, as well as to investigate the propensity of Ir and Rh to insert into C-H versus other types of X-H bonds. Recent experiments have demonstrated that xenon liquefied at -70{degrees}C and 10 atm pressure serves as an inert solvent for the C-H oxidative addition reaction. We have been able to prepare and isolate, for the first time, C-H oxidative addition products formed from high-melting solid substrates such as naphthalene, adamantane, and even cubane; the latter case represents the first observation of C-H oxidative addition at a tertiary C-H bond. Liquid xenon has also allowed us to carry out more conveniently the C-H oxidative addition reactions of low-boiling gases that are difficult to liquefy, such as methane. Recently we have also been able to carry out analogous studies in the gas phase. Under these conditions, ``naked`` rather than solvated Cp*Rh(CO) is formed, and this species reacts with cyclohexane at nearly gas-kinetic rates. Under the conditions, collision between Cp*Rh(CO) and cyclohexane is the slowest step in the overall C-H activation process. In contrast, in solution association of solvent with free Cp*Rh(CO) is so rapid that the step involving C-H bond cleavage in the coordinated alkane complex becomes rate-determining. 3 refs., 5 figs.

  4. Activation of carbon-hydrogen bonds in alkanes and other organic molecules using organotransition metal complexes

    SciTech Connect

    Bergman, R.G.

    1991-10-01

    We have recently begun to investigate the interaction of C-H activating iridium and rhodium complexes with functionalized organic molecules, to determine the effect of functional groups on the process, as well as to investigate the propensity of Ir and Rh to insert into C-H versus other types of X-H bonds. Recent experiments have demonstrated that xenon liquefied at -70{degrees}C and 10 atm pressure serves as an inert solvent for the C-H oxidative addition reaction. We have been able to prepare and isolate, for the first time, C-H oxidative addition products formed from high-melting solid substrates such as naphthalene, adamantane, and even cubane; the latter case represents the first observation of C-H oxidative addition at a tertiary C-H bond. Liquid xenon has also allowed us to carry out more conveniently the C-H oxidative addition reactions of low-boiling gases that are difficult to liquefy, such as methane. Recently we have also been able to carry out analogous studies in the gas phase. Under these conditions, naked'' rather than solvated Cp*Rh(CO) is formed, and this species reacts with cyclohexane at nearly gas-kinetic rates. Under the conditions, collision between Cp*Rh(CO) and cyclohexane is the slowest step in the overall C-H activation process. In contrast, in solution association of solvent with free Cp*Rh(CO) is so rapid that the step involving C-H bond cleavage in the coordinated alkane complex becomes rate-determining. 3 refs., 5 figs.

  5. Multiscale sensing of antibody-antigen interactions by organic transistors and single-molecule force spectroscopy.

    PubMed

    Casalini, Stefano; Dumitru, Andra C; Leonardi, Francesca; Bortolotti, Carlo A; Herruzo, Elena T; Campana, Alessandra; de Oliveira, Rafael F; Cramer, Tobias; Garcia, Ricardo; Biscarini, Fabio

    2015-05-26

    Antibody-antigen (Ab-Ag) recognition is the primary event at the basis of many biosensing platforms. In label-free biosensors, these events occurring at solid-liquid interfaces are complex and often difficult to control technologically across the smallest length scales down to the molecular scale. Here a molecular-scale technique, such as single-molecule force spectroscopy, is performed across areas of a real electrode functionalized for the immunodetection of an inflammatory cytokine, viz. interleukin-4 (IL4). The statistical analysis of force-distance curves allows us to quantify the probability, the characteristic length scales, the adhesion energy, and the time scales of specific recognition. These results enable us to rationalize the response of an electrolyte-gated organic field-effect transistor (EGOFET) operated as an IL4 immunosensor. Two different strategies for the immobilization of IL4 antibodies on the Au gate electrode have been compared: antibodies are bound to (i) a smooth film of His-tagged protein G (PG)/Au; (ii) a 6-aminohexanethiol (HSC6NH2) self-assembled monolayer on Au through glutaraldehyde. The most sensitive EGOFET (concentration minimum detection level down to 5 nM of IL4) is obtained with the first functionalization strategy. This result is correlated to the highest probability (30%) of specific binding events detected by force spectroscopy on Ab/PG/Au electrodes, compared to 10% probability on electrodes with the second functionalization. Specifically, this demonstrates that Ab/PG/Au yields the largest areal density of oriented antibodies available for recognition. More in general, this work shows that specific recognition events in multiscale biosensors can be assessed, quantified, and optimized by means of a nanoscale technique. PMID:25868724

  6. Polymeric biomaterials for nerve regeneration applications: From promoting cellular organization to the delivery of bioactive molecules

    NASA Astrophysics Data System (ADS)

    Delgado-Rivera, Roberto L.

    Thousands of new cases of injury to the central nervous system (CNS) occur each year in the USA and all over the world. However, despite recent advances, at present there is no cure for the resulting paraplegia or quadriplegia. This research is directed towards engineering biomaterial platforms to promote cellular organization at the surface of polymer scaffolds that will be conducive to proper regeneration of injured CNS. In addition, the formulation of a delivery system for neuroactive molecules using polymer-based materials will be evaluated to establish its potential to treat CNS disorders. Initial studies involved the chemical modification of an electrospun nonwoven matrix of nanofibers with fibroblast growth factor 2 (FGF-2). Nanofibers alone up-regulated FGF-2, albeit to a lesser extent than nanofibers covalently modified with FGF-2. These results underscore the importance of both surface topography and growth factor presentation on cellular function. Moreover, that FGF-2 modified nanofibrillar scaffolds may demonstrate utility in tissue engineering applications for replacement and regeneration of damaged tissue following CNS injury or disease. Subsequent research efforts focused on a novel micropatterning technique called microscale plasma-initiated patterning (microPIP). This patterning method uses a polydimethylsiloxane (PDMS) stamp to selectively protect regions of an underlying substrate from oxygen plasma treatment resulting in hydrophobic and hydrophilic regions. FGF-2 and laminin-1 were applied to an electrospun polyamide nanofibrillar matrix following plasma treatment. In this work it, was possible to demonstrate that textured surfaces, such as nanofibrillar scaffolds, can be micropatterned to provide external chemical cues for cellular organization. Finally, a microsphere system capable of encapsulating proteins while minimizing the mechanisms of protein degradation and providing a controlled release was investigated. Microspheres were comprised of

  7. Formation of Complex Organic molecules from Formaldehyde Chemistry in Cometary Ice Analogues

    NASA Astrophysics Data System (ADS)

    Duvernay, fabrice; Vinogradoff, Vassilissa; Danger, Grégoire; Theulé, Patrice; Chiavassa, Thierry

    2015-04-01

    There is convincing evidence that the formation of complex organic molecules occurred in a variety of astrophysical environments. Among them, precursors of biomolecules are of particular significance due to their exobiological implications. Hexamethylenetetramine (HMT, C6H12N4) and the polyoxymethylene (POM, -(CH2-O)n-) are of prime interest since they are supposed to be present in cometary environments. They are also ones of the main components of the organic residue formed from the warming of photolysed interstellar/cometary ice analogs. In this work, we study the warming of water-dominated cometary ice analogs containing formaldehyde (H2CO). Based on infrared and mass spectrometry measurements, and complemented by quantum chemical calculations, we report that NH2CH2OH, HOCH2OH, and POM are the only reaction products when the ice also contains NH3. The branching ratio between the three products strongly depends on the initial H2CO/NH3 concentration ratio. Moreover, the influence of the initial ice composition on the formation of POM oligomers (HO-(CH2O)n-H, n<5) as well as their thermal instability between 200 and 320 K are investigated. Finally, the implications of these results with respect to cometary nucleus chemistry and their impact on POM detection by the Rosetta mission are discussed. In addition, the mechanism for HMT formation in interstellar or cometary ice analogs containing H2CO, NH3, and HCOOH has been determined by combining laboratory experiments and DFT calculations. We show that HMT is thermally formed from H2CO and NH3 activated by HCOOH. Two intermediates has been unambiguously detected: NH2CH2OH and the trimer of CH2NH (1,3,5-triazinane, TMT). Unlike to what it was previously thought, HMT is not an indicator of ice photochemistry, but an indicator of thermal processing of ice. These results strengthen the hypothesis that HMT and its intermediates should be present in comets, where they may be detected with the COSAC or COSIMA instrument of

  8. Rapid heating experiments demonstrate the usefulness of organic molecules as an earthquake thermometer

    NASA Astrophysics Data System (ADS)

    Sheppard, R. E.; Polissar, P. J.; Savage, H. M.

    2012-12-01

    Measuring temperature rise due to an earthquake would elucidate the frictional characteristics of a fault during rapid slip. We developed a new paleothermometer for fault zones using the thermal maturity of organic compounds as a temperature proxy. The kinetics of these reactions are highly nonlinear, and previous experiments to constrain the kinetic parameters have only been accomplished on long time scales. We ran a series of rapid heating experiments designed to determine these parameters specifically on short time scales. Here, we focus on the kinetics of methylphenanthrenes, aromatic molecules whose pattern of methylation changes with thermal maturity. The MPI-1 thermal maturity index is a ratio of methylphenanthrene's refractory 2- and 3-methylphenanthrene isomers relative to the less stable 9- and 1-methylphenanthrene isomers, and thus increases with increasing temperature. Methylphenanthrenes are relevant to the study of fault heating as they are consistently found in faults exhumed from depths shallower than 4km. To address whether methylphenanthrenes react at earthquake rates, we conducted rapid hydrous pyrolysis experiments in a small stainless steel reactor with a carburized inner surface. For each experiment, the reactor was partially filled with water and Woodford Shale, an organic-rich, thermally immature quartzose claystone sampled in central Oklahoma. The reactor was heated for a range of times and temperatures using resistive heating coils. Temperature was controlled using an external thermocouple and a PID controller, while the temperature of the sample was recorded with an internal thermocouple. Steam pressure was monitored using a pressure transducer throughout the experiment. The expelled oil was extracted from the water contained in the reactor using a separatory funnel, and the shale fragments were crushed and extracted via sonication. Both the oil and the shale extractions were then separated using column chromatography. GCMS analysis shows

  9. Morphological study on small molecule acceptor-based organic solar cells with efficiencies beyond 7% (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Ma, Wei; Yan, He

    2015-10-01

    Despite the essential role of fullerenes in achieving best-performance organic solar cells (OSCs), fullerene acceptors have several drawbacks including poor light absorption, high-cost production and purification. For this reason, small molecule acceptor (SMA)-based OSCs have attracted much attention due to the easy tunability of electronic and optical properties of SMA materials. In this study, polymers with temperature dependent aggregation behaviors are combined with various small molecule acceptor materials, which lead to impressive power conversion efficiencies of up to 7.3%. The morphological and aggregation properties of the polymer:small molecule blends are studied in details. It is found that the temperature-dependent aggregation behavior of polymers allows for the processing of the polymer solutions at moderately elevated temperature, and more importantly, controlled aggregation and strong crystallization of the polymer during the film cooling and drying process. This results in a well-controlled and near-ideal polymer:small molecule morphology that is controlled by polymer aggregation during warm casting and thus insensitive to the choice of small molecules. As a result, several cases of highly efficient (PCE between 6-7.3%) SMA OSCs are achieved. The second part of this presentation will describe the morphology of a new small molecule acceptor with a unique 3D structure. The relationship between molecular structure and morphology is revealed.

  10. Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation

    PubMed Central

    García-Fraile, Paula; Benada, Oldrich; Cajthaml, Tomáš; Baldrian, Petr

    2015-01-01

    Understanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55T, which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55T include Bryocella elongata SN10T (95.4% identity), Acidicapsa ligni WH120T (95.2% identity), and Telmatobacter bradus TPB6017T (95.0% identity), revealing that strain S55T should be classified within the phylum Acidobacteria, subdivision 1. Strain S55T is a rod-like bacterium that grows at acidic pH (3 to 6). Its phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicate that strain S55T corresponds to a new genus within the phylum Acidobacteria; thus, we propose the name Terracidiphilus gabretensis gen. nov., sp. nov. (strain S55T = NBRC 111238T = CECT 8791T). This strain produces extracellular enzymes implicated in the degradation of plant-derived biopolymers. Moreover, analysis of the genome sequence of strain S55T also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55T being expressed in the forest soil, especially during winter. Our results suggest an important contribution of T. gabretensis S55T in the carbon cycle in the Picea abies coniferous forest. PMID:26546425

  11. Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation.

    PubMed

    García-Fraile, Paula; Benada, Oldrich; Cajthaml, Tomáš; Baldrian, Petr; Lladó, Salvador

    2016-01-01

    Understanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55(T), which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55(T) include Bryocella elongata SN10(T) (95.4% identity), Acidicapsa ligni WH120(T) (95.2% identity), and Telmatobacter bradus TPB6017(T) (95.0% identity), revealing that strain S55(T) should be classified within the phylum Acidobacteria, subdivision 1. Strain S55(T) is a rod-like bacterium that grows at acidic pH (3 to 6). Its phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicate that strain S55(T) corresponds to a new genus within the phylum Acidobacteria; thus, we propose the name Terracidiphilus gabretensis gen. nov., sp. nov. (strain S55(T) = NBRC 111238(T) = CECT 8791(T)). This strain produces extracellular enzymes implicated in the degradation of plant-derived biopolymers. Moreover, analysis of the genome sequence of strain S55(T) also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55(T) being expressed in the forest soil, especially during winter. Our results suggest an important contribution of T. gabretensis S55(T) in the carbon cycle in the Picea abies coniferous forest. PMID:26546425

  12. Exploiting single photon vacuum ultraviolet photoionization to unravel the synthesis of complex organic molecules in interstellar ices

    NASA Astrophysics Data System (ADS)

    Abplanalp, Matthew J.; Förstel, Marko; Kaiser, Ralf I.

    2016-01-01

    Complex organic molecules (COM) such as aldehydes, ketones, carboxylic acids, esters, and amides are ubiquitous in the interstellar medium, but traditional gas phase astrochemical models cannot explain their formation routes. By systematically exploiting on line and in situ vacuum ultraviolet photoionization coupled with reflectron time of flight mass spectrometry (PI-ReTOF-MS) and combining these data with infrared spectroscopy (FTIR), we reveal that complex organic molecules can be synthesized within interstellar ices that are condensed on interstellar grains via non-equilibrium reactions involving suprathermal hydrogen atoms at temperatures as low as 5 K. By probing for the first time specific structural isomers without their degradation (fragment-free), the incorporation of tunable vacuum ultraviolet photoionization allows for a much greater understanding of reaction mechanisms that exist in interstellar ices compared to traditional methods, thus eliminating the significant gap between observational and laboratory data that existed for the last decades. With the commission of the Atacama Large Millimeter/Submillimeter Array (ALMA), the number of detections of more complex organic molecules in space will continue to grow - including biorelevant molecules connected to the Origins of Life theme - and an understanding of these data will rely on future advances in sophisticated physical chemistry laboratory experiments.

  13. Searching for amino-acid homochirality on Mars with the Mars Organic Molecule Analyzer (MOMA) onboard ExoMars

    NASA Astrophysics Data System (ADS)

    Buch, A.; Freissinet, C.; Sternberg, R.; Brault, A.; Szopa, C.; Claude-Geffroy, C.; Coll, P. J.; Grand, N.; Raulin, F.; Pinick, V.; Goesmann, F.

    2012-12-01

    The joint ESA-Roscosmos Exo-Mars-2018 rover mission plans to seek the signs of a past or a present life on Mars. The Mars Organic Molecule Analyzer (MOMA) experiment onboard theExoMars rover will be a key analytical tool in providing molecular information from Mars solid samples, with a specific focus on the characterization of their organic content. In this purpose, one of MOMA's main instruments is a gas chromatograph-mass spectrometer (GC-MS), which provides a unique ability to characterize a broad range of compounds and allow chemical analyses on volatile and refractory species. The challenge with the analysis of this refractory matter embedded in soil is their primary extraction before their analysis by GC-MS. Since the extraction of organic matter is not possible by liquid solvent extraction, we have developed a method based on the thermodesorption and subsequent derivatization of the organic molecules. The goal of the thermodesorption is to extract the organic matter by heating the sample quickly enough not to degrade its organic content. One of the main focuses is to determine the chirality of this organic matter, notably amino acids. Indeed, on Earth, homochirality of molecules is an indicator for the presence of life. Amino acids appear to bear only the left-handed form (L) in living system. However, other refractory compounds can raise interest: nucleobases, carboxylic acids and PAHs are among molecules supported by life as we know it, and all of them can display chirality. The intrinsic chirality of molecules being thermosensitive, the thermodesorption parameters have been adjusted to occur within a range of temperatures from 150 °C to 300 °C over a period of 30 s to 10 min, depending on the chemical compound. Under these conditions, we have shown that amino acids are not degraded and that their chirality is preserved. Once extracted, refractory molecules with labile hydrogens (e.g. amino acids, nucleobases, carboxylic acids, etc.) are derivatized

  14. Interstellar PAH analogs in the laboratory: A step toward the identification and the quantification of organic molecules in space

    NASA Astrophysics Data System (ADS)

    Biennier, L.; Salama, F.; Gupta, M.; O'Keefe, A.

    In spite of recent progress in our understanding of the organic component of interstellar dust, little has been revealed about the identification and the quantification of large organic molecules in space (e.g., column densities of specific molecular species, physical and chemical processes of formation and destruction, etc...). Experimental studies of "true" cosmic organic analogs are essential to address theses issues. In our laboratory, we have developed a dedicated chamber to generate species under space-like conditions (i.e., free, cold, neutral and ionized species). The chamber is combined with a powerful state-of-the-art instrument to characterize the spectral fingerprints of these molecular species. Polycylic Aromatic Hydrocarbon (PAH) molecules are the precursors/building blocks of complex organic molecules and have been the first targets studied using this innovative approach. Our measurements provide data that can now be directly compared to astronomical spectra of the interstellar (IS) extinction curve and of the diffuse interstellar bands (DIBs), both tracers of cosmic organics. The harsh physical conditions of the diffuse IS medium - characterized by a low temperature, an absence of collisions and strong VUV radiation fields - are simulated in the laboratory by associating a free jet expansion with an ionizing discharge that altogether generate a cold plasma expansion in the chamber. The spectra of these organics are measured using two complementary high sensitivity techniques: Cavity Ring Down Spectroscopy (CRDS) and Multiplex Integrated Cavity Output Spectroscopy (MICOS). These two techniques have been applied to the measurement of the electronic spectrum of a set of representative PAHs such as the cold Naphthalene (C10H_8}) cation, neutral Methylnaphthalene (C11H10}), neutral and ionized Acenaphtene (C12H10), neutral Phenanthrene (C14H10), and neutral and ionized Pyrene (C16H10). These experiments provide unique information on the spectra of free

  15. Increased superconducting transition temperature of a niobium thin film proximity coupled to gold nanoparticles using linking organic molecules.

    PubMed

    Katzir, Eran; Yochelis, Shira; Zeides, Felix; Katz, Nadav; Kalcheim, Yaov; Millo, Oded; Leitus, Gregory; Myasodeyov, Yuri; Shapiro, Boris Ya; Naaman, Ron; Paltiel, Yossi

    2012-03-01

    The superconducting critical temperature, T(C), of thin Nb films is significantly modified when gold nanoparticles (NPs) are chemically linked to the Nb film, with a consistent enhancement when using 3 nm long disilane linker molecules. The T(C) increases by up to 10% for certain linker length and NP size. No change is observed when the nanoparticles are physisorbed with nonlinking molecules. Electron tunneling spectra acquired on the linked NPs below T(C) typically exhibit zero-bias peaks. We attribute these results to a pairing mechanism coupling electrons in the Nb and the NPs, mediated by the organic linkers. PMID:22463444

  16. Organic Molecules and Network Polymers of Intrinsic Microporosity: Structural Characterization via X-ray Scattering and Simulations

    NASA Astrophysics Data System (ADS)

    McDermott, Amanda G.; Abbott, Lauren J.; Del Regno, Annalaura; Msayib, Kadhum J.; Ghanem, Bader S.; Taylor, Rupert; Carta, Mariolino; McKeown, Neil B.; Budd, Peter M.; Siperstein, Flor R.; Colina, Coray M.; Runt, James

    2011-03-01

    Like polymers of intrinsic microporosity (PIMs), organic molecules of intrinsic microporosity (OMIMs) are glassy solids featuring a large concentration of pores smaller than 2 nm and large internal surface area as measured by gas sorption experiments. OMIMs are oligomers designed to fill space inefficiently, consisting of several rigid segments joined at one vertex to produce concave faces. Both X-ray scattering patterns and simulations provide insight into the packing geometry and short-range order of these molecules. We also discuss the interpretation of scattering patterns from two- and three-dimensional network PIMs. Supported by NSF/Materials World Network/EPSRC and the NSF Graduate Research Fellowship Program.

  17. Adsorption of AN Organic Molecule on a Corrugated BN/Rh(111) "nanomesh":. Atomistic Simulation Using Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Gomez Diaz, J.; Seitsonen, A. P.; Iannuzzi, M.; Hutter, J.

    2013-05-01

    We perform modelling of the organic hexa-iodo-cyclohexa-m-phenylene (CHP) molecule on the h-BN/Rh(111) nanomesh [M Corso et al., Science 132, 217 (2004)]. The nanomesh structure consists of a Moiré pattern with a periodicity of 3.2 nm. It forms a template on which the molecules preferentially adsorb in the lower-lying "pores". We employ density functional theory in a slab geometry to investigate the adsorption and the abstraction of iodine atoms of the CHP on the nanomesh.

  18. Increased Superconducting Transition Temperature of a Niobium Thin Film Proximity Coupled to Gold Nanoparticles Using Linking Organic Molecules

    NASA Astrophysics Data System (ADS)

    Katzir, Eran; Yochelis, Shira; Zeides, Felix; Katz, Nadav; Kalcheim, Yaov; Millo, Oded; Leitus, Gregory; Myasodeyov, Yuri; Shapiro, Boris Ya.; Naaman, Ron; Paltiel, Yossi

    2012-03-01

    The superconducting critical temperature, TC, of thin Nb films is significantly modified when gold nanoparticles (NPs) are chemically linked to the Nb film, with a consistent enhancement when using 3 nm long disilane linker molecules. The TC increases by up to 10% for certain linker length and NP size. No change is observed when the nanoparticles are physisorbed with nonlinking molecules. Electron tunneling spectra acquired on the linked NPs below TC typically exhibit zero-bias peaks. We attribute these results to a pairing mechanism coupling electrons in the Nb and the NPs, mediated by the organic linkers.

  19. Lab-on-a-Chip Instrumentation and Method for Detecting Trace Organic and Bioorganic Molecules in Planetary Exploration: The Enceladus Organic Analyzer (EOA)

    NASA Astrophysics Data System (ADS)

    Butterworth, A.; Stockton, A. M.; Turin, P.; Ludlam, M.; Diaz-Aguado, M.; Kim, J.; Mathies, R. A.

    2015-12-01

    Lab-on-a-chip instrumentation is providing an ever more powerful in situ approach for detecting organic molecules relevant for chemical/biochemical evolution in our solar system obviating the cost, risk and long mission duration associated with sample return. Microfabricated analysis systems are particularly feasible when directly sampling from comet comae, or ejecta from icy moons, such as targeting organic molecules in plumes from Enceladus. Furthermore, the superb ppm to ppb sensitivity of chip analyzers, like the Enceladus Organic Analyzer (EOA), coupled with the ability to examine organics with a wide variety of functional groups enhance the probability of detecting organic molecules and determining whether they have a biological origin. The EOA is based on 20 years of research and development of microfabricated capillary electrophoresis (CE) analyzers at Berkeley that provide ppb sensitivity for a wide variety of organic molecules including amino acids, carboxylic acids, amines, aldehydes, ketones and polycyclic aromatic hydrocarbons [1]. Organic molecules are labeled with a fluorescent reagent according to their functional group in a programmable microfluidic processor [2,3] and then separated in a CE system followed by laser-induced fluorescence detection to determine molecular size and concentration. The EOA will be flown through Enceladus plumes and uses a specially designed impact plate/door to capture ice-particles. After closing the door, the material in the capture chamber is dissolved, labeled and analyzed by the microfabricated CE system. Only a few thousand 2 μm diameter particles containing ppm organic concentrations will provide an EOA detectable signal. If amino acids are detected, their chirality is determined because chirality is the best indicator of a biologically produced molecule. We have developed a flight design of this instrument for planetary exploration that is compact (16x16x12 cm), has low mass (3 kg), and requires very low power

  20. Combustion of Organic Molecules by the Thermal Decomposition of Perchlorate Salts: Implications for Organics at the Mars Phoenix Scout Landing Site

    NASA Technical Reports Server (NTRS)

    Ming, D.W.; Morris, R.V.; Niles, B.; Lauer, H.V.; Archer, P.D.; Sutter, B.; Boynton, W.V.; Golden, D.C.

    2009-01-01

    The Mars 2007 Phoenix Scout Mission successfully landed on May 25, 2008 and operated on the northern plains of Mars for 150 sols. The primary mission objective was to study the history of water and evaluate the potential for past and present habitability in Martian arctic ice-rich soil [1]. Phoenix landed near 68 N latitude on polygonal terrain created by ice layers that are a few centimeters under loose soil materials. The Phoenix Mission is assessing the potential for habitability by searching for organic molecules in the ice or icy soils at the landing site. Organic molecules are necessary building blocks for life, although their presence in the ice or soil does not indicate life itself. Phoenix searched for organic molecules by heating soil/ice samples in the Thermal and Evolved-Gas Analyzer (TEGA, [2]). TEGA consists of 8 differential scanning calorimeter (DSC) ovens integrated with a magnetic-sector mass spectrometer with a mass range of 2-140 daltons [2]. Endothermic and exothermic reactions are recorded by the TEGA DSC as samples are heated from ambient to 1000 C. Evolved gases, including any organic molecules and their fragments, are simultaneously measured by the mass spectrometer during heating. Phoenix TEGA data are still under analysis; however, no organic fragments have been identified to date in the evolved gas analysis (EGA). The MECA Wet Chemistry Lab (WCL) discovered a perchlorate salt in the Phoenix soils and a mass 32 peak evolved between 325 and 625 C for one surface sample dubbed Baby Bear [3]. The mass 32 peak is attributed to evolved O2 generated during the thermal decomposition of the perchlorate salt. Perchlorates are very strong oxidizers when heated, so it is possible that organic fragments evolved in the temperature range of 300-600 C were combusted by the O2 released during the thermal decomposition of the perchlorate salt. The byproduct of the combustion of organic molecules is CO2. There is a prominent release of CO2 between 200

  1. Molecular and structural characterization of dissolved organic matter from the deep ocean by FTICR-MS, including hydrophilic nitrogenous organic molecules

    USGS Publications Warehouse

    Reemtsma, T.; These, A.; Linscheid, M.; Leenheer, J.; Spitzy, A.

    2008-01-01

    Dissolved organic matter isolated from the deep Atlantic Ocean and fractionated into a so-called hydrophobic (HPO) fraction and a very hydrophilic (HPI) fraction was analyzed for the first time by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to resolve the molecular species, to determine their exact masses, and to calculate their molecular formulas. The elemental composition of about 300 molecules was identified. Those in the HPO fraction (14C age of 5100 year) are very similar to much younger freshwater fulvic acids, but less aromatic and more oxygenated molecules are more frequent. This trend continues toward the HPI fraction and may indicate biotic and abiotic aging processes that this material experienced since its primary production thousands of years ago. In the HPI fraction series of nitrogenous molecules containing one, two, or three nitrogens were identified by FTICR-MS. Product ion spectra of the nitrogenous molecules suggest that the nitrogen atoms in these molecules are included in the (alicyclic) backbone of these molecules, possibly in reduced form. These mass spectrometric data suggest that a large set of stable fulvic acids is ubiquitous in all aquatic compartments. Although sources may differ, their actual composition and structure appears to be quite similar and largely independent from their source, because they are the remainder of intensive oxidative degradation processes. ?? 2008 American Chemical Society.

  2. Unique organization of solvent molecules within the hexameric capsules of pyrogallol[4]arene in solution.

    PubMed

    Guralnik, Vicky; Avram, Liat; Cohen, Yoram

    2014-11-01

    The hexameric capsules of pyrogallol[4]arene (2b) were prepared in nondeuterated solvents in the absence and presence of adamantane carboxylic acid (3). The small encapsulated molecules were shown to occupy different sites within the same capsule. In the presence of 3, which are also encapsulated in the hexameric capsules, one observes yet another pair of signals for the encapsulated solvent molecules. Different NMR experiments enabled assignment of the different sites within the hexameric capsules of 2b. PMID:25337806

  3. Synchrotron-based soft X-ray spectroscopic studies of the electronic structure of organic semiconducting molecules

    NASA Astrophysics Data System (ADS)

    Demasi, Alexander

    Organic molecules have been the subject of many scientific studies due to their potential for use in a new generation of optoelectronic and semiconducting devices, such as organic photovoltaics and organic light emitting diodes. These studies are motivated by the fact that organic semiconductor devices have several advantages over traditional inorganic semiconductor devices. Unlike inorganic semiconductors, where the electronic properties are a result of the deliberate introduction of dopants to the material, the properties of organic semiconductors are often intrinsic to the molecules themselves. As a result, organic semiconductor devices are frequently less susceptible to contamination by impurities than their inorganic counterparts, which results in the relatively lower cost of producing such devices. Accurate experimental determination of the bulk and surface electronic structure of organic semiconductors is a prerequisite in developing a comprehensive understanding of such materials. The organic materials studied in this thesis were N,N-Ethylene-bis(1,1,1trifluoropentane-2,4-dioneiminato)-copper(ii) (abbreviated Cu-TFAC), aluminum tris-8hydroxyquinoline (A1g3), lithium quinolate (Liq), tetracyanoquinodimethane (TCNQ), and tetrafluorotetracyanoquinodimethane (F4TCNQ). The electronic structures of these materials were measured with several synchrotron-based x-ray spectroscopies. X-ray photoemission spectroscopy was used to measure the occupied total density of states and the core-level states of the aforementioned materials. X-ray absorption spectroscopy (XAS) was used to probe the element-specific unoccupied partial density of states (PDOS); its angle-resolved variant was used to measure the orientation of the molecules in a film and, in some circumstances, to gauge the extent of an organic film's crystallinity. Most notably, x-ray emission spectroscopy (XES) measures the element- specific occupied PDOS and, when aided by XAS, resonant XES can additionally be

  4. Formation, Detection and the Distribution of Complex Organic Molecules with the Atacama Large Millimeter/submillimeter Array (ALMA)

    NASA Astrophysics Data System (ADS)

    Remijan, Anthony John

    2015-08-01

    The formation and distribution of complex organic material in astronomical environments continues to be a focused research area in astrochemistry. For several decades now, emphasis has been placed on the millimeter/submillimeter regime of the radio spectrum for trying to detect new molecular species and to constrain the chemical formation route of complex molecules by comparing and contrasting their relative distributions towards varying astronomical environments. This effort has been extremely laborious as millimeter/submillimeter facilities have been only able to detect and map the distribution of the strongest transition(s) of the simplest organic molecules. Even then, these single transition "chemical maps" have been very low spatial resolution because early millimeter/submillimeter facilities did not have access to broadband spectral coverage or the imaging capabilities to truly ascertain the morphology of the molecular emission. In the era of ALMA, these limitations have been greatly lifted. Broadband spectral line surveys now hold the key to uncovering the full molecular complexity in astronomical environments. In addition, searches for complex organic material is no longer limited to investigating the strongest lines of the simplest molecules toward the strongest sources of emission in the Galaxy. ALMA is issuing a new era of exploration as the search for complex molecules will now be available to an increased suite of sources in the Galaxy and our understanding of the formation of this complex material will be greatly increased as a result. This presentation will highlight the current and future ALMA capabilities in the search for complex molecules towards astronomical environments, highlight the recent searches that ALMA scientists have conducted from the start of ALMA Early Science and provide the motivation for the next suite of astronomical searches to investigate our pre-biotic origins in the universe.

  5. Array formatting of the heat-transfer method (HTM) for the detection of small organic molecules by molecularly imprinted polymers.

    PubMed

    Wackers, Gideon; Vandenryt, Thijs; Cornelis, Peter; Kellens, Evelien; Thoelen, Ronald; De Ceuninck, Ward; Losada-Pérez, Patricia; van Grinsven, Bart; Peeters, Marloes; Wagner, Patrick

    2014-01-01

    In this work we present the first steps towards a molecularly imprinted polymer (MIP)-based biomimetic sensor array for the detection of small organic molecules via the heat-transfer method (HTM). HTM relies on the change in thermal resistance upon binding of the target molecule to the MIP-type receptor. A flow-through sensor cell was developed, which is segmented into four quadrants with a volume of 2.5 μL each, allowing four measurements to be done simultaneously on a single substrate. Verification measurements were conducted, in which all quadrants received a uniform treatment and all four channels exhibited a similar response. Subsequently, measurements were performed in quadrants, which were functionalized with different MIP particles. Each of these quadrants was exposed to the same buffer solution, spiked with different molecules, according to the MIP under analysis. With the flow cell design we could discriminate between similar small organic molecules and observed no significant cross-selectivity. Therefore, the MIP array sensor platform with HTM as a readout technique, has the potential to become a low-cost analysis tool for bioanalytical applications. PMID:24955945

  6. Mitigation of charged impurity effects in graphene field-effect transistors with polar organic molecules (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Worley, Barrett C.; Kim, Seohee; Akinwande, Deji; Rossky, Peter J.; Dodabalapur, Ananth

    2015-09-01

    Recent developments in monolayer graphene production allow its use as the active layer in field-effect transistor technology. Favorable electrical characteristics of monolayer graphene include high mobility, operating frequency, and good stability. These characteristics are governed by such key transport physical phenomena as electron-hole transport symmetry, Dirac point voltage, and charged impurity effects. Doping of graphene occurs during device fabrication, and is largely due to charged impurities located at or near the graphene/substrate interface. These impurities cause scattering of charge carriers, which lowers mobility. Such scattering is detrimental to graphene transistor performance, but our group has shown that coating with fluoropolymer thin films or exposure to polar organic vapors can restore favorable electrical characteristics to monolayer graphene. By partially neutralizing charged impurities and defects, we can improve the mobility by approximately a factor of 2, change the Dirac voltage by fairly large amounts, and reduce the residual carrier density significantly. We hypothesize that this phenomena results from screening of charged impurities by the polar molecules. To better understand such screening interactions, we performed computational chemistry experiments to observe interactions between polar organic molecules and monolayer graphene. The molecules interacted more strongly with defective graphene than with pristine graphene, and the electronic environment of graphene was altered. These computational observations correlate well with our experimental results to support our hypothesis that polar molecules can act to screen charged impurities on or near monolayer graphene. Such screening favorably mitigates charge scattering, improving graphene transistor performance.