Science.gov

Sample records for model gas-phase peptide

  1. Structural exploration and Förster theory modeling for the interpretation of gas-phase FRET measurements: Chromophore-grafted amyloid-β peptides

    NASA Astrophysics Data System (ADS)

    Kulesza, Alexander; Daly, Steven; MacAleese, Luke; Antoine, Rodolphe; Dugourd, Philippe

    2015-07-01

    The distance-dependence of excitation energy transfer, e.g., being described by Förster theory (Förster resonance energy transfer (FRET)), allows the use of optical techniques for the direct observation of structural properties. Recently, this technique has been successfully applied in the gas phase. The detailed interpretation of the experimental FRET results, however, relies on the comparison with structural modeling. We therefore present a complete first-principles modeling approach that explores the gas-phase structure of chromophore-grafted peptides and achieves accurate predictions of FRET efficiencies. We apply the approach to amyloid-β 12-28 fragments, known to be involved in amyloid plaque formation connected to Alzheimer's disease. We sample structures of the peptides that are grafted with 5-carboxyrhodamine 575 (Rh575) and QSY-7 chromophores by means of replica-exchange molecular dynamics simulations upon an Amber-type forcefield parametrization as a function of the charge state. The generated ensembles provide chromophore-distance and -orientation distributions which are used with the spectral parameters of the Rh575/QSY-7 chromophores to model FRET-efficiencies for the systems. The theoretical values agree with the experimental average "action"-FRET efficiencies and motivate to use the herein reported parametrization, sampling, and FRET-modeling technique in future studies on the structural properties and aggregation-behavior of related systems.

  2. Structural exploration and Förster theory modeling for the interpretation of gas-phase FRET measurements: Chromophore-grafted amyloid-β peptides.

    PubMed

    Kulesza, Alexander; Daly, Steven; MacAleese, Luke; Antoine, Rodolphe; Dugourd, Philippe

    2015-07-14

    The distance-dependence of excitation energy transfer, e.g., being described by Förster theory (Förster resonance energy transfer (FRET)), allows the use of optical techniques for the direct observation of structural properties. Recently, this technique has been successfully applied in the gas phase. The detailed interpretation of the experimental FRET results, however, relies on the comparison with structural modeling. We therefore present a complete first-principles modeling approach that explores the gas-phase structure of chromophore-grafted peptides and achieves accurate predictions of FRET efficiencies. We apply the approach to amyloid-β 12-28 fragments, known to be involved in amyloid plaque formation connected to Alzheimer's disease. We sample structures of the peptides that are grafted with 5-carboxyrhodamine 575 (Rh575) and QSY-7 chromophores by means of replica-exchange molecular dynamics simulations upon an Amber-type forcefield parametrization as a function of the charge state. The generated ensembles provide chromophore-distance and -orientation distributions which are used with the spectral parameters of the Rh575/QSY-7 chromophores to model FRET-efficiencies for the systems. The theoretical values agree with the experimental average "action"-FRET efficiencies and motivate to use the herein reported parametrization, sampling, and FRET-modeling technique in future studies on the structural properties and aggregation-behavior of related systems. PMID:26178129

  3. Theoretical Modeling of the Chirality Discrimination of Enantiomers by Nanotubular Cyclic Peptides using Gas-Phase Photoelectron Spectroscopy: An ONIOM Spectroscopic Calculations.

    PubMed

    Farrokhpour, H; Karachi, S; Chermahini, A Najafi

    2016-09-01

    In the present work, the chirality recognition of the enantiomers of a chiral molecule (1-phenyl-1-propanol) interacting with a nanotubular cyclic peptide (E-type cyclic decapeptide) was investigated by their ionization in the gas phase, theoretically. The absolute energy difference between the interaction of the S- and R-enantiomer with the cyclic peptide, calculated at the M06-2X/6-311++G(d, p) level of theory, was 4.70 kcal·mol(-1). Two different schemes of "Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM)" method such as (quantum mechanics (QM):molecular mechanics (MM)) and (QM:QM) were employed to study the effect of the interaction on the gas-phase ionization energies of the enantiomers and cyclic peptide, separately. The symmetry-adapted cluster/configuration interaction (SAC-CI) methodology was used for the calculation of the ionization energies. It was found that the difference between the interactions of R- and S-enantiomer with the cyclic peptide caused different changes in the photoelectron spectrum of each enantiomer so that these changes could be used for the chirality discrimination of the enantiomers in the gas phase. Similarly, the photoelectron spectrum of the cyclic peptide interacting with the R and S-enantiomer were calculated, separately, and it was observed that the difference in the interaction with the R- and S-enantiomer created different changes in the spectrum of cyclic peptide. Finally, it was shown that the difference in the interaction of cyclic peptide with the enantiomers of a chiral molecule in the gas phase can be used for the identification of enantiomers in the gas phase by the direct ionization. PMID:27500312

  4. Solution Versus Gas-Phase Modification of Peptide Cations with NHS-Ester Reagents

    NASA Astrophysics Data System (ADS)

    Mentinova, Marija; Barefoot, Nathan Z.; McLuckey, Scott A.

    2012-02-01

    A comparison between solution and gas phase modification of primary amine sites in model peptide cations with N-hydroxysuccinimide (NHS) ester reagents is presented. In all peptides, the site of modification in solution was directed to the N-terminus by conducting reactions at pH = 5, whereas for the same peptides, a lysine residue was preferentially modified in the gas phase. The difference in pKa values of the N-terminus and ɛ-amino group of the lysine allows for a degree of control over sites of protonation of the peptides in aqueous solution. With removal of the dielectric and multiple charging of the peptide ions in the gas phase, the accommodation of excess charge can affect the preferred sites of reaction. Interaction of the lone pair of the primary nitrogen with a proton reduces its nucleophilicity and, as a result, its reactivity towards NHS-esters. While no evidence for reaction of the N-terminus with sulfo-NHS-acetate was noted in the model peptide cations, a charge inversion experiment using bis[sulfosuccinimidyl] suberate, a cross-linking reagent with two sulfo-NHS-ester functionalities, showed modification of the N-terminus. Hence, an unprotonated N-terminus can serve as a nucleophile to displace NHS, which suggests that its lack of reactivity with the peptide cations is likely due to the participation of the N-terminus in solvating excess charge.

  5. Metal-ligand redox reactions in gas-phase quaternary peptide-metal complexes by electrospray ionization mass spectrometry

    NASA Astrophysics Data System (ADS)

    Vaisar, T.; Gatlin, C. L.; Turecek, F.

    1997-03-01

    The dipeptides Phe-Leu, Leu-Phe, Leu-Ala, and Ala-Leu form quaternary complexes of the type [Cu(II)(peptide - 2H+M)bpy]+ in the gas phase when electrosprayed in the presence of Cu(II) salts, 2.2'-bipyridyl (bpy), and an alkali hydroxide (MOH). The gas-phase complexes decarboxylate on collisional activation at low ion kinetic energies. The resulting ions undergo unusual eliminations of neutral Na, K, and Rb, which depend on the peptide structure. The ionization energy of the decarboxylated Phe-Leu-Cu-bpy complex was bracketed at 4.2 eV. Other collision-induced dissociations also depend on the alkali metal ion and the peptide structure. Ab initio calculations on a model system are reported and used to discuss the electronic properties of the peptide complexes.

  6. Gas-phase Ion Isomer Analysis Reveals the Mechanism of Peptide Sequence Scrambling

    PubMed Central

    Jia, Chenxi; Wu, Zhe; Lietz, Christopher B.; Liang, Zhidan; Cui, Qiang; Li, Lingjun

    2014-01-01

    Peptide sequence scrambling during mass spectrometry-based gas-phase fragmentation analysis causes misidentification of peptides and proteins. Thus, there is a need to develop an efficient approach to probing the gas-phase fragment ion isomers related to sequence scrambling and the underlying fragmentation mechanism, which will facilitate the development of bioinformatics algorithm for proteomics research. Herein, we report on the first use of electron transfer dissociation (ETD)-produced diagnostic fragment ions to probe the components of gas-phase peptide fragment ion isomers. In combination with ion mobility spectrometry (IMS) and formaldehyde labeling, this novel strategy enables qualitative and quantitative analysis of b-type fragment ion isomers. ETD fragmentation produced diagnostic fragment ions indicative of the precursor ion isomer components, and subsequent IMS analysis of b ion isomers provided their quantitative and structural information. The isomer components of three representative b ions (b9, b10, and b33 from three different peptides) were accurately profiled by this method. IMS analysis of the b9 ion isomers exhibited dynamic conversion among these structures. Furthermore, molecular dynamics simulation predicted theoretical drift time values which were in good agreement with experimentally measured values. Our results strongly support the mechanism of peptide sequence scrambling via b ion cyclization, and provide the first experimental evidence to support that the conversion from molecular precursor ion to cyclic b ion (M→cb) pathway is less energetically (or kinetically) favored. PMID:24313304

  7. Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler

    NASA Astrophysics Data System (ADS)

    Shaffer, Christopher J.; Andrikopoulos, Prokopis C.; Řezáč, Jan; Rulíšek, Lubomír; Tureček, František

    2016-04-01

    Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific 13C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)+ ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H]+ ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase.

  8. Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler.

    PubMed

    Shaffer, Christopher J; Andrikopoulos, Prokopis C; Řezáč, Jan; Rulíšek, Lubomír; Tureček, František

    2016-04-01

    Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific (13)C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)(+) ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H](+) ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase. Graphical Abstract ᅟ. PMID:26817657

  9. Influence of salt bridge interactions on the gas-phase stability of DNA/peptide complexes

    NASA Astrophysics Data System (ADS)

    Alves, Sandra; Woods, Amina; Delvolvé, Alice; Tabet, Jean Claude

    2008-12-01

    Negative ion mode electrospray ionization mass spectrometry was used to study DNA duplexes-peptide interaction. In the present study, we show that peptides that contain two adjacent basic residues interact noncovalently with DNA single strand or duplex. Fragmentation of the complexes between peptides containing basic residues and DNA were studied under collisions and showed unexpected dissociation pathways, as previously reported for peptide-peptide interactions. The binary complexes are dissociated either along fragmentation of the covalent bonds of the peptide backbone and/or along the single DNA strand backbone cleavage without disruption of noncovalent interaction, which demonstrates the strong binding of peptide to the DNA strand. Sequential MS/MS and MSn were further performed on ternary complexes formed between duplexes and peptides to investigate the nature of interaction. The CID spectra showed as major pathway the disruption of the noncovalent interactions and the formation of binary complexes and single-strand ions, directed by the nucleic acid gas-phase acidity. Indeed, a preferential formation of complexes with thymidine containing single strands is observed. An alternative pathway is also detected, in which complexes are dissociated along the covalent bond of the peptide and/or DNA according to the basicity. Our experimental data suggest the presence of strong salt bridge interactions between DNA and peptides containing basic residues.

  10. UV/Vis Action Spectroscopy and Structures of Tyrosine Peptide Cation Radicals in the Gas Phase.

    PubMed

    Viglino, Emilie; Shaffer, Christopher J; Tureček, František

    2016-06-20

    We report the first application of UV/Vis photodissociation action spectroscopy for the structure elucidation of tyrosine peptide cation radicals produced by oxidative intramolecular electron transfer in gas-phase metal complexes. Oxidation of Tyr-Ala-Ala-Ala-Arg (YAAAR) produces Tyr-O radicals by combined electron and proton transfer involving the phenol and carboxyl groups. Oxidation of Ala-Ala-Ala-Tyr-Arg (AAAYR) produces a mixture of cation radicals involving electron abstraction from the Tyr phenol ring and N-terminal amino group in combination with hydrogen-atom transfer from the Cα positions of the peptide backbone. PMID:27159034

  11. Molecular Dynamics Simulation for the Dynamics and Kinetics of Folding Peptides in the Gas Phase.

    PubMed

    Litinas, Iraklis; Koutselos, Andreas D

    2015-12-31

    The conformations of flexible molecular species, such as oligomers and oligopeptides, and their interconversion in the gas phase have been probed by ion mobility spectrometry measurements. The ion motion is interpreted through the calculation of effective cross sections in the case of stable conformations of the macromolecules. However, when the molecular structures transform to each other as the ions collide with gas atoms during their flight through the drift tube, the introduction of an average cross section is required. To provide a direct way for the reproduction of the ion motion, we employ a nonequilibrium molecular dynamics simulation method and consider a molecular model that consists of two connected stiff cylindrical bodies interacting through an intramolecular model potential. With this procedure we have calculated the ion mobility as a function of temperature for a prototype peptide that converts between a helical and an extended globular form. The results are in good agreement with ion mobility spectrometry data confirming that an angular vibration coordinate can be used for the interpretation of the shifting of the drift-time distributions at high temperatures. The approach produces mean kinetic energies as well as various combined distributions of the ion degrees of freedom. It is easily applied to flexible macromolecular ions and can be extended to include additional degrees of freedom. PMID:26641107

  12. Gas-phase diffusion in porous media: Comparison of models

    SciTech Connect

    Webb, S.W.

    1998-09-01

    Two models are commonly used to analyze gas-phase diffusion in porous media in the presence of advection, the Advective-Dispersive Model (ADM) and the Dusty-gas Model (DGM). The ADM, which is used in TOUGH2, is based on a simple linear addition of advection calculated by Darcy`s law and ordinary diffusion using Fick`s law with a porosity-tortuosity-gas saturation multiplier to account for the porous medium. Another approach for gas-phase transport in porous media is the Dusty-Gas Model. This model applies the kinetic theory of gases to the gaseous components and the porous media (or dust) to combine transport due to diffusion and advection that includes porous medium effects. The two approaches are compared in this paper.

  13. Native like helices in a specially designed β peptide in the gas phase.

    PubMed

    Schubert, Franziska; Pagel, Kevin; Rossi, Mariana; Warnke, Stephan; Salwiczek, Mario; Koksch, Beate; von Helden, Gert; Blum, Volker; Baldauf, Carsten; Scheffler, Matthias

    2015-02-21

    In the natural peptides, helices are stabilized by hydrogen bonds that point backward along the sequence direction. Until now, there is only little evidence for the existence of analogous structures in oligomers of conformationally unrestricted β amino acids. We specifically designed the β peptide Ac-(β(2)hAla)6-LysH(+) to form native like helical structures in the gas phase. The design follows the known properties of the peptide Ac-Ala6-LysH(+) that forms a α helix in isolation. We perform ion-mobility mass-spectrometry and vibrational spectroscopy in the gas phase, combined with state-of-the-art density-functional theory simulations of these molecular systems in order to characterize their structure. We can show that the straightforward exchange of alanine residues for the homologous β amino acids generates a system that is generally capable of adopting native like helices with backward oriented H-bonds. By pushing the limits of theory and experiments, we show that one cannot assign a single preferred structure type due to the densely populated energy landscape and present an interpretation of the data that suggests an equilibrium of three helical structures. PMID:25611682

  14. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation.

    PubMed

    Baldauf, Carsten; Rossi, Mariana

    2015-12-16

    The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field. PMID:26598600

  15. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation

    NASA Astrophysics Data System (ADS)

    Baldauf, Carsten; Rossi, Mariana

    2015-12-01

    The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.

  16. Hydrogen Attachment/Abstraction Dissociation (HAD) of Gas-Phase Peptide Ions for Tandem Mass Spectrometry.

    PubMed

    Takahashi, Hidenori; Sekiya, Sadanori; Nishikaze, Takashi; Kodera, Kei; Iwamoto, Shinichi; Wada, Motoi; Tanaka, Koichi

    2016-04-01

    Dissociation of gas-phase peptide ions through interaction with low-energy hydrogen (H) radical (∼0.15 eV) was observed with a quadrupole ion trap mass spectrometry. The H radical generated by thermal dissociation of H2 molecules passing through a heated tungsten capillary (∼2000 °C) was injected into the ion trap containing target peptide ions. The fragmentation spectrum showed abundant c-/z- and a-/x-type ions, attributable to H attachment/abstraction to/from peptide ion. Because the low-energy neutral H radical initiated the fragmentation, the charge state of the precursor ion was maintained during the dissociation. As a result, precursor ions of any charge state, including singly charged positive and negative ions, could be analyzed for amino acid sequence. The sequence coverage exceeding 90% was obtained for both singly protonated and singly deprotonated substance P peptide. This mass spectrometry also preserved labile post-translational modification bonds. The modification sites of triply phosphorylated peptide (kinase domain of insulin receptor) were identified with the sequence coverage exceeding 80%. PMID:27002918

  17. Multiscale Aspects of Modeling Gas-Phase Nanoparticle Synthesis

    PubMed Central

    Buesser, B.; Gröhn, A.J.

    2013-01-01

    Aerosol reactors are utilized to manufacture nanoparticles in industrially relevant quantities. The development, understanding and scale-up of aerosol reactors can be facilitated with models and computer simulations. This review aims to provide an overview of recent developments of models and simulations and discuss their interconnection in a multiscale approach. A short introduction of the various aerosol reactor types and gas-phase particle dynamics is presented as a background for the later discussion of the models and simulations. Models are presented with decreasing time and length scales in sections on continuum, mesoscale, molecular dynamics and quantum mechanics models. PMID:23729992

  18. Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features.

    PubMed

    Kopysov, Vladimir; Makarov, Alexander; Boyarkin, Oleg V

    2016-03-17

    Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by a combination of UV cold ion spectroscopy and high-resolution mass spectrometry, to identify the main conformers of gas-phase peptides and to recover individual UV absorption and mass spectra of all of these conformers in a single laser scan. We first validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S. The revealed characteristic structural difference between the conformers of the latter identifies some of the previously calculated structures of gramicidin S as the most likely geometries of its remaining unsolved conformer. PMID:26950179

  19. IRMPD Spectroscopy: Evidence of Hydrogen Bonding in the Gas Phase Conformations of Lasso Peptides and their Branched-Cyclic Topoisomers.

    PubMed

    Jeanne Dit Fouque, Kevin; Lavanant, Hélène; Zirah, Séverine; Steinmetz, Vincent; Rebuffat, Sylvie; Maître, Philippe; Afonso, Carlos

    2016-06-01

    Lasso peptides are natural products characterized by a mechanically interlocked topology. The conformation of lasso peptides has been probed in the gas phase using ion mobility-mass spectrometry (IM-MS) which showed differences in the lasso and their unthreaded branched-cyclic topoisomers depending on the ion charge states. To further characterize the evolution of gas phase conformations as a function of the charge state and to assess associated changes in the hydrogen bond network, infrared multiple photon dissociation (IRMPD) action spectroscopy was carried out on two representative lasso peptides, microcin J25 (MccJ25) and capistruin, and their branched-cyclic topoisomers. For the branched-cyclic topoisomers, spectroscopic evidence of a disruption of neutral hydrogen bonds were found when comparing the 3+ and 4+ charge states. In contrast, for the lasso peptides, the IRMPD spectra were found to be similar for the two charge states, suggesting very little difference in gas phase conformations upon addition of a proton. The IRMPD data were thus found consistent and complementary to IM-MS, confirming the stable and compact structure of lasso peptides in the gas phase. PMID:27171649

  20. Gas Phase Model of Surface Reactions for N{2} Afterglows

    NASA Astrophysics Data System (ADS)

    Marković, V. Lj.; Petrović, Z. Lj.; Pejović, M. M.

    1996-07-01

    The adequacy of the homogeneous gas phase model as a representation of the surface losses of diffusing active particles in gas phase is studied. As an example the recent data obtained for the surface recombination coefficients are reanalyzed. The data were obtained by the application of the breakdown delay times which consists of the measurements of the breakdown delay times t_d as a function of the afterglow period tau. It was found that for the conditions of our experiment, the diffusion should not be neglected as the final results are significantly different when obtained by approximate gas phase representation and by exact numerical solution to the diffusion equation. While application of the gas phase effective coefficients to represent surface losses gives an error in the value of the recombination coefficient, it reproduces correctly other characteristics such as order of the process which can be obtained from simple fits to the experimental data. Dans cet article, nous étudions la validité du modèle approximatif représentant les pertes superficielles des particules actives qui diffusent de la phase gazeuse comme pertes dans la phase homogène du gaz. Les données actuelles du coefficient de recombination en surface sont utilisées par cette vérification . Les données experimentales sont obtenues en utilisant la technique qui consiste en la mesure du temps de retard du début de la décharge en fonction de la période de relaxation. Nous avons trouvé que, pour nos conditions expérimentales, la diffusion ne peut être négligée. Aussi, les résultats finals sont considérablement différents quand ils sont obtenus en utilisant le modèle approximatif par comparaison aves les résultats obtenus par la solution numérique exacte de l'équation de la diffusion. L'application des coefficients effectifs dans la phase gaseuse pour la présentation des pertes superficielles donne, pour les coefficients de la recombinaison, des valeurs qui diffèrent en

  1. Gas-phase ion/ion reactions of peptides and proteins: acid/base, redox, and covalent chemistries

    PubMed Central

    Prentice, Boone M.

    2013-01-01

    Gas-phase ion/ion reactions are emerging as useful and flexible means for the manipulation and characterization of peptide and protein biopolymers. Acid/base-like chemical reactions (i.e., proton transfer reactions) and reduction/oxidation (redox) reactions (i.e., electron transfer reactions) represent relatively mature classes of gas-phase chemical reactions. Even so, especially in regards to redox chemistry, the widespread utility of these two types of chemistries is undergoing rapid growth and development. Additionally, a relatively new class of gas-phase ion/ion transformations is emerging which involves the selective formation of functional-group-specific covalent bonds. This feature details our current work and perspective on the developments and current capabilities of these three areas of ion/ion chemistry with an eye towards possible future directions of the field. PMID:23257901

  2. Determination of the gas-phase acidities of cysteine-polyalanine peptides using the extended kinetic method.

    PubMed

    Tan, John P; Ren, Jianhua

    2007-02-01

    We determined the gas-phase acidities of two cysteine-polyalanine peptides, HSCA3 and HSCA4, using a triple-quadrupole mass spectrometer through application of the extended kinetic method with full entropy analysis. Five halogenated carboxylic acids were used as the reference acids. The negatively charged proton-bound dimers of the deprotonated peptides with the conjugate bases of the reference acids were generated by electrospray ionization. Collision-induced dissociation (CID) experiments were carried out at three collision energies. The enthalpies of deprotonation (Delta(acid)H) of the peptides were derived according to the linear relationship between the logarithms of the CID product ion branching ratios and the differences of the gas-phase acidities. The values were determined to be Delta(acid)H(HSCA3) = 317.3 +/- 2.4 kcal/mol and Delta(acid)H (HSCA4) = 316.2 +/- 3.9 kcal/mol. Large entropy effects (Delta(DeltaS) = 13-16 cal/mol K) were observed for these systems. Combining the enthalpies of deprotonation with the entropy term yielded the apparent gas-phase acidities (Delta(acid)G(app)) of 322.1 +/- 2.4 kcal/mol (HSCA3) and 320.1 +/- 3.9 kcal/mol (HSCA4), in agreement with the results obtained from the CID-bracketing experiments. Compared with that in the isolated cysteine residue, the thiol group in HSCA3,4 has a stronger gas-phase acidity by about 20 kcal/mol. This increased acidity is likely due to the stabilization of the negatively charged thiolate group through internal solvation. PMID:17067812

  3. The gas-phase thermal chemistry of tetralin and related model systems

    SciTech Connect

    Malandra, J.

    1993-05-01

    The thesis is divided into 5 papers: gas-phase thermal decomposition of tetralin; flash vacuum pyrolysis of 3-benzocycloheptenone and 1,3, 4,5-tetrahydro-2-benzothiepin-2,2-dioxide (model systems for gas-phase pyrolysis of tetralin); high-temperature gas-phase reactions of o-allylbenzyl radicals generated by flash vacuum pyrolysis of is(o-allylbenzyl) oxalate; flash vacuum pyrolysis of 1,4-diphenylbutane; and flash vacuum pyrolysis of o-allyltoluene, o-(3-butenyl)toluene and o-(pentenyl)toluene were also used.

  4. Electron Transfer versus Proton Transfer in Gas-Phase Ion/Ion Reactions of Polyprotonated Peptides

    PubMed Central

    Gunawardena, Harsha P.; He, Min; Chrisman, Paul A.; Pitteri, Sharon J.; Hogan, Jason M.; Hodges, Brittany D. M.; McLuckey, Scott A.

    2005-01-01

    The ion/ion reactions of several dozen reagent anions with triply protonated cations of the model peptide KGAILKGAILR have been examined to evaluate predictions of a Landau–Zener-based model for the likelihood for electron transfer. Evidence for electron transfer was provided by the appearance of fragment ions unique to electron transfer or electron capture dissociation. Proton transfer and electron transfer are competitive processes for any combination of anionic and cationic reactants. For reagent anions in reactions with protonated peptides, proton transfer is usually significantly more exothermic than electron transfer. If charge transfer occurs at relatively long distances, electron transfer should, therefore, be favored on kinetic grounds because the reactant and product channels cross at greater distances, provided conditions are favorable for electron transfer at the crossing point. The results are consistent with a model based on Landau–Zener theory that indicates both thermodynamic and geometric criteria apply for electron transfer involving polyatomic anions. Both the model and the data suggest that electron affinities associated with the anionic reagents greater than about 60–70 kcal/mol minimize the likelihood that electron transfer will be observed. Provided the electron affinity is not too high, the Franck–Condon factors associated with the anion and its corresponding neutral must not be too low. When one or the other of these criteria is not met, proton transfer tends to occur essentially exclusively. Experiments involving ion/ion attachment products also suggest that a significant barrier exists to the isomerization between chemical complexes that, if formed, lead to either proton transfer or electron transfer. PMID:16144411

  5. Multiple gas-phase conformations of proline-containing peptides: is it always cis/trans isomerization?

    PubMed

    Lietz, Christopher B; Chen, Zhengwei; Yun Son, Chang; Pang, Xueqin; Cui, Qiang; Li, Lingjun

    2016-08-01

    Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structures of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental "signature" has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra is observed. Despite the high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y's wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross-sections of [M + 4H](4+) ions yields the cis/trans "signature", molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross-section arise with equal frequency. We believe that this work further underscores the importance of theoretical calculations in IM-MS structural assignments. PMID:27434776

  6. Fragmentation mechanism of UV-excited peptides in the gas phase

    SciTech Connect

    Zabuga, Aleksandra V. Kamrath, Michael Z.; Boyarkin, Oleg V.; Rizzo, Thomas R.

    2014-10-21

    We present evidence that following near-UV excitation, protonated tyrosine- or phenylalanine–containing peptides undergo intersystem crossing to produce a triplet species. This pathway competes with direct dissociation from the excited electronic state and with dissociation from the electronic ground state subsequent to internal conversion. We employ UV-IR double-resonance photofragment spectroscopy to record conformer-specific vibrational spectra of cold peptides pre-excited to their S{sub 1} electronic state. The absorption of tunable IR light by these electronically excited peptides leads to a drastic increase in fragmentation, selectively enhancing the loss of neutral phenylalanine or tyrosine side-chain, which are not the lowest dissociation channels in the ground electronic state. The recorded IR spectra evolve upon increasing the time delay between the UV and IR pulses, reflecting the dynamics of the intersystem crossing on a timescale of ∼80 ns and <10 ns for phenylalanine- and tyrosine-containing peptides, respectively. Once in the triplet state, phenylalanine-containing peptides may live for more than 100 ms, unless they absorb IR photons and undergo dissociation by the loss of an aromatic side-chain. We discuss the mechanism of this fragmentation channel and its possible implications for photofragment spectroscopy and peptide photostability.

  7. Electronic Relaxation of the Phenylalanine Residue in Gas Phase Peptides: Role of the Neighbouring Amide Groups in the Photophysics

    NASA Astrophysics Data System (ADS)

    Loquais, Y.; Biswal, H. S.; Tardivel, B.; Brenner, V.; Mons, M.; Gloaguen, E.; Jouvet, C.; Broquier, M.; Malis, M.; Ljubic, I.; Doslic, N.

    2012-06-01

    Protein absorption in the near UV is mainly due to the presence of aromatic systems on the side chain of three residues: phenylalanine, tryptophan and tyrosine. It is generally expected that the photophysics of these UV chromophores depends on their immediate environment within the molecule and thus on the conformation of these flexible molecules. This property may in particular be used as an optical diagnostic of the conformational state of the peptide chain. The structure of peptide chains isolated in the gas phase can be characterized by UV and IR laser spectroscopy. These measurements allow us to distinguish the spectral contributions of the different conformers and thus provide us with an elegant way to address the issue of the conformational dependence on the photophysics. For this purpose, the dynamics of relaxation of the ππ* excited state of several peptides containing a phenylalanine residue have been studied using two-colour resonant two-photon ionization (2C-R2PI) in the ns time scale at CEA and ps at CLUPS and laser-induced fluorescence as well. The lifetime of the ππ* excited state is found to strongly depend on the conformation adopted by the molecule and on the excess energy in the excited state, with measured lifetimes ranging from 1 ns to 80 ns. W. Chin; F. Piuzzi; I. Dimicoli and M. Mons, Phys. Chem. Chem. Phys., 8, pp 1033-1048 (2006)

  8. Gas-Phase Structure of Amyloid-β (12 - 28) Peptide Investigated by Infrared Spectroscopy, Electron Capture Dissociation and Ion Mobility Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Le, Thi Nga; Poully, Jean Christophe; Lecomte, Frédéric; Nieuwjaer, Nicolas; Manil, Bruno; Desfrançois, Charles; Chirot, Fabien; Lemoine, Jerome; Dugourd, Philippe; van der Rest, Guillaume; Grégoire, Gilles

    2013-12-01

    The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.

  9. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

    2014-06-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm-1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  10. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    PubMed Central

    Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

    2014-01-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm−1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides. PMID:24929378

  11. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    SciTech Connect

    Carr, J. K.; Roy, S.; Skinner, J. L.; Zabuga, A. V.; Rizzo, T. R.

    2014-06-14

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala){sub 5}-Lys-H{sup +} in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly {sup 13}C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and {sup 13}C{sup 18}O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm{sup −1} for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  12. Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study.

    PubMed

    Pepin, Robert; Petrone, Alessio; Laszlo, Kenneth J; Bush, Matthew F; Li, Xiaosong; Tureček, František

    2016-07-21

    Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections. PMID:27389035

  13. Conformations of Prolyl-Peptide Bonds in the Bradykinin 1-5 Fragment in Solution and in the Gas Phase.

    PubMed

    Voronina, Liudmila; Masson, Antoine; Kamrath, Michael; Schubert, Franziska; Clemmer, David; Baldauf, Carsten; Rizzo, Thomas

    2016-07-27

    The dynamic nature of intrinsically disordered peptides makes them a challenge to characterize by solution-phase techniques. In order to gain insight into the relation between the disordered state and the environment, we explore the conformational space of the N-terminal 1-5 fragment of bradykinin (BK[1-5](2+)) in the gas phase by combining drift tube ion mobility, cold-ion spectroscopy, and first-principles simulations. The ion-mobility distribution of BK[1-5](2+) consists of two well-separated peaks. We demonstrate that the conformations within the peak with larger cross-section are kinetically trapped, while the more compact peak contains low-energy structures. This is a result of cis-trans isomerization of the two prolyl-peptide bonds in BK[1-5](2+). Density-functional theory calculations reveal that the compact structures have two very different geometries with cis-trans and trans-cis backbone conformations. Using the experimental CCSs to guide the conformational search, we find that the kinetically trapped species have a trans-trans configuration. This is consistent with NMR measurements performed in a solution, which show that 82% of the molecules adopt a trans-trans configuration and behave as a random coil. PMID:27366919

  14. R vs. S fluoroproline ring substitution: trans/cis effects on the formation of b2 ions in gas-phase peptide fragmentation.

    PubMed

    Bernier, Matthew C; Chamot-Rooke, Julia; Wysocki, Vicki H

    2016-01-21

    The b2 structures of model systems Xxx-Flp-Ala (Flp = 4R-fluoroproline) and Xxx-flp-Ala (flp = 4S-fluoroproline) (where Xxx is Val or Tyr) were studied by action IRMPD spectroscopy. Proline ring substitutions influence the trans/cis isomerization of the precursor ion, resulting in different b2 fragment ion structures by collision induced dissociation. Vibrational spectra of the b2 ions of Val-Flp and Val-flp exhibit highly intense bands at ~1970 cm(-1), revealing that the dominant ion in each case is an oxazolone. The major difference between the spectra of b2 ions for R vs. S fluoroproline is a collection of peaks at 1690 and 1750 cm(-1), characteristic of a diketopiperazine structure, which were only present in the 4S-fluoroproline (flp) cases. This suggests only one b2 ion structure (oxazolone) is being formed for Flp-containing peptides, whereas flp-containing peptides produce a mixture of a dominant oxazolone with a lower population of diketopiperazine. In solution, Flp is known to possess a higher trans percentage in the N-terminally adjacent peptide bond, with flp inducing a greater proportion of the cis conformation. The diketopiperazine formation observed here correlates directly with the Ktrans/cis trend previously shown in solution, highlighting that the trans/cis isomerization likelihood for proline residues modified in the 4(th) position is retained in the gas-phase. PMID:26690386

  15. Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations

    NASA Astrophysics Data System (ADS)

    Pluhařová, Eva; Marsalek, Ondrej; Schmidt, Burkhard; Jungwirth, Pavel

    2012-11-01

    The salt bridge formation and stability in the terminated lysine-glutamate dipeptide is investigated in water clusters of increasing size up to the limit of bulk water. Proton transfer dynamics between the acidic and basic side chains is described by DFT-based Born-Oppenheimer molecular dynamics simulations. While the desolvated peptide prefers to be in its neutral state, already the addition of a single water molecule can trigger proton transfer from the glutamate side chain to the lysine side chain, leading to a zwitterionic salt bridge state. Upon adding more water molecules we find that stabilization of the zwitterionic state critically depends on the number of hydrogen bonds between side chain termini, the water molecules, and the peptidic backbone. Employing classical molecular dynamics simulations for larger clusters, we observed that the salt bridge is weakened upon additional hydration. Consequently, long-lived solvent shared ion pairs are observed for about 30 water molecules while solvent separated ion pairs are found when at least 40 or more water molecules hydrate the dipeptide. These results have implications for the formation and stability of salt bridges at partially dehydrated surfaces of aqueous proteins.

  16. Effect of the Basic Residue on the Energetics, Dynamics and Mechanisms of Gas- Phase Fragmentation of Protonated Peptides

    SciTech Connect

    Laskin, Julia; Yang, Zhibo; Song, Tao; Lam, Corey; Chu, Ivan K.

    2010-11-17

    The effect of the basic residue on the energetics, dynamics and mechanisms of backbone fragmentation of protonated peptides was investigated. Time- and collision energy-resolved surface-induced dissociation (SID) of singly protonated peptides with the N-terminal arginine residue and their analogs, in which arginine is replaced with less basic lysine and histidine residues was examined using in a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). SID experiments demonstrated very different kinetics of formation of several primary product ions of peptides with and without arginine residue. The energetics and dynamics of these pathways were determined from the RRKM modeling of the experimental data. Comparison between the kinetics and energetics of fragmentation of arginine-containing peptides and the corresponding methyl ester derivatives provides important information on the effect of dissociation pathways involving salt bridge (SB) intermediates on the observed fragmentation behavior. It is found that because pathways involving SB intermediates are characterized by low threshold energies, they efficiently compete with classical oxazolone pathways of arginine-containing peptides on a long timescale of the FT-ICR instrument. In contrast, fragmentation of histidine- and lysine-containing peptides is largely determined by classical oxazolone pathways. Because SB pathways are characterized by negative activation entropies, fragmentation of arginine-containing peptides is kinetically hindered and observed at higher collision energies as compared to their lysine- and histidine-containing analogs.

  17. CASCADER: An m-chain gas-phase radionuclide transport and fate model. [CASCADER Model

    SciTech Connect

    Lindstrom, F.T.; Cawlfield, D.E.; Emer, D.F.; Shott, G.J.; Donahue, M.E.

    1992-06-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes as they are advected and/or dispersed. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. CASCADER is a gas-phase, one space dimensional transport and fate model for an m-chain of radionuclides in very dry soil. This model contains barometric pressure-induced advection and diffusion together with linear irreversible and linear reversible sorption for each radionuclide. The advocation velocity is derived from an embedded air-pumping submodel. The airpumping submodel is based on an assumption of isothermal conditions and is barometric pressure driven. CASCADER allows the concentration of source radionuclides to decay via the classical Bateman chain of simple, first-order kinetic processes. The transported radionuclides also decay via first-order processes while in the soil. A mass conserving, flux-type inlet and exit set of boundary conditions is used. The user must supply the initial distribution for the parent radionuclide in the soil. The initial daughter distribution is found using equilibrium rules. The model is user friendly as it uses a prompt-driven, free-form input. The code is ANSI standard Fortran 77.

  18. Gas-phase reactivity and molecular modeling studies on triply protonated dodecapeptides that contain four basic residues.

    PubMed

    Cassady, C J

    1998-07-01

    Gas-phase deprotonation and hydrogen/deuterium (H/D) exchange reactions for ions from three model dodecapeptides were studied by Fourier transform ion cyclotron resonance mass spectrometry. Molecular dynamics calculations were employed to provide information on conformations and Coulomb energies. The peptides, (KGG)4, (K2G4)2, and K4G8, each contain four high basicity lysine residues and eight low basicity glycine residues; however, in the present work only three lysine residues were protonated. Proton transfer reactions with a series of reference amines revealed apparent gas-phase acidities in a narrow range of 207.3-209.6 kcal/mol, with deprotonation efficiencies following the order [K4G8 + 3H]3+ > [(KGG)4 + 3H]3+ > [(K2G4)2 + 3H]3+. The three ions also react similarly with d4-methanol: each exchanged a maximum of 23-25 of their 25 labile hydrogens, with the first 15-17 exchanges occurring at rate constants of (1.6-2.6) x 10(-11) cm3 molecule-1 s-1. The experimental results agree with molecular modeling findings of similar conformations and Coulomb energies for the three peptide ions. The [M + 3H]3+ data are compared to data obtained previously in our laboratory for the "fully" protonated [M + 4H]4+ (Zhang, X.; Ewing, N. P.; Cassady, C. J. Int. J. Mass Spectrom. Ion Phys., in press). For (KGG)4 and (K2G4)2, there is a marked difference in H/D exchange reactivity between 3+ ions and 4+ ions. The 4+ ions, which have diffuse conformations, slowly exchange only 14 hydrogens, whereas their more compact 3+ counterparts exchange 23-25 hydrogens at a 5-times greater rate. In contrast, the 3+ and 4+ ions of K4G8 have similar compact conformations and exchange reactivity. The results indicate that a multiply hydrogen-bonded intermediate between the deuterating reagent and the peptide ion is necessary for facile H/D exchange. The slower, incomplete H/D exchange of [(KGG)4 + 4H]4+ and [(K2G4)2 + 4H]4+ is attributed to the inability of their protonated lysine n

  19. CASCADER: An M-chain gas-phase radionuclide transport and fate model

    SciTech Connect

    Lindstrom, F.T.; Cawlfield, D.E.; Emer, D.F.; Shott, G.J.; Donahue, M.E.

    1993-02-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and diffusion. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. CASCADER is a gas-phase, one-space dimensional transport and fate model for M-chain radionuclides in very dry homogeneous or heterogeneous soil. This model contains barometric pressure-induced advection and diffusion together with linear irreversible and linear reversible sorption for each radionuclide. The advection velocity is derived from an embedded air-pumping submodel. The air-pumping submodel is based on an assumption of isothermal conditions, which is driven by barometric pressure. CASCADER allows the concentration of source radionuclides to decay via the classical Bateman chain of simple, first-order kinetic processes. The transported radionuclides also decay via first-order processes while in the soil. A mass conserving, flux-type inlet and exit set of boundary conditions are used. The user must supply the initial distribution for the parent radionuclide in the soil. The initial daughter distribution is found using equilibrium rules. The model is user friendly as it uses a prompt-driven, free-form input. The code is ANSI standard Fortran 77.

  20. The modeling of gas phase permeation through iron and nickel membranes

    NASA Technical Reports Server (NTRS)

    Kuhn, David K.; Shanabarger, Mickey R.

    1989-01-01

    The gas phase permeation of hydrogen through metal membranes encompasses many kinetic processes. This paper reviews a permeation model which incorporates second order gas-surface reaction kinetics with simple bulk diffusion. The model is used to investigate the effect of this particular surface reaction of steady-state permeation. The dependence of the steady-state permeation flux on temperature, pressure, and thickness of the membrane has been calculated. The model predicts that the bulk controlled steady-state flux will change to a surface limited steady-state flux as either the temperature or thickness of the membrane is reduced. Finally, using independently derived parameters, the model is compared with permeation measurements on iron and nickel membranes.

  1. Enantioselective Collision-Activated Dissociation of Gas-Phase Tryptophan Induced by Chiral Recognition of Protonated uc(l)-Alanine Peptides

    NASA Astrophysics Data System (ADS)

    Fujihara, Akimasa; Matsuyama, Hiroki; Tajiri, Michiko; Wada, Yoshinao; Hayakawa, Shigeo

    2016-06-01

    Enantioselective dissociation in the gas phase is important for enantiomeric enrichment and chiral transmission processes in molecular clouds regarding the origin of homochirality in biomolecules. Enantioselective collision-activated dissociation (CAD) of tryptophan (Trp) and the chiral recognition ability of uc(l)-alanine peptides (uc(l)-Ala n ; n = 2-4) were examined using a linear ion trap mass spectrometer. CAD spectra of gas-phase heterochiral H+(uc(d)-Trp)(uc(l)-Ala n ) and homochiral H+(uc(l)-Trp)(uc(l)-Ala n ) noncovalent complexes were obtained as a function of the peptide size n. The H2O-elimination product was observed in CAD spectra of both heterochiral and homochiral complexes for n = 2 and 4, and in homochiral H+(uc(l)-Trp)(uc(l)-Ala3), indicating that the proton is attached to the uc(l)-alanine peptide, and H2O loss occurs from H+(uc(l)-Ala n ) in the noncovalent complexes. H2O loss did not occur in heterochiral H+(uc(d)-Trp)(uc(l)-Ala3), where NH3 loss and (H2O + CO) loss were the primary dissociation pathways. In heterochiral H+(uc(d)-Trp)(uc(l)-Ala3), the protonation site is the amino group of uc(d)-Trp, and NH3 loss and (H2O + CO) loss occur from H+(uc(d)-Trp). uc(l)-Ala peptides recognize uc(d)-Trp through protonation of the amino group for peptide size n = 3. NH3 loss and (H2O + CO) loss from H+(uc(d)-Trp) proceeds via enantioselective CAD in gas-phase heterochiral H+(uc(d)-Trp)(uc(l)-Ala3) at room temperature, whereas uc(l)-Trp dissociation was not observed in homochiral H+(uc(l)-Trp)(uc(l)-Ala3). These results suggest that enantioselective dissociation induced by chiral recognition of uc(l)-Ala peptides through protonation could play an important role in enantiomeric enrichment and chiral transmission processes of amino acids.

  2. Simulation of a turbulent spray flame using coupled PDF gas phase and spray flamelet modeling

    SciTech Connect

    Ge, Hai-Wen; Gutheil, Eva

    2008-04-15

    A joint mixture fraction-enthalpy probability density function (PDF) is proposed for the simulation of turbulent spray flames. The PDF transport equation is deduced and modeled. The interaction-by-exchange-with-the-mean (IEM) model that has been developed for gas-phase flows is extended to describe molecular mixing in nonreactive and reactive spray flows. The joint PDF transport equation is solved by a hybrid finite-volume and Lagrangian Monte Carlo method. Standard spray and turbulence models are used to describe the gas phase and the liquid phase. A turbulent methanol/air spray flame is simulated using the present method. Detailed chemistry is implemented through the spray flamelet model. The precalculated spray flamelet library for methanol/air combustion comprises 23 species and 168 elementary reactions. Thus, the model is capable of predicting the formation of radicals and of pollutants. Different values for the model constant C{sub {phi}} in the IEM model are tested. The numerical results for the gas velocity, the gas temperature, and the mass fraction of methanol vapor are compared with experimental data in the literature. Good agreement with experiment is obtained when C{sub {phi}}=2.0. Marginal PDFs of mixture fraction, enthalpy, and gas temperature are presented. The computed PDFs of mixture fraction are compared with the presumed standard {beta} function and modified {beta} function. The results show that the standard {beta} function fails to reproduce bimodal shapes observed in transported PDF computation, while the modified {beta} function, fits the computed PDFs very well. Moreover, joint PDFs of mixture fraction and enthalpy are presented and analyzed. The enthalpy and mixture fraction are strongly correlated. The samples that deviate from the linear correlation are due to the energy consumption of local spray evaporation. (author)

  3. Electron Transfer Reduction of the Diazirine Ring in Gas-Phase Peptide Ions. On the Peculiar Loss of [NH4O] from Photoleucine

    NASA Astrophysics Data System (ADS)

    Marek, Aleš; Shaffer, Christopher J.; Pepin, Robert; Slováková, Kristina; Laszlo, Kenneth J.; Bush, Matthew F.; Tureček, František

    2015-03-01

    Electron transfer to gas-phase peptide ions with diazirine-containing amino acid residue photoleucine (L*) triggers diazirine ring reduction followed by cascades of residue-specific radical reactions. Upon electron transfer, substantial fractions of (GL*GGR +2H)+● cation-radicals undergo elimination of [NH4O] radicals and N2H2 molecules from the side chain. The side-chain dissociations are particularly prominent on collisional activation of long-lived (GL*GGR +2H)+● cation-radicals formed by electron transfer dissociation of noncovalent peptide-18-crown-6-ether ion complexes. The ion dissociation products were characterized by multistage tandem mass spectrometry (MSn) and ion mobility measurements. The elimination of [NH4O] was elucidated with the help of 2H, 15 N, and 18O-labeled peptide ions and found to specifically involve the amide oxygen of the N-terminal residue. The structures, energies, and electronic states of the peptide radical species were elucidated by a combination of near-UV photodissociation experiments and electron structure calculations combining ab initio and density functional theory methods. Electron transfer reaching the ground electronic states of charge reduced (GL*GGR +2H)+● cation-radicals was found to reduce the diazirine ring. In contrast, backbone N - Cα bond dissociations that represent a 60%-75% majority of all dissociations because of electron transfer are predicted to occur from excited electronic states.

  4. Measuring Uptake Coefficients and Henry's Law Constants of Gas-Phase Species with Models for Secondary Organic Aerosol

    NASA Astrophysics Data System (ADS)

    Fairhurst, M. C.; Waring-Kidd, C.; Ezell, M. J.; Finlayson-Pitts, B. J.

    2014-12-01

    Volatile organic compounds (VOC) are oxidized in the atmosphere and their products contribute to secondary organic aerosol (SOA) formation. These particles have been shown to have effects on visibility, climate, and human health. Current models typically under-predict SOA concentrations from field measurements. Underestimation of these concentrations could be a result of how models treat particle growth. It is often assumed that particles grow via instantaneous thermal equilibrium partitioning between liquid particles and gas-phase species. Recent work has shown that growth may be better represented by irreversible, kinetically limited uptake of gas-phase species onto more viscous, tar-like SOA. However, uptake coefficients for these processes are not known. The goal of this project is to measure uptake coefficients and solubilities for different gases onto models serving as proxies for SOA and determine how they vary based on the chemical composition of the gas and the condensed phase. Experiments were conducted using two approaches: attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy and a flow system coupled to a mass spectrometer. The ATR crystal was coated with the SOA proxy and the gas-phase species introduced via a custom flow system. Uptake of the gas-phase species was characterized by measuring the intensity of characteristic IR bands as a function of time, from which a Henry's law constant and initial estimate of uptake coefficients could be obtained. Uptake coefficients were also measured in a flow system where the walls of the flow tube were coated with the SOA proxy and gas-phase species introduced via a moveable inlet. Uptake coefficients were derived from the decay in gas-phase species measured by mass spectrometry. The results of this work will establish a structure-interaction relationship for uptake of gases into SOA that can be implemented into regional and global models.

  5. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization

    NASA Astrophysics Data System (ADS)

    Pepin, Robert; Laszlo, Kenneth J.; Marek, Aleš; Peng, Bo; Bush, Matthew F.; Lavanant, Helène; Afonso, Carlos; Tureček, František

    2016-07-01

    Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions.

  6. Modeled occupational exposures to gas-phase medical laser-generated air contaminants.

    PubMed

    Lippert, Julia F; Lacey, Steven E; Jones, Rachael M

    2014-01-01

    Exposure monitoring data indicate the potential for substantive exposure to laser-generated air contaminants (LGAC); however the diversity of medical lasers and their applications limit generalization from direct workplace monitoring. Emission rates of seven previously reported gas-phase constituents of medical laser-generated air contaminants (LGAC) were determined experimentally and used in a semi-empirical two-zone model to estimate a range of plausible occupational exposures to health care staff. Single-source emission rates were generated in an emission chamber as a one-compartment mass balance model at steady-state. Clinical facility parameters such as room size and ventilation rate were based on standard ventilation and environmental conditions required for a laser surgical facility in compliance with regulatory agencies. All input variables in the model including point source emission rates were varied over an appropriate distribution in a Monte Carlo simulation to generate a range of time-weighted average (TWA) concentrations in the near and far field zones of the room in a conservative approach inclusive of all contributing factors to inform future predictive models. The concentrations were assessed for risk and the highest values were shown to be at least three orders of magnitude lower than the relevant occupational exposure limits (OELs). Estimated values do not appear to present a significant exposure hazard within the conditions of our emission rate estimates. PMID:24762065

  7. An Unexpected Gas-Phase Binding Motif for Metal Dication Complexation with Peptides: Irmpd Spectroscopic Structure Determination

    NASA Astrophysics Data System (ADS)

    Dunbar, Robert C.; Steill, Jeffrey; Polfer, Nicolas; Berden, Giel; Oomens, Jos

    2011-06-01

    The favorable orientation of the amide linkage and the aromatic side chain of N-terminal Phe or Trp leads to several favorable motifs for metal ion binding to dipeptides, having distinct characteristics in the IR spectrum. Infrared multiple photon photodissociation spectroscopy using the FELIX free electron laser has enabled clear resolution of these isomeric forms. The spectral patterns of complexes of small dications (Mg2+, Ni2+ and Co2+) reveal an unexpected new isomeric form, in which the metal ion displaces the amide hydrogen, forming a metal-nitrogen bond with covalent character which is unprecedented in such gas-phase complexes. Spectra of the ions were acquired by irradiating the cell of the Fourier-transform ion cyclotron resonance mass spectrometer with infrared light from the FELIX laser at wavelengths in the approximate range 500 to 1900 Cm-1.

  8. Peptide bond formation through gas-phase reactions in the interstellar medium: formamide and acetamide as prototypes

    SciTech Connect

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

    2014-09-20

    A theoretical study of the reactions of NH{sub 4}{sup +} with formaldehyde and CH{sub 5}{sup +} with formamide is carried out. The viability of these gas-phase ion-molecule reactions as possible sources of formamide and acetamide under the conditions of interstellar medium is evaluated. We report a theoretical estimation of the reaction enthalpies and an analysis of their potential energy surfaces. Formation of protonated formamide from the reaction between ammonium cation and formaldehyde is an exothermic process, but all the channels located on the potential energy surface leading to this product present net activation energies. For the reaction between methanium and formamide, different products are possible from a thermodynamic point of view. An analysis of its potential energy surface showed that formation of protonated acetamide and amino acetaldehyde takes place through barrier-free paths. Therefore, this reaction could be a feasible source of acetamide and amino acetaldehyde in space.

  9. CHEMICAL TRANSFORMATION MODULES FOR EULERIAN ACID DEPOSITION MODELS. VOLUME 1. THE GAS-PHASE CHEMISTRY

    EPA Science Inventory

    This study focuses on the review and evaluation of mechanistic and kinetic data for the gas-phase reactions that lead to the production of acidic substances in the environment. A master mechanism is designed that treats oxides, sulfur dioxide, ozone, hydrogen peroxide, ammonia, t...

  10. Un-catalyzed peptide bond formation between two monomers of glycine, alanine, serine, threonine, and aspartic acid in gas phase: a density functional theory study

    NASA Astrophysics Data System (ADS)

    Bhunia, Snehasis; Singh, Ajeet; Ojha, Animesh K.

    2016-05-01

    In the present report, un-catalyzed peptide bond formation between two monomers of glycine (Gly), alanine (Ala), serine (Ser), threonine (Thr), and aspartic acid (Asp) has been investigated in gas phase via two steps reaction mechanism and concerted mechanism at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. The peptide bond is formed through a nucleophilic reaction via transition states, TS1 and TS2 in stepwise mechanism. The TS1 reveals formation of a new C-N bond while TS2 illustrate the formation of C=O bond. In case of concerted mechanism, C-N bond is formed by a single four-centre transition state (TS3). The energy barrier is used to explain the involvement of energy at each step of the reaction. The energy barrier (20-48 kcal/mol) is required for the transformation of reactant state R1 to TS1 state and intermediate state I1 to TS2 state. The large value of energy barrier is explained in terms of distortion and interaction energies for stepwise mechanism. The energy barrier of TS3 in concerted mechanism is very close to the energy barrier of the first transition state (TS1) of the stepwise mechanism for the formation of Gly-Gly and Ala-Ala di- peptide. However, in case of Ser-Ser, Thr-Thr and Asp-Asp di-peptide, the energy barrier of TS3 is relatively high than that of the energy barrier of TS1 calculated at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. In both the mechanisms, the value of energy barrier calculated at B3LYP/6-31G(d,p) level of theory is greater than that of the value calculated at M062X/6-31G(d,p) level of theory.

  11. Energetics and structural characterization of isomers using ion mobility and gas-phase H/D exchange: Learning from lasso peptides.

    PubMed

    Hanozin, Emeline; Morsa, Denis; De Pauw, Edwin

    2015-08-01

    State-of-the-art characterization of proteins using MS namely relies on fragmentation methods that allow exploring featured dissociative reaction pathways. These pathways are often initiated by a series of potentially informative mass-constant conformational changes that are nonetheless frequently overlooked by lack of adequate investigation techniques. In the present study, we propose a methodology to readily address both structural and energetic aspects of stereoisomerization reactions using ion mobility coupled with MS. To this end, a commercial spectrometer was used as a reactor comprising an energy resolved collisional activation step intended at promoting controlled conformational changes and a structural assignment step dedicated to the identification of the generated isomers. This identification relies on ion mobility and other on-line coupled techniques, namely an originally designed gas-phase H/D exchange experiment. We here apply this methodology to characterize the isomerization kinetics of capistruin, a 19-residue long lasso-folded peptide. We expect this approach to bring insights into the physical origin of global dissociation thresholds monitored in MS/MS experiments and to set a promising basis for quantitative investigations of the stability of different molecular folds. PMID:25821205

  12. Chemical models of interstellar gas-grain processes. II - The effect of grain-catalysed methane on gas phase evolution

    NASA Technical Reports Server (NTRS)

    Brown, Paul D.; Charnley, S. B.

    1991-01-01

    The effects on gas phase chemistry which result from the continuous desorption of methane molecules from grain surfaces are studied. Significant and sustained enhancements in the abundances of several complex hydrocarbon molecules are found, in good agreement with their observed values in TMC-1. The overall agreement is, however, just as good for the case of zero CH4 desorption efficiency. It is thus impossible to determine from the models whether or not the grain-surface production of methane is responsible for the observed abundances of some hydrocarbon molecules.

  13. CASCADER: An M-chain gas-phase radionuclide transport and fate model. Volume 4 -- Users guide to CASCADR9

    SciTech Connect

    Cawlfield, D.E.; Emer, D.F.; Lindstrom, F.T.; Shott, G.J.

    1993-09-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and/or dispersion. Additionally during the transport of parent and daughter radionuclides in soil, radionuclide decay may occur. This version of CASCADER called CASCADR9 starts with the concepts presented in volumes one and three of this series. For a proper understanding of how the model works, the reader should read volume one first. Also presented in this volume is a set of realistic scenarios for buried sources of radon gas, and the input and output file structure for CASCADER9.

  14. Investigating Differences in Isoprene Oxidation Chemistry Between Gas-Phase Mechanisms Using a Constrained Chemical Box Model

    NASA Astrophysics Data System (ADS)

    Marvin, M. R.; Wolfe, G. M.; Salawitch, R. J.; Canty, T. P.; Hanisco, T. F.; Kaiser, J.; Keutsch, F. N.; Graus, M.; Warneke, C.; De Gouw, J. A.; Gilman, J.; Lerner, B. M.; Peischl, J.; Veres, P. R.; Min, K. E.; Holloway, J. S.; Aikin, K. C.; Ryerson, T. B.; Roberts, J. M.; Brown, S. S.; Pollack, I. B.; Hatch, C. D.; Lee, B. H.; Lopez-Hilfiker, F.; Thornton, J. A.; Diskin, G. S.; Sachse, G. W.; Huey, L. G.; Liu, X.; Wisthaler, A.; Mikoviny, T.; Wennberg, P. O.; St Clair, J.; Crounse, J.; Teng, A.

    2015-12-01

    Oxidation of isoprene by OH can significantly influence concentrations of important atmospheric pollutants such as ozone and secondary organic aerosols, but the chemistry that describes the relationships between these species is complex and not fully understood. Debate on the topic has led to differences in the isoprene oxidation schemes of several gas-phase chemical mechanisms currently applied in air chemistry models. We use the University of Washington Chemical Model (UWCMv3) to evaluate these mechanisms with respect to isoprene chemistry based on observations from the SENEX and SEAC4RS aircraft campaigns. The campaigns provide constraints on compounds measured over the Southeast United States, where isoprene concentrations are high and other conditions (e.g., NOx levels) vary widely. The payloads for both missions include observations of a wide range of isoprene oxidation products, which can provide insight into specific oxidation pathways. Analysis will focus on the characterization and comparison of isoprene oxidation chemistry for established gas-phase mechanisms that are prevalent in atmospheric modeling today, including the Carbon Bond mechanism (CB05 and CB6r2) and the Master Chemical Mechanism (versions 3.2 and 3.3).

  15. CASCADER: An M-chain gas-phase radionuclide transport and fate model. Volume 3: Heterogeneous layered porous media

    SciTech Connect

    Lindstrom, F.T.; Cawlfield, D.E.; Emer, D.F.; Shott, G.J.; Donahue, M.E.

    1993-02-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and diffusion. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. CASCADER is a gas-phase, one-space dimensional transport and fate model for M-chain radionuclides in very dry homogeneous or heterogeneous soil. This model contains barometric pressure-induced advection and diffusion together with linear irreversible and linear reversible sorption for each radionuclide. The advection velocity is derived from an embedded air-pumping submodel. The air-pumping submodel is based on an assumption of isothermal conditions, which is driven by barometric pressure. CASCADER allows the concentration of source radionuclides to decay via the classical Bateman chain of simple, first-order kinetic processes. The transported radionuclides also decay via first-order processes while in the soil. A mass conserving, flux-type inlet and exit set of boundary conditions are used. The user must supply the initial distribution for the parent radionuclide in the soil. The initial daughter distribution is found using equilibrium rules. The model is user friendly as it uses a prompt-driven, free-form input. The code is ANSI standard Fortran 77.

  16. CASCADER: An m-chain gas-phase radionuclide transport and fate model. Volume 1, Basic physics and mathematics

    SciTech Connect

    Lindstrom, F.T.; Cawlfield, D.E.; Emer, D.F.; Shott, G.J.; Donahue, M.E.

    1992-06-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes as they are advected and/or dispersed. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. CASCADER is a gas-phase, one space dimensional transport and fate model for an m-chain of radionuclides in very dry soil. This model contains barometric pressure-induced advection and diffusion together with linear irreversible and linear reversible sorption for each radionuclide. The advocation velocity is derived from an embedded air-pumping submodel. The airpumping submodel is based on an assumption of isothermal conditions and is barometric pressure driven. CASCADER allows the concentration of source radionuclides to decay via the classical Bateman chain of simple, first-order kinetic processes. The transported radionuclides also decay via first-order processes while in the soil. A mass conserving, flux-type inlet and exit set of boundary conditions is used. The user must supply the initial distribution for the parent radionuclide in the soil. The initial daughter distribution is found using equilibrium rules. The model is user friendly as it uses a prompt-driven, free-form input. The code is ANSI standard Fortran 77.

  17. Gas-phase ion-molecule reactions: a model for the determination of biologically reactive electrophilic contaminants in the environment.

    PubMed

    Freeman, J A; Johnson, J V; Yost, R A; Kuehl, D W

    1994-06-01

    A promising instrumental technique has been investigated to rapidly screen complex environmental samples for chemical contaminants having the propensity to covalently bond to biomacromolecules such as DNA. Radical molecular ions of pyridine, a model compound for nucleophilic bases of DNA, were mass-selected and allowed to react with electrophilic environmental contaminants in the collision cell of a triple quadrupole mass spectrometer. Analytes were introduced into the collision cell via a gas chromatographic column. Reactive chemicals are then characterized by scanning Q3 to identify associative reaction products. A good qualitative correlation was observed for the gas-phase reactivity of a series of electrophilic reagents with both their alkylating reactivity in solution (4-(4-nitrobenzyl)pyridine) and AMES test mutagenicity which had been previously published. Femtomole limits of detection for specific associative reaction products were demonstrated. Gas-phase reactions of ions of environmental contaminants (introduced into the source) with neutral pyridine (in the collision cell) were also investigated. Reactions of the radical molecular ion of the allyl reagents with neutral pyridine were similar to results from the mass-selected reaction of the pyridine radical molecular ion with neutral allylic reagents. PMID:8030792

  18. The sensitivity of gas-phase models of dense interstellar clouds to changes in dissociative recombination branching ratios

    NASA Technical Reports Server (NTRS)

    Millar, T. J.; Defrees, D. J.; Mclean, A. D.; Herbst, E.

    1988-01-01

    The approach of Bates to the determination of neutral product branching ratios in ion-electron dissociative recombination reactions has been utilized in conjunction with quantum chemical techniques to redetermine branching ratios for a wide variety of important reactions of this class in dense interstellar clouds. The branching ratios have then been used in a pseudo time-dependent model calculation of the gas phase chemistry of a dark cloud resembling TMC-1 and the results compared with an analogous model containing previously used branching ratios. In general, the changes in branching ratios lead to stronger effects on calculated molecular abundances at steady state than at earlier times and often lead to reductions in the calculated abundances of complex molecules. However, at the so-called 'early time' when complex molecule synthesis is most efficient, the abundances of complex molecules are hardly affected by the newly used branching ratios.

  19. Dissolved gas transport in the presence of a trapped gas phase: Experimental evaluation of a two-dimensional kinetic model

    SciTech Connect

    Donaldson, J.H.; Istok, J.D.; O`Reilly, K.T.

    1998-01-01

    Quantitative information on dissolved gas transport in ground water aquifers is needed for a variety of site characterization and remedial design applications. The objective of this study was to gain further understanding of dissolved gas transport in the presence of trapped gas in the pore space of an otherwise water saturated porous medium, using a combination of laboratory experiments and numerical modeling. Transport experiments were conducted in a large-scale laboratory physical aquifer model containing a homogeneous sandpack. Tracer (Br{sup {minus}}) and dissolved gas (O{sub 2} or H{sub 2}) plumes were created using a two-well injection/extraction scheme and then were allowed to drift in a uniform flow field. Plume locations and shapes were monitored by measuring tracer and dissolved gas concentrations as a function of position within the sandpack and time. In all experiments, partitioning of the dissolved gases between the mobile ground water and stationary trapped gas phases resulted in substantial retardation and tailing of the dissolved O{sub 2} and H{sub 2} plumes relative to the Br{sup {minus}} plumes. Most observed plume features could be reproduced in simulations performed with a numerical model that combined the advection-dispersion equation with diffusion controlled mass transfer of dissolved gas between the mobile aqueous and stationary trapped gas phases. Fitted values of the volumetric trapped gas content and mass transfer coefficient ranged from 0.04 to 0.08 and from 10{sup {minus}6} to 10{sup {minus}5} sec{sup {minus}1}, respectively. Sensitivity analyses were used to examine how systematic variations in these parameters would be expected to affect dissolved gas transport under a range of potential field conditions. The experimental and modeling results indicate that diffusion controlled mass transfer should be considered when predicting dissolved gas transport in ground water aquifers in the presence of trapped gas.

  20. Gas Phase Nanoparticle Synthesis

    NASA Astrophysics Data System (ADS)

    Granqvist, Claes; Kish, Laszlo; Marlow, William

    This book deals with gas-phase nanoparticle synthesis and is intended for researchers and research students in nanomaterials science and engineering, condensed matter physics and chemistry, and aerosol science. Gas-phase nanoparticle synthesis is instrumental to nanotechnology - a field in current focus that raises hopes for environmentally benign, resource-lean manufacturing. Nanoparticles can be produced by many physical, chemical, and even biological routes. Gas-phase synthesis is particularly interesting since one can achieve accurate manufacturing control and hence industrial viability.

  1. An Effective Continuum Model for the Liquid-to-Gas Phase Change in a Porous Medium Driven by Solute Diffusion: II. Constant Liquid Withdrawal Rates

    SciTech Connect

    Tsimpanogiannis, Ioannis N.; Yortsos, Yanis C.

    2001-08-15

    This report describes the development of an effective continuum model to describe the nucleation and subsequent growth of a gas phase from a supersaturated, slightly compressible binary liquid in a porous medium, driven by solute diffusion.This report also focuses on the processes resulting from the withdrawal of the liquid at a constant rate. As before, the model addresses two stages before the onset of bulk gas flow, nucleation and gas phase growth. Because of negligible gradients due to gravity or viscous forces, the critical gas saturation, is only a function of the nucleation fraction.

  2. Implementation and evaluation of online gas-phase chemistry within a regional climate model (RegCM-CHEM4)

    SciTech Connect

    Shalaby, A. K.; Zakey, A. S.; Tawfik, A. B.; Solmon, F.; Giorgi, Filippo; Stordal, F.; Sillman, S.; Zaveri, Rahul A.; Steiner, A. L.

    2012-05-22

    The RegCM-CHEM4 is a new online climate-chemistry model based on the International Centre for Theoretical Physics (ICTP) regional climate model (RegCM4). Tropospheric gas-phase chemistry is integrated into the climate model using the condensed version of the Carbon Bond Mechanism (CBM-Z; Zaveri and Peters, 1999) with a fast solver based on radical balances. We evaluate the model over Continental Europe for two different time scales: (1) an event-based analysis of the ozone episode associated with the heat wave of August 2003 and (2) a climatological analysis of a sixyear simulation (2000-2005). For the episode analysis, model simulations show good agreement with European Monitoring and Evaluation Program (EMEP) observations of hourly ozone over different regions in Europe and capture ozone concentrations during and after the August 2003 heat wave event. For long-term climate simulations, the model captures the seasonal cycle of ozone concentrations with some over prediction of ozone concentrations in non-heat wave summers. Overall, the ozone and ozone precursor evaluation shows the feasibility of using RegCM-CHEM4 for decadal-length simulations of chemistry-climate interactions.

  3. SENSITIVITY OF THE CMAQ MERCURY MODEL TO GAS-PHASE OXIDATION CHEMISTRY

    EPA Science Inventory

    Simulations of the Community Multi-scale Air Quality (CMAQ) model for mercury have shown the vast majority of the mercury deposited in the United States to be in the form of oxidized mercury. However, most of this simulated oxidized mercury was the result of atmospheric oxidatio...

  4. Modeling Interactions Among Turbulence, Gas-Phase Chemistry, Soot and Radiation Using Transported PDF Methods

    NASA Astrophysics Data System (ADS)

    Haworth, Daniel

    2013-11-01

    The importance of explicitly accounting for the effects of unresolved turbulent fluctuations in Reynolds-averaged and large-eddy simulations of chemically reacting turbulent flows is increasingly recognized. Transported probability density function (PDF) methods have emerged as one of the most promising modeling approaches for this purpose. In particular, PDF methods provide an elegant and effective resolution to the closure problems that arise from averaging or filtering terms that correspond to nonlinear point processes, including chemical reaction source terms and radiative emission. PDF methods traditionally have been associated with studies of turbulence-chemistry interactions in laboratory-scale, atmospheric-pressure, nonluminous, statistically stationary nonpremixed turbulent flames; and Lagrangian particle-based Monte Carlo numerical algorithms have been the predominant method for solving modeled PDF transport equations. Recent advances and trends in PDF methods are reviewed and discussed. These include advances in particle-based algorithms, alternatives to particle-based algorithms (e.g., Eulerian field methods), treatment of combustion regimes beyond low-to-moderate-Damköhler-number nonpremixed systems (e.g., premixed flamelets), extensions to include radiation heat transfer and multiphase systems (e.g., soot and fuel sprays), and the use of PDF methods as the basis for subfilter-scale modeling in large-eddy simulation. Examples are provided that illustrate the utility and effectiveness of PDF methods for physics discovery and for applications to practical combustion systems. These include comparisons of results obtained using the PDF method with those from models that neglect unresolved turbulent fluctuations in composition and temperature in the averaged or filtered chemical source terms and/or the radiation heat transfer source terms. In this way, the effects of turbulence-chemistry-radiation interactions can be isolated and quantified.

  5. High Resolution Stark Spectroscopy of Model Donor-Acceptor Aminobenzonitriles in the Gas Phase.

    NASA Astrophysics Data System (ADS)

    Fleisher, Adam J.; Clements, Casey L.; Bird, Ryan G.; Pratt, David W.; Alvarez-Valtierra, Leonardo

    2011-06-01

    Electronic communication between donor-acceptor systems is prevalent in many chemical processes. Unfortunately, an accurate description of the changes in molecular geometry responsible for intramolecular charge transfer (ICT) is difficult to ascertain. Reported here are the S0, LA, and LB electronic state structures and dipole moments of two model ICT systems, 4-(1H-pyrrol-l-yl)benzonitrile (PBN) and 4-(1-pyrrolidinyl)benzonitrile (PDBN), as measured by rotationally resolved electronic spectroscopy. As was observed for phenylpyrrole, the unsaturted rings of PBN become collectively more planar following excitation with UV light, in support of the planar ICT model. However, in PDBN the twist/inversion angle between rings is nearly zero in both the ground and excited electronic states. The unperturbed dipole moments measured here, taken in conjunction with available solvatochromism data, provide an estimate for the polarization, dispersion, and charge transfer contributions to solvent-mediated excited state stabilization. J.A. Thomas, J.W. Young, A.J. Fleisher, L. Álvarez-Valtierra, and D.W. Pratt, J. Phys. Chem. Lett. 1, 2017 (2010).

  6. Modeling-gas phase reactions in indoor environments using computational fluid dynamics

    NASA Astrophysics Data System (ADS)

    Sørensen, Dan Nørtoft; Weschler, Charles J.

    This CFD modeling study examines the concentrations of two gaseous compounds that react in an indoor setting to produce a hypothetical product. The reactants are ozone and either d-limonene or α-terpinene (which reacts with ozone about 40 times faster than d-limonene). In addition to two different terpenes, the scenarios include two air exchange rates (0.5 and 2.0 h-1). The terpene is introduced as a floor source with an emission pattern similar to a floor-care product. These four scenarios have been set in a fairly large two-dimensional room (13.6×40.6 m) with a supply at the top of the left wall and an exhaust at the bottom of the right wall. The room has been deliberately scaled so that the Reynolds numbers for key flow regimes match those of a room in which the calculated flow field has been validated against measured data. It has been further assumed that ozone interacts with room surfaces while the terpenes do not. The results show that for all four scenarios, under steady-state conditions, there are large concentration gradients within the room for both reactants and product. To some extent this is due to imperfect mixing. However, it also reflects that reactions occur at different rates across the room (because of varying reactant concentrations) and that the time available for reactions to occur varies with the room location (because the "age of the air" varies from point to point). Locally, within the room, the concentrations calculated by the CFD method differ significantly from those calculated by a one-compartment mass-balance model assuming perfect mixing.

  7. The gas-phase chemistry of carbon chains in dark cloud chemical models

    NASA Astrophysics Data System (ADS)

    Loison, Jean-Christophe; Wakelam, Valentine; Hickson, Kevin M.; Bergeat, Astrid; Mereau, Raphael

    2014-01-01

    We review the reactions between carbon chain molecules and radicals, namely Cn, CnH, CnH2, C2n+1O, CnN, HC2n+1N, with C, N and O atoms. Rate constants and branching ratios for these processes have been re-evaluated using experimental and theoretical literature data. In total 8 new species have been introduced, 41 new reactions have been proposed and 122 rate coefficients from kida.uva.2011 have been modified. We test the effect of the new rate constants and branching ratios on the predictions of gas-grain chemical models for dark cloud conditions using two different C/O elemental ratios. We show that the new rate constants produce large differences in the predicted abundances of carbon chains since the formation of long chains is less effective. The general agreement between the model predictions and observed abundances in the dark cloud TMC-1 (CP) is improved by the new network and we find that C/O ratios of 0.7 and 0.95 both produce a similar agreement for different times. The general agreement for L134N (N) is not significantly changed. The current work specifically highlights the importance of O + CnH and N + CnH reactions. As there are very few experimental or theoretical data for the rate constants of these reactions, we highlight the need for experimental studies of the O + CnH and N + CnH reactions, particularly at low temperature.

  8. Gas-Phase Reactions of Glyceraldehyde and 1,3-Dihydroxyacetone as Models for Levoglucosan Conversion during Biomass Gasification.

    PubMed

    Fukutome, Asuka; Kawamoto, Haruo; Saka, Shiro

    2016-04-01

    Levoglucosan, the major intermediate in wood gasification, is decomposed selectively to C1/C2 fragments at 550-600 °C. Kinetic analyses suggest that radical chain mechanisms with the involvement of short-lived carbonyl intermediates explain the lower production of larger fragments. To address this hypothesis, the gas-phase reactivities of glyceraldehyde (Gald), 1,3-dihydroxyacetone (DHA), and glycerol, as simple C3 model compounds, were compared at 400-800 °C under N2 flow at residence times of 0.9-1.4 s. Retro-aldol fragmentation and dehydration proceeded for the pyrolysis of Gald/DHA at 400 °C, far below the 600 °C decomposition point of glycerol. Pyrolysis of Gald/DHA generated exclusively syngas (CO and H2). On the basis of the results of theoretical calculations, the effects of carbonyl intermediates on reactivity were explained by postulating uni- and bimolecular reactions, although the bimolecular reactions became less effective at elevated temperatures. PMID:26893057

  9. Modeling Gas-phase Glyoxal and Associated Secondary Organic Aerosol Formation in a Megacity using WRF/Chem

    NASA Astrophysics Data System (ADS)

    Wang, K.; Hodzic, A.; Barth, M. C.; Jimenez, J. L.; Volkamer, R.; Ervens, B.; Zhang, Y.

    2011-12-01

    Organic aerosol (OA) as one of a major fine particulate matter in the atmosphere plays an important role in air pollution, human health, and climate forcing. OA is composed of directly emitted primary organic aerosol and chemically produced secondary organic aerosols (SOA). Despite much recent progress in understanding SOA formation, current air quality models cannot explain the magnitude and growth of atmospheric SOA, due to high uncertainties in sources, properties, and chemical reactions of precursors and formation pathways of SOA. Recent laboratory and modeling studies showed that glyoxal may serve as an important SOA precursor in the condensed solution of inorganic or organic aerosol particles (e.g., ammonium sulfate, fulvic acid, and amino acids). In this study, the Weather Research and Forecasting model with chemistry (WRF/Chem) is modified to account for the latest observed gas-phase yields of glyoxal from various volatile organic compounds (VOCs) and the associated SOA formation in the aqueous aerosol phase. The SOA formation in the aqueous aerosol phase is implemented using two approaches. In the first approach, two simplified parameterizations are used to represent the lumped particle-phase chemical processes under dark conditions and photochemical surface uptake. In the second approach, more detailed kinetic glyoxal reactions such as reversible glyoxal uptake, dimer formation of glyoxal, and oligomerization are treated and resolved explicitly. The updated WRF/Chem is assessed over the Mexico City and the surrounding region during March 2006 using the MILAGRO campaign data. Various observations such as organic matter from Aerodyne Aerosol Mass Spectrometer and VOCs from Proton-transfer Ion Trap Mass Spectrometry were compared. The preliminary results showed that the addition of the SOA formation from glyoxal in aqueous particles brings SOA predictions into a better agreement with field observations, in particular in presence of high relative humidity

  10. Impact of gas-phase mechanisms on Weather Research Forecasting Model with Chemistry (WRF/Chem) predictions: Mechanism implementation and comparative evaluation

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Chen, Yaosheng; Sarwar, Golam; Schere, Kenneth

    2012-01-01

    Gas-phase mechanisms provide important oxidant and gaseous precursors for secondary aerosol formation. Different gas-phase mechanisms may lead to different predictions of gases, aerosols, and aerosol direct and indirect effects. In this study, WRF/Chem-MADRID simulations are conducted over the continental United States for July 2001, with three different gas-phase mechanisms, a default one (i.e., CBM-Z) and two newly implemented ones (i.e., CB05 and SAPRC-99). Simulation results are evaluated against available surface observations, satellite data, and reanalysis data. The model with these three gas-phase mechanisms gives similar predictions of most meteorological variables in terms of spatial distribution and statistics, but large differences exist in shortwave radiation and temperature and relative humidity at 2 m at individual sites under cloudy conditions, indicating the importance of aerosol semi-direct and indirect effects on these variables. Large biases exist in the simulated wind speed at 10 m, cloud water path, cloud optical thickness, and precipitation, due to uncertainties in current cloud microphysics and surface layer parameterizations. Simulations with all three gas-phase mechanisms well reproduce surface concentrations of O3, CO, NO2, and PM2.5, and column NO2. Larger biases exist in the surface concentrations of nitrate and organic matter (OM) and in the spatial distribution of column CO, tropospheric ozone residual, and aerosol optical depth, due to uncertainties in primary OM emissions, limitations in model representations of chemical transport, and radiative processes. Different gas-phase mechanisms lead to different predictions of mass concentrations of O3 (up to 5 ppb), PM2.5 (up to 0.5 μg m-3), secondary inorganic PM2.5 species (up to 1.1 μg m-3), organic PM (up to 1.8 μg m-3), and number concentration of PM2.5 (up to 2 × 104 cm-3). Differences in aerosol mass and number concentrations further lead to sizeable differences in simulated

  11. Reactivity of OH and CH3OH Between 22 and 64 K: Modelling the Gas Phase Production of CH3O in Barnard 1B

    PubMed Central

    Antiñolo, M.; Agúndez, M.; Jiménez, E.; Ballesteros, B.; Canosa, A.; Dib, G. El; Albaladejo, J.; Cernicharo, J.

    2016-01-01

    In the last years, ultra-low temperature chemical kinetic experiments have demonstrated that some gas-phase reactions are much faster than previously thought. One example is the reaction between OH and CH3OH, which has been recently found to be accelerated at low temperatures yielding CH3O as main product. This finding opened the question of whether the CH3O observed in the dense core Barnard 1b could be formed by the gas-phase reaction of CH3OH and OH. Several chemical models including this reaction and grain-surface processes have been developed to explain the observed abundance of CH3O with little success. Here we report for the first time rate coefficients for the gas-phase reaction of OH and CH3OH down to a temperature of 22 K, very close to those in cold interstellar clouds. Two independent experimental set-ups based on the supersonic gas expansion technique coupled to the pulsed laser photolysis-laser induced fluorescence technique were used to determine rate coefficients in the temperature range 22-64 K. The temperature dependence obtained in this work can be expressed as k(22-64 K) = (3.6 ± 0.1) × 10−12(T/300 K)−(1.0±0.2) cm3 molecule−1 s−1. Implementing this expression in a chemical model of a cold dense cloud results in CH3O/CH3OH abundance ratios similar or slightly lower than the value of ∼ 3 × 10−3 observed in Barnard 1b. This finding confirms that the gas-phase reaction between OH and CH3OH is an important contributor to the formation of interstellar CH3O. The role of grain-surface processes in the formation of CH3O, although it cannot be fully neglected, remains controversial. PMID:27279655

  12. Reactivity of OH and CH3OH between 22 and 64 K: Modeling the Gas Phase Production of CH3O in Barnard 1b

    NASA Astrophysics Data System (ADS)

    Antiñolo, M.; Agúndez, M.; Jiménez, E.; Ballesteros, B.; Canosa, A.; El Dib, G.; Albaladejo, J.; Cernicharo, J.

    2016-05-01

    In recent years, ultra-low temperature chemical kinetic experiments have demonstrated that some gas-phase reactions are much faster than was previously thought. One example is the reaction between OH and CH3OH, which has recently been found to be accelerated at low temperatures yielding CH3O as its main product. This finding raised the question of whether or not the CH3O observed in the dense core Barnard 1b could be formed by the gas-phase reaction of CH3OH and OH. Several chemical models including this reaction and grain-surface processes have been developed to explain the observed abundance of CH3O, but they have met with little success. Here, we report for the first time the rate coefficients for the gas-phase reaction of OH and CH3OH down to a temperature of 22 K, which is very close to the temperature in cold interstellar clouds. Two independent experimental set-ups based on the supersonic gas expansion technique coupled to the pulsed laser photolysis laser-induced fluorescence technique were used to determine the rate coefficients in the temperature range 22–64 K. The temperature dependence obtained in this work can be expressed as k(22–64 K) = {(3.6+/- 0.1)× {10}-12(T/300{{K}})}-(1.0+/- 0.2) cm3 molecule‑1 s‑1. Implementing this expression in a chemical model of a cold, dense cloud results in CH3O/CH3OH abundance ratios similar to or slightly lower than the value of ∼3 × 10‑3 observed in Barnard 1b. This finding confirms that the gas-phase reaction between OH and CH3OH is an important contributor to the formation of interstellar CH3O. The role of grain-surface processes in the formation of CH3O, although it cannot be fully neglected, remains controversial.

  13. Gas phase ultraviolet and infrared spectroscopy on a partial peptide of β2-adrenoceptor SIVSF-NH2 by a laser desorption supersonic jet technique.

    PubMed

    Ishiuchi, Shun-Ichi; Yamada, Kohei; Oba, Hikari; Wako, Hiromichi; Fujii, Masaaki

    2016-08-17

    Laser desorption supersonic jet laser spectroscopy has been applied to a penta-peptide, Ser-Ile-Val-Ser-Phe-NH2 (SIVSF-NH2), which is a partial sequence of a binding site in a β2-adrenaline receptor protein. By comparing the resonance enhanced multiphoton ionization spectrum with the ultraviolet-ultraviolet hole burning (HB) spectrum, it is concluded that only a single conformer exists. The infrared (IR) spectrum of the X-H stretching region, measured by IR dip spectroscopy, shows that all of the OH and NH groups form hydrogen bonds. The structure of SIVSF-NH2 is assigned by the combination of a force field calculation (CONFLEX) and quantum chemical calculations both in S0 and S1. Over 20 000 stable conformations, given by CONFLEX, are classified into 6987 groups and 1068 groups in which all of the NH and OH bonds are hydrogen-bonded are selected. The most stable structure in each group was geometrically optimized by density functional theory (DFT) calculations, and theoretical IR spectra were calculated for the conformers for which the energies are within 10 kJ mol(-1) of the most stable one. It has been found that the most stable and the secondmost stable conformers well-reproduce the observed IR spectrum. The vibrational frequencies in S1 were also calculated for these two conformers. According to the reproduction of the vibrational frequencies in the HB spectrum, the structure of SIVSF-NH2 is assigned to the most stable conformer, which forms a hydrogen-bonded structure corresponding to a compact, distorted version of the beta hairpin of peptides and proteins. PMID:27498750

  14. CASCADER: An m-chain gas-phase radionuclide transport and fate model. Volume 2, User`s manual for CASCADR8

    SciTech Connect

    Cawlfield, D.E.; Been, K.B.; Emer, D.F.; Lindstrom, F.T.; Shott, G.J.

    1993-06-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and/or diffusion. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. This is volume two to the CASCADER series, titled CASCADR8. It embodies the concepts presented in volume one of this series. To properly understand how the CASCADR8 model works, the reader should read volume one first. This volume presents the input and output file structure for CASCADR8, and a set of realistic scenarios for buried sources of radon gas.

  15. Nonaligned carbon nanotubes anchored on porous alumina: formation, process modeling, gas-phase analysis, and field-emission properties.

    PubMed

    Lysenkov, Dmitry; Engstler, Jörg; Dangwal, Arti; Popp, Alexander; Müller, Günter; Schneider, Jörg J; Janardhanan, Vinod M; Deutschmann, Olaf; Strauch, Peter; Ebert, Volker; Wolfrum, Jürgen

    2007-06-01

    We have developed a chemical vapor deposition (CVD) process for the catalytic growth of carbon nanotubes (CNTs), anchored in a comose-type structure on top of porous alumina substrates. The mass-flow conditions of precursor and carrier gases and temperature distributions in the CVD reactor were studied by transient computational fluid dynamic simulation. Molecular-beam quadrupole mass spectroscopy (MB-QMS) has been used to analyze the gas phase during ferrocene CVD under reaction conditions (1073 K) in the boundary layer near the substrate. Field-emission (FE) properties of the nonaligned CNTs were measured for various coverages and pore diameters of the alumina. Samples with more dense CNT populations provided emitter-number densities up to 48,000 cm(-2) at an electric field of 6 V microm(-1). Samples with fewer but well-anchored CNTs in 22-nm pores yielded the highest current densities. Up to 83 mA cm(-2) at 7 V microm(-1) in dc mode and more than 200 mA cm(-2) at 11 V microm(-1) in pulsed diode operation have been achieved from a cathode size of 24 mm2. PMID:17514768

  16. Gas-phase diffusion in porous media: Evaluation of an advective- dispersive formulation and the dusty-gas model including comparison to data for binary mixtures

    SciTech Connect

    Webb, S.W.

    1996-05-01

    Two models for gas-phase diffusion and advection in porous media, the Advective-Dispersive Model (ADM) and the Dusty-Gas Model (DGM), are reviewed. The ADM, which is more widely used, is based on a linear addition of advection calculated by Darcy`s Law and ordinary diffusion using Fick`s Law. Knudsen diffusion is often included through the use of a Klinkenberg factor for advection, while the effect of a porous medium on the diffusion process is through a porosity-tortuosity-gas saturation multiplier. Another, more comprehensive approach for gas-phase transport in porous media has been formulated by Evans and Mason, and is referred to as the Dusty- Gas Model (DGM). This model applies the kinetic theory of gases to the gaseous components and the porous media (or ``dust``) to develop an approach for combined transport due to ordinary and Knudsen diffusion and advection including porous medium effects. While these two models both consider advection and diffusion, the formulations are considerably different, especially for ordinary diffusion. The various components of flow (advection and diffusion) are compared for both models. Results from these two models are compared to isothermal experimental data for He-Ar gas diffusion in a low-permeability graphite. Air-water vapor comparisons have also been performed, although data are not available, for the low-permeability graphite system used for the helium-argon data. Radial and linear air-water heat pipes involving heat, advection, capillary transport, and diffusion under nonisothermal conditions have also been considered.

  17. Receptors useful for gas phase chemical sensing

    DOEpatents

    Jaworski, Justyn W; Lee, Seung-Wuk; Majumdar, Arunava; Raorane, Digvijay A

    2015-02-17

    The invention provides for a receptor, capable of binding to a target molecule, linked to a hygroscopic polymer or hydrogel; and the use of this receptor in a device for detecting the target molecule in a gaseous and/or liquid phase. The invention also provides for a method for detecting the presence of a target molecule in the gas phase using the device. In particular, the receptor can be a peptide capable of binding a 2,4,6-trinitrotoluene (TNT) or 2,4,-dinitrotoluene (DNT).

  18. Evidence for α-helices in the gas phase: a case study using Melittin from honey bee venom.

    PubMed

    Florance, Hannah V; Stopford, Andrew P; Kalapothakis, Jason M; McCullough, Bryan J; Bretherick, Andrew; Barran, Perdita E

    2011-09-01

    Gas phase methodologies are increasingly used to study the structure of proteins and peptides. A challenge to the mass spectrometrist is to preserve the structure of the system of interest intact and unaltered from solution into the gas phase. Small peptides are very flexible and can present a number of conformations in solution. In this work we examine Melittin a 26 amino acid peptide that forms the active component of honey bee venom. Melittin is haemolytic and has been shown to form an α-helical tetrameric structure by X-ray crystallography [M. Gribskov et al., The RCSB Protein Data Bank, 1990] and to be helical in high concentrations of methanol. Here we use ion mobility mass spectrometry, molecular dynamics and gas-phase HDX to probe its structure in the gas phase and specifically interrogate whether the helical form can be preserved. All low energy calculated structures possess some helicity. In our experiments we examine the peptide following nano-ESI from solutions with varying methanol content. Ion mobility gives collision cross sections (CCS) that compare well with values found from molecular modelling and from other reported structures, but with inconclusive results regarding the effect of solvent. There is only a slight increase in CCS with charge, showing minimal coloumbically driven unfolding. HDX supports preservation of some helical content into the gas phase and again shows little difference in the exchange rates of species sprayed from different solvents. The [M + 3H](3+) species has two exchanging populations both of which exhibit faster exchange rates than observed for the [M + 2H](2+) species. One interpretation for these results is that the time spent being analysed is sufficient for this peptide to form a helix in the 'ultimate' hydrophobic environment of a vacuum. PMID:21701716

  19. EPA GAS PHASE CHEMISTRY CHAMBER STUDIES

    EPA Science Inventory

    Gas-phase smog chamber experiments are being performed at EPA in order to evaluate a number of current chemical mechanisms for inclusion in EPA regulatory and research models. The smog chambers are 9000 L in volume and constructed of 2-mil teflon film. One of the chambers is co...

  20. Impact of Gas-Phase Mechanisms on Weather Research Forecasting Model with Chemistry (WRF/Chem) Predictions: Mechanism Implementation and Comparative Evaluation

    EPA Science Inventory

    Gas-phase mechanisms provide important oxidant and gaseous precursors for secondary aerosol formation. Different gas-phase mechanisms may lead to different predictions of gases, aerosols, and aerosol direct and indirect effects. In this study, WRF/Chem-MADRID simulations are cond...

  1. Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase SN2 Reaction of Acetate Ion with 1,2-Dichloroethane

    PubMed Central

    Valero, Rosendo; Song, Lingchun; Gao, Jiali; Truhlar, Donald G.

    2009-01-01

    Diabatic models are widely employed for studying chemical reactivity in condensed phases and enzymes, but there has been little discussion of the pros and cons of various diabatic representations for this purpose. Here we discuss and contrast six different schemes for computing diabatic potentials for a charge rearrangement reaction. They include (i) the variational diabatic configurations (VDC) constructed by variationally optimizing individual valence bond structures and (ii) the consistent diabatic configurations (CDC) obtained by variationally optimizing the ground-state adiabatic energy, both in the nonorthogonal molecular orbital valence bond (MOVB) method, along with the orthogonalized (iii) VDC-MOVB and (iv) CDC-MOVB models. In addition, we consider (v) the fourfold way (based on diabatic molecular orbitals and configuration uniformity), and (vi) empirical valence bond (EVB) theory. To make the considerations concrete, we calculate diabatic electronic states and diabatic potential energies along the reaction path that connects the reactant and the product ion-molecule complexes of the gas-phase bimolecular nucleophilic substitution (SN2) reaction of 1,2-dichloethane (DCE) with acetate ion, which is a model reaction corresponding to the reaction catalyzed by haloalkane dehalogenase. We utilize ab initio block-localized molecular orbital theory to construct the MOVB diabatic states and ab initio multi-configuration quasidegenerate perturbation theory to construct the fourfold-way diabatic states; the latter are calculated at reaction path geometries obtained with the M06-2X density functional. The EVB diabatic states are computed with parameters taken from the literature. The MOVB and fourfold-way adiabatic and diabatic potential energy profiles along the reaction path are in qualitative but not quantitative agreement with each other. In order to validate that these wave-function-based diabatic states are qualitatively correct, we show that the reaction

  2. Gas-phase chemical dynamics

    SciTech Connect

    Weston, R.E. Jr.; Sears, T.J.; Preses, J.M.

    1993-12-01

    Research in this program is directed towards the spectroscopy of small free radicals and reactive molecules and the state-to-state dynamics of gas phase collision, energy transfer, and photodissociation phenomena. Work on several systems is summarized here.

  3. Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: the case of the halide ions F-, Cl-, and Br-.

    PubMed

    Trumm, Michael; Martínez, Yansel Omar Guerrero; Réal, Florent; Masella, Michel; Vallet, Valérie; Schimmelpfennig, Bernd

    2012-01-28

    In this work, we investigate the hydration of the halide ions fluoride, chloride, and bromide using classical molecular dynamics simulations at the 10 ns scale and based on a polarizable force-field approach, which treats explicitly the cooperative bond character of strong hydrogen bond networks. We have carried out a thorough analysis of the ab initio data at the MP2 or CCSD(T) level concerning anion/water clusters in gas phase to adjust the force-field parameters. In particular, we consider the anion static polarizabilities computed in gas phase using large atomic basis sets including additional diffuse functions. The information extracted from trajectories in solution shows well structured first hydration shells formed of 6.7, 7.0, and 7.6 water molecules at about 2.78 Å, 3.15 Å, and 3.36 Å for fluoride, chloride, and bromide, respectively. These results are in excellent agreement with the latest neutron- and x-ray diffraction studies. In addition, our model reproduces several other properties of halide ions in solution, such as diffusion coefficients, description of hydration processes, and exchange reactions. Moreover, it is also able to reproduce the electrostatic properties of the anions in solution (in terms of anion dipole moment) as reported by recent ab initio quantum simulations. All the results show the ability of the proposed model in predicting data, as well as the need of accounting explicitly for the cooperative character of strong hydrogen bonds to reproduce ab initio potential energy surfaces in a mean square sense and to build up a reliable force field. PMID:22299893

  4. Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: The case of the halide ions F-, Cl-, and Br-

    NASA Astrophysics Data System (ADS)

    Trumm, Michael; Martínez, Yansel Omar Guerrero; Réal, Florent; Masella, Michel; Vallet, Valérie; Schimmelpfennig, Bernd

    2012-01-01

    In this work, we investigate the hydration of the halide ions fluoride, chloride, and bromide using classical molecular dynamics simulations at the 10 ns scale and based on a polarizable force-field approach, which treats explicitly the cooperative bond character of strong hydrogen bond networks. We have carried out a thorough analysis of the ab initio data at the MP2 or CCSD(T) level concerning anion/water clusters in gas phase to adjust the force-field parameters. In particular, we consider the anion static polarizabilities computed in gas phase using large atomic basis sets including additional diffuse functions. The information extracted from trajectories in solution shows well structured first hydration shells formed of 6.7, 7.0, and 7.6 water molecules at about 2.78 Å, 3.15 Å, and 3.36 Å for fluoride, chloride, and bromide, respectively. These results are in excellent agreement with the latest neutron- and x-ray diffraction studies. In addition, our model reproduces several other properties of halide ions in solution, such as diffusion coefficients, description of hydration processes, and exchange reactions. Moreover, it is also able to reproduce the electrostatic properties of the anions in solution (in terms of anion dipole moment) as reported by recent ab initio quantum simulations. All the results show the ability of the proposed model in predicting data, as well as the need of accounting explicitly for the cooperative character of strong hydrogen bonds to reproduce ab initio potential energy surfaces in a mean square sense and to build up a reliable force field.

  5. Atomic-scale modeling of chemical vapor deposition processes from new complicated gas-phase mixtures for micro- and nanoelectronic applications

    NASA Astrophysics Data System (ADS)

    Makhviladze, T. M.; Sarychev, M. E.

    2009-01-01

    Low-pressure chemical vapor deposition (CVD) is one of the most important processes for obtaining thin films widely used in semiconductor and in IC technology. Because of the baffling complexity of deposition process the usually-used approaches in CVD modeling include a great number of empiric non-calculated parameters, and this drawback becomes a grave disadvantage if one needs to model the process with new reagents and materials which were not used before. So we place primary emphasis upon the development of non-empirical deposition models that rely on phenomenological theories and experimental data only to a minimal extent. We are presenting the atomistic-scale models and software package throughout the entire deposition process that are based mainly on the first principles and ab initio methods. The main modeling stages are studied and discussed in detail, namely: atomistic modeling of gas-phase and surface reactions, determination of the basic chemical and physical mechanisms for the considered gas mixtures, calculations of the reactions rates for elementary reactions and acts, Monte Carlo and/or molecular dynamics simulation of the thin film growth, and modeling of macrokinetic processes in realistic deposition flow-reactor chamber. The modeling results for thin films deposition from actual gas mixtures are given. The physical properties of films as well as their stoichiometric composition and structure in dependence of process conditions are discussed.

  6. Gas-phase evaluation of the online NMMB/BSC-CTM model over Europe for 2010 in the framework of the AQMEII-Phase2 project

    NASA Astrophysics Data System (ADS)

    Badia, A.; Jorba, O.

    2015-08-01

    The Air Quality Model Evaluation International Initiative Phase2 aims to intercompare online coupled regional-scale models over North America and Europe. The NMMB/BSC Chemical Transport Model (NMMB/BSC-CTM) is a fully online integrated system for meso- to global-scale applications under development at the Barcelona Supercomputing Center. The NMMB/BSC-CTM is applied to Europe for the year 2010 in the framework of the AQMEII-Phase2 intercomparison exercise. This paper presents a spatial, temporal and vertical evaluation of the gas-phase model results. This is the first time that the model has been evaluated on a regional scale over a whole annual cycle. The model is compared with available ground-based monitoring stations for relevant reactive gases, ozonesondes, and OMI and MOPITT satellite retrievals of NO2 and CO. A comparative analysis of the present results and several European model evaluations is also presented here. The seasonal cycle for O3, NO2, SO2 and CO is successfully reproduced by the model. The O3 daily mean and daily maximum correlations for the analysed period are r = 0.68 and r = 0.75, respectively. The OMI tropospheric NO2 column retrievals are well reproduced, capturing the most polluted areas over Europe throughout the whole year. Modelled SO2 and CO surface concentrations are generally underestimated, especially during the winter months. Two different vertical configurations of the model (24 and 48 vertical layers) are also analysed. Although model results are very similar, the simulation configured with 48 vertical layers provides better results regarding surface O3 concentrations during summer. Compared to previous model evaluations, the NMMB/BSC-CTM's performance corresponds to state-of-the-art regional air quality models.

  7. Transient-state studies and neural modeling of the removal of a gas-phase pollutant mixture in a biotrickling filter.

    PubMed

    López, M Estefanía; Boger, Zvi; Rene, Eldon R; Veiga, María C; Kennes, Christian

    2014-03-30

    The removal efficiency (RE) of gas-phase hydrogen sulfide (H), methanol (M) and α-pinene (P) in a biotrickling filter (BTF) was modeled using artificial neural networks (ANNs). The inlet concentrations of H, M, P, unit flow and operation time were used as the model inputs, while the outputs were the RE of H, M and P, respectively. After testing and validating the results, an optimal network topology of 5-8-3 was obtained. The model predictions were analyzed using Casual index (CI) values. M removal in the BTF was influenced positively by the inlet concentration of M in mixture (CI=3.79), while the removal of P and H were influenced more by the time of BTF operation (CI=25.36, 15.62). The BTF was subjected to different types of short-term shock-loads: 5-h shock-load of HMP mixture simultaneously, and 2.5-h shock-load of either H, M, or P, individually. It was observed that, short-term shock-loads of individual pollutants (M or H) did not significantly affect their own removal, but the removal of P was affected by 50%. The results from this study also show the sensitiveness of the well-acclimated BTF to handle sudden load variations and also revival capability of the BTF when pre-shock conditions were restored. PMID:24315813

  8. Monitoring CO2 gas-phase injection in a shallow sand aquifer using cross borehole GPR and modeled with T2VOC multi-phase code

    NASA Astrophysics Data System (ADS)

    Lassen, R. N.; Jensen, K.; Looms, M. C.; Sonnenborg, T.; Gudbjerg, J.

    2013-12-01

    Risk assessment of potential leakage is an important issue that needs attention in designing effective storage schemes for CO2 storage. Leaking gas may threat groundwater resources and be a liability if pooled up in buildings. We have designed an experiment where we were track the movement of an injected CO2 gas-phase using cross borehole GPR in an unconfined sandy aquifer located in the southwestern part of Denmark. The geology at the field site has been determined using GPR- data, natural gamma ray logging in boreholes, cores sampled with a Geoprobe soil-sampling tool and grain size analysis of the cores. From these measurements the field site geology can be divided into three geological zones. The first zone is an approximately 4 m fine aeolian sand; the second zone is poorly sorted glacial deposits dominated by sand down to 9 m; and the the last zone from 9 m and down consist of well-sorted medium melt water sand. In total we conducted four short injection experiments all of them producing very similar results. The screen of the injection well was 10 m below ground level or 8 m below the water table. An array of six GPR boreholes was installed around the injection well and downwards of dominating gas flow direction. GPR-data were acquired in zero-offset (1D) and multiple-offset (2D) configurations prior and during the injection. All sets of GPR data showed that a plume developed at the depth of the injection screen and that the injected gas primarily spread towards South-East and never breach a barrier around 5 m depth. This corresponded very well with the natural gamma logs, which resulted in higher readings from 4-6.5 m depth. The grain size analyses confirmed that there is a fine sediment layer throughout the area at 4-6 meters depth. We guesstimated van Genucthen parameters from the grain size analysis and used as input to the numerical model and GPR data were used for calibration. The numerical model enabled us to test minimum entry pressure required for

  9. Analysis of uncertainties in the regional acid deposition model, version 2 (RADM2), gas-phase chemical mechanism. Final report

    SciTech Connect

    Gao, D.; Milford, J.B.; Stockwell, W.R.

    1996-04-01

    This report describes the results of a detailed analysis of uncertainties in the RADM2 chemical mechanism, which was developed by Stockwell et al. (1990) for use in urban and regional scale models of the formation and transport of ozone and other photochemical air pollutants. The uncertainty analysis was conducted for box model simulations of chemical conditions representing summertime smog episodes in polluted rural and urban areas. Estimated uncertainties in the rate parameters and product yields of the mechanism were propagated through the simulations using Monte Carlo analysis with a Latin Hypercube Sampling scheme. Uncertainty estimates for the mechanism parameters were compiled from published reviews, supplemented as necessary by original estimates. Correlations between parameters were considered in the analysis as appropriate.

  10. Back Propagation Neural Network Model for Predicting the Performance of Immobilized Cell Biofilters Handling Gas-Phase Hydrogen Sulphide and Ammonia

    PubMed Central

    Rene, Eldon R.; López, M. Estefanía; Kim, Jung Hoon; Park, Hung Suck

    2013-01-01

    Lab scale studies were conducted to evaluate the performance of two simultaneously operated immobilized cell biofilters (ICBs) for removing hydrogen sulphide (H2S) and ammonia (NH3) from gas phase. The removal efficiencies (REs) of the biofilter treating H2S varied from 50 to 100% at inlet loading rates (ILRs) varying up to 13 g H2S/m3·h, while the NH3 biofilter showed REs ranging from 60 to 100% at ILRs varying between 0.5 and 5.5 g NH3/m3·h. An application of the back propagation neural network (BPNN) to predict the performance parameter, namely, RE (%) using this experimental data is presented in this paper. The input parameters to the network were unit flow (per min) and inlet concentrations (ppmv), respectively. The accuracy of BPNN-based model predictions were evaluated by providing the trained network topology with a test dataset and also by calculating the regression coefficient (R2) values. The results from this predictive modeling work showed that BPNNs were able to predict the RE of both the ICBs efficiently. PMID:24307999

  11. A model for gas phase chemistry in interstellar clouds. II - Nonequilibrium effects and effects of temperature and activation energies

    NASA Technical Reports Server (NTRS)

    Prasad, S. S.; Huntress, W. T., Jr.

    1980-01-01

    The chemical evolution of diffuse and dense interstellar clouds is examined via the time-dependent model outlined by Prasad and Huntress (1980). This paper presents specific results for CH, CO, CH4, O2, CH2O, CN, C2, C2H, HC3N, and NH3. Comparison with observations and predictions of other contemporary models show that cloud temperature plays a very important role through the inverse temperature dependence of radiative association reactions and through activation energies in neutral reactions and selected ion-molecule reactions. The observed fractional abundance of CN with respect to H2 and more accurate recent laboratory data on CN + O and CN + O2 reactions suggest that there is an unidentified, yet efficient, mechanism for conversion of O and O2 into polyatomic species. C2H and HC3N are synthesized early in the history of dense clouds. The value of the fractional abundance of C2H remains high, because as the cloud cools down the activation energy in the C2H + O reaction closes down this most important loss channel. A rapidly decreasing fractional abundance of O with time can also accomplish the same result. The value of the fractional abundance of HC3N remains high because it is an unreactive molecule and probably does not condense readily onto grains.

  12. Gas Phase Reactivity of Carboxylates with N-Hydroxysuccinimide Esters

    NASA Astrophysics Data System (ADS)

    Peng, Zhou; McGee, William M.; Bu, Jiexun; Barefoot, Nathan Z.; McLuckey, Scott A.

    2015-01-01

    N-hydroxysuccinimide (NHS) esters have been used for gas-phase conjugation reactions with peptides at nucleophilic sites, such as primary amines (N-terminus, ɛ-amine of lysine) or guanidines, by forming amide bonds through a nucleophilic attack on the carbonyl carbon. The carboxylate has recently been found to also be a reactive nucleophile capable of initiating a similar nucleophilic attack to form a labile anhydride bond. The fragile bond is easily cleaved, resulting in an oxygen transfer from the carboxylate-containing species to the reagent, nominally observed as a water transfer. This reactivity is shown for both peptides and non-peptidic species. Reagents isotopically labeled with O18 were used to confirm reactivity. This constitutes an example of distinct differences in reactivity of carboxylates between the gas phase, where they are shown to be reactive, and the solution phase, where they are not regarded as reactive with NHS esters.

  13. Gas-phase chemistry in Oxidation Flow Reactors for the study of secondary organic aerosols systematically examined by modeling

    NASA Astrophysics Data System (ADS)

    Peng, Z.; Day, D. A.; Ortega, A. M.; Hu, W.; Palm, B. B.; Li, R.; De Gouw, J. A.; Brune, W. H.; Jimenez, J. L.

    2014-12-01

    Oxidation Flow Reactors (OFRs) using OH produced from low-pressure Hg lamps at 254 nm (OFR254) or both 185 and 254 nm (OFR185) are commonly used in atmospheric chemistry and other fields. OFR254 requires addition of externally formed O3 since OH is formed mainly from O3 photolysis, while OFR185 does not since OH can also be formed from H2O photolysis. In this study we use a plug-flow kinetic model to investigate OFR properties under a very wide range of conditions applicable to both field and laboratory studies. We show that radical chemistry in OFRs can be characterized as a function of 3 main parameters: UV light intensity, H2O concentration, and total external OH reactivity (e.g. from VOCs, NOx, and SO2). In OFR185, OH exposure is more sensitive to external OH reactivity than in OFR254, because injected O3 in OFR254 greatly promotes the recycling of HO2 to OH, making external perturbations to the radical chemistry less significant. The uncertainties of modeled OH, O3, and H2O2 due to uncertain kinetic parameters are within 40% in most cases. Sensitivity analysis shows that most of the uncertainty is contributed by photolysis and reactions involving OH and HO2, e.g. 2HO2→H2O2+O2 and OH+O3→HO2+O2. Reactants of atmospheric interest are dominantly consumed by OH, except some biogenics that can have substantial contributions from O3. Other highly reactive species (UV photons, O(1D), and O(3P)) only contribute for some species under conditions low H2O concentration and/or high external OH reactivity, which can be avoided by experimental planning. OFR185 and OFR254 are comparable in terms of non-OH oxidants' influence. In OFRs NO is fast oxidized. RO2 fate is similar to that in the atmosphere under low NO conditions. A comprehensive comparison of OFRs with typical environmental chamber studies with UV blacklights and with the atmosphere is also performed. OFRs' key advantages are their short experimental time scales, portability to field sites, and generally good

  14. REMOVAL OF ALDEHYDES FROM INDOOR AIR: ELUCIDATING ADSORPTION MECHANISMS, MODELING COMPETITIVE ADSORPTION, AND PREDICTING REMOVAL IN GAS-PHASE AIR CLEANERS

    EPA Science Inventory

    This research project will identify specific chemical and physical characteristics of activated carbon surfaces that promote the removal of gas-phase, polar organic pollutants. It is expected that basic and acidic functional groups will influence aldehyde adsorption through di...

  15. A new model for multiply charged adduct formation between peptides and anions in electrospray mass spectrometry.

    PubMed

    Liu, Xiaohua; Cole, Richard B

    2011-12-01

    A new model has been developed to account for adduct formation on multiply charged peptides observed in negative ion electrospray mass spectrometry. To obtain a stable adduct, the model necessitates an approximate matching of apparent gas-phase basicity (GB(app)) of a given proton bearing site on the peptide with the gas-phase basicity (GB) of the anion attaching at that site. Evidence supporting the model is derived from the fact that for [Glu] Fibrinopeptide B, higher GB anions dominated in adducts observed at higher negative charge states, whereas lower GB anions appeared predominately in lower charge state adducts. Singly charged adducts were only observed for lower GB anions: HSO(4)(-), I(-), CF(3)COO(-). Ions that have medium GBs (NO(3) (-), Br(-), H(2)PO(4)(-)) only form adducts having -2 charge states, whereas Cl(-) (higher GB) can form adducts having -3 charge states. The model portends that (1) carboxylate groups are much more basic than available amino groups; (2) apparent GBs of the various carboxylate groups on peptides do not vary substantially from one another; and (3) apparent GBs of the individual carboxylate and amino sites do not behave independently. This model was developed for negative ion attachment but an analogous mechanism is also proposed for the positive ion mode wherein (1) binding of a neutral at an amino site polarizes this amino group, but hardly affects apparent GBs of other sites; (2) proton addition (charge state augmentation) at one site can decrease the instrinsic GBs of other potential protonation sites and lower their apparent GBs. PMID:21997579

  16. A New Model for Multiply Charged Adduct Formation Between Peptides and Anions in Electrospray Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Liu, Xiaohua; Cole, Richard B.

    2011-12-01

    A new model has been developed to account for adduct formation on multiply charged peptides observed in negative ion electrospray mass spectrometry. To obtain a stable adduct, the model necessitates an approximate matching of apparent gas-phase basicity (GBapp) of a given proton bearing site on the peptide with the gas-phase basicity (GB) of the anion attaching at that site. Evidence supporting the model is derived from the fact that for [Glu] Fibrinopeptide B, higher GB anions dominated in adducts observed at higher negative charge states, whereas lower GB anions appeared predominately in lower charge state adducts. Singly charged adducts were only observed for lower GB anions: HSO{4/-}, I-, CF3COO-. Ions that have medium GBs (NO{3/-}, Br-, H2PO{4/-}) only form adducts having -2 charge states, whereas Cl- (higher GB) can form adducts having -3 charge states. The model portends that (1) carboxylate groups are much more basic than available amino groups; (2) apparent GBs of the various carboxylate groups on peptides do not vary substantially from one another; and (3) apparent GBs of the individual carboxylate and amino sites do not behave independently. This model was developed for negative ion attachment but an analogous mechanism is also proposed for the positive ion mode wherein (1) binding of a neutral at an amino site polarizes this amino group, but hardly affects apparent GBs of other sites; (2) proton addition (charge state augmentation) at one site can decrease the instrinsic GBs of other potential protonation sites and lower their apparent GBs.

  17. A model of the gas-phase chemistry of boron nitride CVC from BCl{sub 3} and NH{sub 3}

    SciTech Connect

    Allendorf, M.D.; Melius, C.F.; Osterheld, T.H.

    1995-12-01

    The kinetics of gas-phase reactions occurring during the CVD of boron nitride (BN) from BCl{sub 3} and NH{sub 3} are investigated using an elementary reaction mechanism whose rate constants were obtained from theoretical predictions and literature sources. Plug-flow calculations using this mechanism predict that unimolecular decomposition of BCl{sub 3} is not significant under typical CVD conditions, but that some NH{sub 3} decomposition may occur, especially for deposition occurring at atmospheric pressure. Reaction of BCl{sub 3} with NH{sub 3} is rapid under CVD conditions and yields species containing both boron and nitrogen. One of these compounds, Cl{sub 2}BNH{sub 2}, is predicted to be a key gas-phase precursor to BN.

  18. Rate processes in gas phase

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1983-01-01

    Reaction-rate theory and experiment are given a critical review from the engineers' point of view. Rates of heavy-particle, collision-induced reaction in gas phase are formulated in terms of the cross sections and activation energies for reaction. The effect of cross section function shape and of excited state contributions to reaction both cause the slope of Arrhenius plots to differ from the true activation energy, except at low temperature. The master equations for chemically reacting gases are introduced, and dissociation and ionization reactions are shown to proceed primarily from excited states about kT from the dissociation or ionization limit. Collision-induced vibration, vibration-rotation, and pure rotation transitions are treated, including three-dimensional effects and conservation of energy, which have usually been ignored. The quantum theory of transitions at potential surface crossing is derived, and results are found to be in fair agreement with experiment in spite of some questionable approximations involved.

  19. The bimolecular gas-phase reaction of protonated alkyldipeptides with acetonylacetone

    NASA Astrophysics Data System (ADS)

    Gur, Erez H.; de Koning, L. J.; Nibbering, N. M. M.

    1997-11-01

    The gas-phase reaction of protonated alkyldipeptides with acetonylacetone has been studied in a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer. The reaction is identified as the gas-phase analogue of Paal-Knorr pyrrole synthesis. Under thermal conditions, the reaction complex loses a water molecule during a condensation reaction, which couples the dipeptide to the acetonylacetone molecule via an imine bond. Low energy collisional activation of the long-lived imine product ion induces additional loss of a water molecule to form the protonated 2,5-dimethylpyrrole derivative of the dipeptide. Detailed insight into the mechanism is obtained by a comparison of the reactivity of various alkyldipeptides with model compounds with amino functional groups. The reaction is catalysed by the peptide carbonyl groups, which assist in the protonation of the acetonylacetone carbonyl oxygen atoms, making the acetonylacetone carbonyl carbon atoms susceptible to nucleophilic attack by the peptide amino group. From both the previously studied bimolecular hydrogen-deuterium exchange behaviour and the presently studied reaction with acetonylacetone, it follows that the bimolecular reactivity of protonated alkyldipeptides is related to the extent of mobility of the proton within the reactive complex.

  20. Oscillatory burning of solid propellants including gas phase time lag.

    NASA Technical Reports Server (NTRS)

    T'Ien, J. S.

    1972-01-01

    An analysis has been performed for oscillatory burning of solid propellants including gas phase time lag. The gaseous flame is assumed to be premixed and laminar with a one-step overall chemical reaction. The propellant is assumed to decompose according to the Arrenhius Law, with no condensed phase reaction. With this model, strong gas phase resonance has been found in certain cases at the characteristic gas-phase frequencies, but the peaking of the acoustic admittance is in the direction favoring the damping of pressure waves. At still higher frequencies, moderate wave-amplifying ability was found. The limit of low frequency response obtained previously by Denison and Baum was recovered, and the limitations of the quasi-steady theory were investigated.

  1. Analysis of the gas phase reactivity of chlorosilanes.

    PubMed

    Ravasio, Stefano; Masi, Maurizio; Cavallotti, Carlo

    2013-06-27

    Trichlorosilane is the most used precursor to deposit silicon for photovoltaic applications. Despite of this, its gas phase and surface kinetics have not yet been completely understood. In the present work, it is reported a systematic investigation aimed at determining what is the dominant gas phase chemistry active during the chemical vapor deposition of Si from trichlorosilane. The gas phase mechanism was developed calculating the rate constant of each reaction using conventional transition state theory in the rigid rotor-harmonic oscillator approximation. Torsional vibrations were described using a hindered rotor model. Structures and vibrational frequencies of reactants and transition states were determined at the B3LYP/6-31+G(d,p) level, while potential energy surfaces and activation energies were computed at the CCSD(T) level using aug-cc-pVDZ and aug-cc-pVTZ basis sets extrapolating to the complete basis set limit. As gas phase and surface reactivities are mutually interlinked, simulations were performed using a microkinetic surface mechanism. It was found that the gas phase reactivity follows two different routes. The disilane mechanism, in which the formation of disilanes as reaction intermediates favors the conversion between the most stable monosilane species, and the radical pathway, initiated by the decomposition of Si2HCl5 and followed by a series of fast propagation reactions. Though both mechanisms are active during deposition, the simulations revealed that above a certain temperature and conversion threshold the radical mechanism provides a faster route for the conversion of SiHCl3 into SiCl4, a reaction that favors the overall Si deposition process as it is associated with the consumption of HCl, a fast etchant of Si. Also, this study shows that the formation of disilanes as reactant intermediates promotes significantly the gas phase reactivity, as they contribute both to the initiation of radical chain mechanisms and provide a catalytic route for

  2. Magnetic field dependence of the product yields of cycloheptanone photolysis in the dilute gas phase

    NASA Astrophysics Data System (ADS)

    Stich, E. M.; Baumeister, W. F.; Huber, J. Robert

    1984-07-01

    The product yields of the gas-phase photolysis of cycloheptanone were measured in magnetic fields up to 10 kG. The magnetic-field effect is explained in terms of the radical pair model. A reaction mechanism is proposed that explains the magnetic field dependence, pressure dependence, and excitation enegy dependence of the gas-phase photochemistry of cycloheptanone.

  3. Self-Assembled Multimetallic/Peptide Complexes: Structures and Unimolecular Reactions of [Mn (GlyGly-H)2n-1 ](+) and Mn+1 (GlyGly-H2n ](2+) Clusters in the Gas Phase.

    PubMed

    Moghaddam, Maryam B; Jami-Alahmadi, Yasaman; Fridgen, Travis D

    2015-10-26

    The unimolecular chemistry and structures of self-assembled complexes containing multiple alkaline-earth-metal dications and deprotonated GlyGly ligands are investigated. Singly and doubly charged ions [Mn (GlyGly-H)n-1 ](+) (n=2-4), [Mn+1 (GlyGly-H)2n ](2+) (n=2,4,6), and [M(GlyGly-H)GlyGly](+) were observed. The losses of 132 Da (GlyGly) and 57 Da (determined to be aminoketene) were the major dissociation pathways for singly charged ions. Doubly charged Mg(2+) clusters mainly lost GlyGly, whereas those containing Ca(2+) or Sr(2+) also underwent charge separation. Except for charge separation, no loss of metal cations was observed. Infrared multiple photon dissociation spectra were the most consistent with the computed IR spectra for the lowest energy structures, in which deprotonation occurs at the carboxyl acid groups and all amide and carboxylate oxygen atoms are complexed to the metal cations. The N-H stretch band, observed at 3350 cm(-1) , is indicative of hydrogen bonding between the amine nitrogen atoms and the amide hydrogen atom. This study represents the first into large self-assembled multimetallic complexes bound by peptide ligands. PMID:26279054

  4. Modelling water molecules inside cyclic peptide nanotubes

    NASA Astrophysics Data System (ADS)

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2016-03-01

    Cyclic peptide nanotubes occur during the self-assembly process of cyclic peptides. Due to the ease of synthesis and ability to control the properties of outer surface and inner diameter by manipulating the functional side chains and the number of amino acids, cyclic peptide nanotubes have attracted much interest from many research areas. A potential application of peptide nanotubes is their use as artificial transmembrane channels for transporting ions, biomolecules and waters into cells. Here, we use the Lennard-Jones potential and a continuum approach to study the interaction of a water molecule in a cyclo[(- D-Ala- L-Ala)_4-] peptide nanotube. Assuming that each unit of a nanotube comprises an inner and an outer tube and that a water molecule is made up of a sphere of two hydrogen atoms uniformly distributed over its surface and a single oxygen atom at the centre, we determine analytically the interaction energy of the water molecule and the peptide nanotube. Using this energy, we find that, independent of the number of peptide units, the water molecule will be accepted inside the nanotube. Once inside the nanotube, we show that a water molecule prefers to be off-axis, closer to the surface of the inner nanotube. Furthermore, our study of two water molecules inside the peptide nanotube supports the finding that water molecules form an array of a 1-2-1-2 file inside peptide nanotubes. The theoretical study presented here can facilitate thorough understanding of the behaviour of water molecules inside peptide nanotubes for applications, such as artificial transmembrane channels.

  5. Chemical Models of Peptide Formation in Translation

    PubMed Central

    Watts, R. Edward; Forster, Anthony C.

    2010-01-01

    Ribosomal incorporations of N-alkyl amino acids including proline are slower than incorporations of non-N-alkyl L-amino acids. The “chemical reactivity hypothesis” proposes that these results, and the exclusion of non-proline N-alkyl amino acids from the genetic code, are explained by intrinsic chemical reactivities of the amino acid nucleophiles. However, there is little data on the reactivities relevant to physiological conditions. Here, we use non-enzymatic, aqueous-based assays to model 11 amino acid nucleophiles in dipeptide formation. The relative rates in the non-enzymatic and translation systems correlate well, supporting the chemical reactivity hypothesis and arguing that peptide bond formation, not accommodation, is rate limiting for natural Pro-tRNAPro isoacceptors. The effects of N-substitution sterics, side chain sterics, induction and pKa were evaluated in the chemical model. The dominant factor affecting relative rates was found to be N-substitution sterics. PMID:20141197

  6. Electrothermal vaporization, part 1: gas phase chemistry

    NASA Astrophysics Data System (ADS)

    Majidi, Vahid; Xu, Ning; Smith, Robert G.

    2000-01-01

    This manuscript is the first of a two-part publication on evaluation of vaporization and atomization processes in electrothermal vaporizers (ETV). Part 1 is specifically focused on gas phase (and heterogeneous) chemistry in ETVs. Molecular absorption spectroscopy and thermogravimetric analysis (in conjunction with gas-phase mass spectrometry) are used to investigate the vaporization of Mg, Ca, Sr, Ba, Co and Ni (chloride and nitrate salts). Graphite, Pt, and Ta were used as substrate material for vaporizers to elucidate some observations of gas-phase chemistry. The experiments in Part I and II of this series are intentionally performed using wall vaporization to closely mimic the conditions used when ETV is employed as a sample introduction device.

  7. Liquid-gas phase transition in nuclear matter including strangeness

    SciTech Connect

    Wang, P.; Leinweber, D.B.; Williams, A.G.; Thomas, A.W.

    2004-11-01

    We apply the chiral SU(3) quark mean field model to study the properties of strange hadronic matter at finite temperature. The liquid-gas phase transition is studied as a function of the strangeness fraction. The pressure of the system cannot remain constant during the phase transition, since there are two independent conserved charges (baryon and strangeness number). In a range of temperatures around 15 MeV (precise values depending on the model used) the equation of state exhibits multiple bifurcates. The difference in the strangeness fraction f{sub s} between the liquid and gas phases is small when they coexist. The critical temperature of strange matter turns out to be a nontrivial function of the strangeness fraction.

  8. Comparing the gas-phase fragmentation reactions of protonated and radical cations of the tripeptides GXR

    NASA Astrophysics Data System (ADS)

    Wee, Sheena; O'Hair, Richard A. J.; McFadyen, W. David

    2004-05-01

    Electrospray ionization (ESI) mass spectrometry of methanolic solutions of mixtures of the copper salt (2,2':6',2''-terpyridine)copper(II) nitrate monohydrate ([Cu(II)(tpy)(NO3)2].H2O) and a tripeptide GXR (where X = 1 of the 20 naturally occurring amino acids) yielded [Cu(II)(tpy)(GXR)][radical sign]2+ ions, which were then subjected to collision induced dissociation (CID). In all but one case (GRR), these [Cu(II)(tpy)(GXR)][radical sign]2+ ions fragment to form odd electron GXR[radical sign]+ radical cations with sufficient abundance to examine their gas-phase fragmentation reactions. The GXR[radical sign]+ radical cations undergo a diverse range of fragmentation reactions which depend on the nature of the side chain of X. Many of these reactions can be rationalized as arising from the intermediacy of isomeric distonic ions in which the charge (i.e. proton) is sequestered by the highly basic arginine side chain and the radical site is located at various positions on the tripeptide including the peptide back bone and side chains. The radical sites in these distonic ions often direct the fragmentation reactions via the expulsion of small radicals (to yield even electron ions) or small neutrals (to form radical cations). Both classes of reaction can yield useful structural information, allowing for example, distinction between leucine and isoleucine residues. The gas-phase fragmentation reactions of the GXR[radical sign]+ radical cations are also compared to their even electron [GXR+H]+ and [GXR+2H]2+ counterparts. The [GXR+H]+ ions give fewer sequence ions and more small molecule losses while the [GXR+2H]2+ ions yield more sequence information, consistent with the [`]mobile proton model' described in previous studies. In general, all three classes of ions give complementary structural information, but the GXR[radical sign]+ radical cations exhibit a more diverse loss of small species (radicals and neutrals). Finally, links between these gas-phase results and key

  9. Gas-Phase Infrared; JCAMP Format

    National Institute of Standards and Technology Data Gateway

    SRD 35 NIST/EPA Gas-Phase Infrared; JCAMP Format (PC database for purchase)   This data collection contains 5,228 infrared spectra in the JCAMP-DX (Joint Committee for Atomic and Molecular Physical Data "Data Exchange") format.

  10. Continuous-Flow Gas-Phase Bioreactors

    NASA Technical Reports Server (NTRS)

    Wise, Donald L.; Trantolo, Debra J.

    1994-01-01

    Continuous-flow gas-phase bioreactors proposed for biochemical, food-processing, and related industries. Reactor contains one or more selected enzymes dehydrated or otherwise immobilized on solid carrier. Selected reactant gases fed into reactor, wherein chemical reactions catalyzed by enzyme(s) yield product biochemicals. Concept based on discovery that enzymes not necessarily placed in traditional aqueous environments to function as biocatalysts.

  11. Modeling vapor uptake induced mobility shifts in peptide ions observed with transversal modulation ion mobility spectrometry-mass spectrometry.

    PubMed

    Rawat, Vivek K; Vidal-de-Miguel, Guillermo; Hogan, Christopher J

    2015-10-21

    Low field ion mobility spectrometry-mass spectrometry (IMS-MS) techniques exhibit low orthogonality, as inverse mobility often scales with mass to charge ratio. This inadequacy can be mitigated by adding vapor dopants, which may cluster with analyte ions and shift their mobilities by amounts independent of both mass and mobility of the ion. It is therefore important to understand the interactions of vapor dopants with ions, to better quantify the extent of dopant facilitated mobility shifts. Here, we develop predictive models of vapor dopant facilitated mobility shifts, and compare model calculations to measurements of mobility shifts for peptide ions exposed to variable gas phase concentrations of isopropanol. Mobility measurements were made at atmospheric pressure and room temperature using a recently developed transversal modulation ion mobility spectrometer (TMIMS). Results are compared to three separate models, wherein mobility shifts due to vapor dopants are attributed to changes in gas composition and (I) no vapor dopant uptake is assumed, (II) site-specific dopant uptake by the ion is assumed (approximated via a Langmuir adsorption model), and (III) site-unspecific dopant uptake by the ion is assumed (approximated via a classical nucleation model). We find that mobility shifts in peptide ions are in excellent agreement with model II, site-specific binding predictions. Conversely, mobility shifts of tetraalkylammonium ions from previous measurements were compared with these models and best agreement was found with model III predictions, i.e. site-unspecific dopant uptake. PMID:26051323

  12. Information-driven modeling of protein-peptide complexes.

    PubMed

    Trellet, Mikael; Melquiond, Adrien S J; Bonvin, Alexandre M J J

    2015-01-01

    Despite their biological importance in many regulatory processes, protein-peptide recognition mechanisms are difficult to study experimentally at the structural level because of the inherent flexibility of peptides and the often transient interactions on which they rely. Complementary methods like biomolecular docking are therefore required. The prediction of the three-dimensional structure of protein-peptide complexes raises unique challenges for computational algorithms, as exemplified by the recent introduction of protein-peptide targets in the blind international experiment CAPRI (Critical Assessment of PRedicted Interactions). Conventional protein-protein docking approaches are often struggling with the high flexibility of peptides whose short sizes impede protocols and scoring functions developed for larger interfaces. On the other side, protein-small ligand docking methods are unable to cope with the larger number of degrees of freedom in peptides compared to small molecules and the typically reduced available information to define the binding site. In this chapter, we describe a protocol to model protein-peptide complexes using the HADDOCK web server, working through a test case to illustrate every steps. The flexibility challenge that peptides represent is dealt with by combining elements of conformational selection and induced fit molecular recognition theories. PMID:25555727

  13. Revisiting a many-body model for water based on a single polarizable site: From gas phase clusters to liquid and air/liquid water systems

    NASA Astrophysics Data System (ADS)

    Réal, Florent; Vallet, Valérie; Flament, Jean-Pierre; Masella, Michel

    2013-09-01

    We present a revised version of the water many-body model TCPE [M. Masella and J.-P. Flament, J. Chem. Phys. 107, 9105 (1997)], which is based on a static three charge sites and a single polarizable site to model the molecular electrostatic properties of water, and on an anisotropic short range many-body energy term specially designed to accurately model hydrogen bonding in water. The parameters of the revised model, denoted TCPE/2013, are here developed to reproduce the ab initio energetic and geometrical properties of small water clusters (up to hexamers) and the repulsive water interactions occurring in cation first hydration shells. The model parameters have also been refined to reproduce two liquid water properties at ambient conditions, the density and the vaporization enthalpy. Thanks to its computational efficiency, the new model range of applicability was validated by performing simulations of liquid water over a wide range of temperatures and pressures, as well as by investigating water liquid/vapor interfaces over a large range of temperatures. It is shown to reproduce several important water properties at an accurate enough level of precision, such as the existence liquid water density maxima up to a pressure of 1000 atm, the water boiling temperature, the properties of the water critical point (temperature, pressure, and density), and the existence of a "singularity" temperature at about 225 K in the supercooled regime. This model appears thus to be particularly well-suited for characterizing ion hydration properties under different temperature and pressure conditions, as well as in different phases and interfaces.

  14. Revisiting a many-body model for water based on a single polarizable site: from gas phase clusters to liquid and air/liquid water systems.

    PubMed

    Réal, Florent; Vallet, Valérie; Flament, Jean-Pierre; Masella, Michel

    2013-09-21

    We present a revised version of the water many-body model TCPE [M. Masella and J.-P. Flament, J. Chem. Phys. 107, 9105 (1997)], which is based on a static three charge sites and a single polarizable site to model the molecular electrostatic properties of water, and on an anisotropic short range many-body energy term specially designed to accurately model hydrogen bonding in water. The parameters of the revised model, denoted TCPE/2013, are here developed to reproduce the ab initio energetic and geometrical properties of small water clusters (up to hexamers) and the repulsive water interactions occurring in cation first hydration shells. The model parameters have also been refined to reproduce two liquid water properties at ambient conditions, the density and the vaporization enthalpy. Thanks to its computational efficiency, the new model range of applicability was validated by performing simulations of liquid water over a wide range of temperatures and pressures, as well as by investigating water liquid/vapor interfaces over a large range of temperatures. It is shown to reproduce several important water properties at an accurate enough level of precision, such as the existence liquid water density maxima up to a pressure of 1000 atm, the water boiling temperature, the properties of the water critical point (temperature, pressure, and density), and the existence of a "singularity" temperature at about 225 K in the supercooled regime. This model appears thus to be particularly well-suited for characterizing ion hydration properties under different temperature and pressure conditions, as well as in different phases and interfaces. PMID:24070292

  15. A new method for measurement of gas-phase ammonia and amines in air

    NASA Astrophysics Data System (ADS)

    Dawson, M. L.; Gomez, A.; Arquero, K. D.; Perraud, V. M.; Finlayson-Pitts, B. J.

    2013-12-01

    Accurately predicting particle formation and growth from gas phase precursors is an essential component of modeling the impact of particulate matter on human health, visibility and climate. While the reactions of ammonia with nitric and sulfuric acids to form particulate nitrate and sulfate particles is well known, it has been recently recognized that gas-phase amines, even at low ppb levels, significantly enhance particle formation from common atmospheric acids. As a result, accurate data on the sources, sinks and typical background concentrations of gas-phase amines, are crucial to predicting new particle formation in the atmosphere. However, gas-phase amines are notoriously difficult to measure, as they have a tendency to stick to surfaces, including sampling lines and inlets. In addition, background amine concentrations in the atmosphere are typically a few ppb or lower, requiring low detection limits for ambient sampling techniques. Here we report the development of a simple, reliable method for detection of gas-phase amines at atmospherically relevant concentrations using collection on a cation exchange sorbent followed by in-line extraction and ion chromatography. Gas-phase standards of several amines and ammonia are used to characterize the technique and results from ambient samples in an agricultural area are presented. The application of this technique to field measurements as well as to laboratory measurements of new particle formation from gas-phase ammonia and amines are discussed.

  16. Gas phase chemistry of chlorine nitrate

    SciTech Connect

    Okumura, M.; Moore, T.A.; Crellin, K.C.

    1995-12-31

    Chlorine nitrate (ClONO{sub 2}) is a reservoir of both ClO{sub x} and NO{sub x} radicals in Earth`s stratosphere, and its decomposition is important in determining the abundance of stratospheric ozone. We present experimental and theoretical studies that explore the mechanisms and dynamics of processes leading to ClONO{sub 2} destruction in the stratosphere. Molecular beam photodissociation experiments have been performed to determine the decomposition pathways of ClONO{sub 2} upon excitation at 308 nm and to explore the possibility of a long-lived excited state. We have also investigated the reaction of chlorine nitrate with chloride ions Cl{sup -} in the gas phase. The gas phase ionic reaction may elucidate ionic mechanisms of heterogeneous reactions occurring on the surfaces of Polar Stratospheric Cloud particles and also raise doubts about proposed schemes to mitigate ozone depletion by electrifying the stratosphere.

  17. Gas phase chemistry of the transactinides

    NASA Astrophysics Data System (ADS)

    Türler, A.

    1999-01-01

    In the past few years the gas phase chemistry of the first three transactinide elements rutherfordium (element 104), dubnium (element 105) and seaborgium (element 106) has been studied experimentally using OLGA, the On-line Gas chemistry Apparatus, developed at Paul Scherrer Institute. In each experiment, the investigated transactinide element was identified by measuring the characteristic decay properties of its isotopes. In the chemistry of rutherfordium and dubnium evidence for relativistic effects were found, as predicted previously in theoretical calculations. For the first time, the volatility of Sg oxychlorides in comparison to its lighter homologues W and Mo was measured. Also, the half-lives and SF-branches of the nuclides 265Sg and 266Sg were determined. Finally, prospects for a chemical separation of bohrium (element 107) and hassium (element 108) using gas phase chemistry will be discussed.

  18. The gas-phase acidity of nitrocyclopropane

    NASA Astrophysics Data System (ADS)

    Bartmess, John E.; Wilson, Burton; Sorensen, Daniel N.; Bloor, John E.

    1992-09-01

    Nitrocyclopropane is 10.5 kcal mol-1 weaker as an acid in the gas phase than its open-chain analog, 2-nitropropane. This is attributed to the conflicting hybridization requirements for carbanion stabilization by the cyclopropyl ring and by the nitro group. Based on reactivities, the deprotonated form does not ring-open to either the 2-nitroallyl anion or the 1-nitroallyl anion.

  19. Gas-Phase Photoionization Of A Protein

    NASA Astrophysics Data System (ADS)

    Milosavljevic, A. R.; Giuliani, A.; Nicolas, C.; Gil, J.-F.; Lemaire, J.; Refregiers, M.; Nahon, L.

    2010-07-01

    We present preliminary results on gas phase photoionization of electrosprayproduced multiply protonated cytochrome c protein (104 amino acids; ˜12.4 kDa), which has been achieved with a newly developed experimental system for spectroscopy of electrosprayed ions in a linear quadrupole ion trap using a monochromatized vacuum ultraviolet (VUV) synchrotron radiation and tandem mass spectrometry method. The investigation of proteins in the gas phase, where they are free of the influence of counterions and solvent molecules, offer a possibility to understand their intrinsic molecular properties. However, due to limited both ion densities and available number of photons, the use of synchrotron radiation for the trapped ions spectroscopy is a rather challenging task. The feasibility of coupling a Fourier transform ion cyclotron resonance ion trap with soft x-ray synchrotron beamline and the first successful use of synchrotron radiation for spectroscopy of electrosprayed negative ions stored in a three-dimensional quadrupole ion trap have been demonstrated only recently (R. Thissen et al., 2008, Phys. Rev. Lett., 100, 223001; A. Giulliani et al., Proc. 57th ASMS Conf., Philadelphia, 2009). The present results are the first reported on photoionization of kDa species in the gas phase and are valuable regarding both a fundamental interest of accessing physical properties of large biological ions isolated in vacuo and potential development of a new technique for proteomics.

  20. Infrared spectroscopic and modeling studies of H2/CH4 microwave plasma gas phase from low to high pressure and power

    NASA Astrophysics Data System (ADS)

    Rond, C.; Hamann, S.; Wartel, M.; Lombardi, G.; Gicquel, A.; Röpcke, J.

    2014-09-01

    InfraRed Tunable Diode Laser Absorption Spectroscopy technique has been implemented in a H2/CH4 Micro-Wave (MW frequency f = 2.45 GHz) plasma reactor dedicated to diamond deposition under high pressure and high power conditions. Parametric studies such as a function of MW power, pressure, and admixtures of methane have been carried out on a wide range of experimental conditions: the pressure up to 270 mbar and the MW power up to 4 kW. These conditions allow high purity Chemical Vapor Deposition diamond deposition at high growth rates. Line integrated absorption measurements have been performed in order to monitor hydrocarbon species, i.e., CH3, CH4, C2H2, C2H4, and C2H6. The densities of the stable detected species were found to vary in the range of 1012-1017 molecules cm-3, while the methyl radical CH3 (precursor of diamond growth under these conditions) measured into the plasma bulk was found up to 1014 molecules cm-3. The experimental densities have been compared to those provided by 1D-radial thermochemical model for low power and low pressure conditions (up to 100 mbar/2 kW). These densities have been axially integrated. Experimental measurements under high pressure and power conditions confirm a strong increase of the degree of dissociation of the precursor, CH4, associated to an increase of the C2H2 density, the most abundant reaction product in the plasma.

  1. Infrared spectroscopic and modeling studies of H{sub 2}/CH{sub 4} microwave plasma gas phase from low to high pressure and power

    SciTech Connect

    Rond, C. Lombardi, G.; Gicquel, A.; Hamann, S.; Röpcke, J.; Wartel, M.

    2014-09-07

    InfraRed Tunable Diode Laser Absorption Spectroscopy technique has been implemented in a H{sub 2}/CH{sub 4} Micro-Wave (MW frequency f = 2.45 GHz) plasma reactor dedicated to diamond deposition under high pressure and high power conditions. Parametric studies such as a function of MW power, pressure, and admixtures of methane have been carried out on a wide range of experimental conditions: the pressure up to 270 mbar and the MW power up to 4 kW. These conditions allow high purity Chemical Vapor Deposition diamond deposition at high growth rates. Line integrated absorption measurements have been performed in order to monitor hydrocarbon species, i.e., CH{sub 3}, CH{sub 4}, C{sub 2}H{sub 2}, C{sub 2}H{sub 4}, and C{sub 2}H{sub 6}. The densities of the stable detected species were found to vary in the range of 10{sup 12}–10{sup 17} molecules cm{sup −3}, while the methyl radical CH{sub 3} (precursor of diamond growth under these conditions) measured into the plasma bulk was found up to 10{sup 14} molecules cm{sup −3}. The experimental densities have been compared to those provided by 1D-radial thermochemical model for low power and low pressure conditions (up to 100 mbar/2 kW). These densities have been axially integrated. Experimental measurements under high pressure and power conditions confirm a strong increase of the degree of dissociation of the precursor, CH{sub 4}, associated to an increase of the C{sub 2}H{sub 2} density, the most abundant reaction product in the plasma.

  2. A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation

    PubMed Central

    Kang, Myungshim

    2010-01-01

    A pairwise preferential interaction model (PPIM), based on Kirkwood–Buff integrals, is developed to quantify and characterize the interactions between some of the functional groups commonly observed in peptides. The existing experimental data are analyzed to determine the preferential interaction (PI) parameters for different amino acid and small peptide systems in aqueous solutions. The PIs between the different functional groups present in the peptides are then isolated and quantified by assuming simple pairwise additivity. The PPIM approach provides consistent estimates for the pair interactions between the same functional groups obtained from different solute molecules. Furthermore, these interactions appear to be chemically intuitive. It is argued that this type of approach can provide valuable information concerning specific functional group correlations which could give rise to peptide aggregation. PMID:20694045

  3. Conformational preferences of flavone and isoflavone in the gas phase, aqueous solution and organic solution

    NASA Astrophysics Data System (ADS)

    Ishiki, Hamilton Mitsugu; Alemán, Carlos; Galembeck, Sérgio Emanuel

    1998-05-01

    Flavone and isoflavone are an important class of secondary metabolites that are widely distributed in nature. In this Letter we have determined the conformational preferences of each compound in the gas phase, aqueous solution and organic solution. Gas-phase calculations were performed using AM1, MNDO, HF/3-21G, HF/6-31G(d) and B3-LYP/6-31G(d) calculations. Besides solution calculations were performed using the MST solvation model.

  4. Oxidation of Methionine Residues in Polypeptide Ions Via Gas-Phase Ion/Ion Chemistry

    NASA Astrophysics Data System (ADS)

    Pilo, Alice L.; McLuckey, Scott A.

    2014-06-01

    The gas-phase oxidation of methionine residues is demonstrated here using ion/ion reactions with periodate anions. Periodate anions are observed to attach in varying degrees to all polypeptide ions irrespective of amino acid composition. Direct proton transfer yielding a charge-reduced peptide ion is also observed. In the case of methionine and, to a much lesser degree, tryptophan-containing peptide ions, collisional activation of the complex ion generated by periodate attachment yields an oxidized peptide product (i.e., [M + H + O]+), in addition to periodic acid detachment. Detachment of periodic acid takes place exclusively for peptides that do not contain either a methionine or tryptophan side chain. In the case of methionine-containing peptides, the [M + H + O]+ product is observed at a much greater abundance than the proton transfer product (viz., [M + H]+). Collisional activation of oxidized Met-containing peptides yields a signature loss of 64 Da from the precursor and/or product ions. This unique loss corresponds to the ejection of methanesulfenic acid from the oxidized methionine side chain and is commonly used in solution-phase proteomics studies to determine the presence of oxidized methionine residues. The present work shows that periodate anions can be used to `label' methionine residues in polypeptides in the gas phase. The selectivity of the periodate anion for the methionine side chain suggests several applications including identification and location of methionine residues in sequencing applications.

  5. Helix versus sheet formation in a small peptide

    NASA Astrophysics Data System (ADS)

    Peng, Yong; Hansmann, Ulrich H.

    2003-10-01

    Segments with the amino acid sequence EKAYLRT (glutamine-lysine-alanine-tyrosine-leucine-arginine-threonine) appear in naturally occurring proteins both in α-helices and β-sheets. For this reason, we have used this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both the solvated molecule and EKAYLRT in gas phase form an α-helix when not interacting with other molecules. However, in the vicinity of a β-strand, the peptide forms a β-strand. Because of this change in secondary structure our peptide may provide a simple model for the α→β transition that is supposedly related to the outbreak of prion diseases and similar illnesses.

  6. Gas phase thermochemistry of organogermanium compounds

    SciTech Connect

    Engel, J.P.

    1993-12-07

    A variety of silyl- and alkyl-germylene precursors have been synthesized and subsequently pyrolyzed in the gas phase. Arrhenius parameters were obtained employing a pulsed-stirred flow reactor for these unimolecular decompositions. These precursors are divided into two major categories by mechanism of germylene extrusion: {alpha}-elimination precursors and germylacetylenes. The extrusion of germylenes from germylacetylene precursors is of primary interest. A mechanism is proposed employing a germacyclopropene intermediate. Evidence supporting this mechanism is presented. In the process of exploring germylacetylenes as germylene precursors, an apparent dyatropic rearrangement between germanium and silicon was observed. This rearrangement was subsequently explored.

  7. 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.

  8. Base pair analogs in the gas phase.

    PubMed

    Roscioli, Joseph R; Pratt, David W

    2003-11-25

    A rotationally resolved electronic spectrum of the gas-phase dimer 2-aminopyridine.2-pyridone, an analog of the adenine.thymine base pair, has been observed and assigned, leading to precise measurements of its moments of inertia and preliminary determinations of its structure. A Watson-Crick configuration results, with N...H-N and N-H...O hydrogen bond lengths of 2.898 and 2.810 A, respectively. The two bases are found not to be coplanar; a dihedral angle of 6.1 degrees between the base planes is also estimated from the measured moments of inertia. Possible chemical and biological implications of these results are discussed. PMID:14612563

  9. Gas-phase protonation thermochemistry of adenosine.

    PubMed

    Touboul, David; Bouchoux, Guy; Zenobi, Renato

    2008-09-18

    The goal of this work was to obtain a detailed insight on the gas-phase protonation energetic of adenosine using both mass spectrometric experiments and quantum chemical calculations. The experimental approach used the extended kinetic method with nanoelectrospray ionization and collision-induced dissociation tandem mass spectrometry. This method provides experimental values for proton affinity, PA(adenosine) = 979 +/- 1 kJ.mol (-1), and for the "protonation entropy", Delta p S degrees (adenosine) = S degrees (adenosineH +) - S degrees (adenosine) = -5 +/- 5 J.mol (-1).K (-1). The corresponding gas-phase basicity is consequently equal to: GB(adenosine) = 945 +/- 2 kJ.mol (-1) at 298K. Theoretical calculations conducted at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) level, including 298 K enthalpy correction, predict a proton affinity value of 974 kJ.mol (-1) after consideration of isodesmic proton transfer reactions with pyridine as the reference base. Moreover, computations clearly showed that N3 is the most favorable protonation site for adenosine, due to a strong internal hydrogen bond involving the hydroxyl group at the 2' position of the ribose sugar moiety, unlike observations for adenine and 2'-deoxyadenosine, where protonation occurs on N1. The existence of negligible protonation entropy is confirmed by calculations (theoretical Delta p S degrees (adenosine) approximately -2/-3 J.mol (-1).K (-1)) including conformational analysis and entropy of hindered rotations. Thus, the calculated protonation thermochemical properties are in good agreement with our experimental measurements. It may be noted that the new PA value is approximately 10 kJ.mol (-1) lower than the one reported in the National Institute of Standards and Technology (NIST) database, thus pointing to a correction of the tabulated protonation thermochemistry of adenosine. PMID:18720985

  10. Application of peptide-mediated ring current shifts to the study of neurophysin-peptide interactions: a partial model of the neurophysin-peptide complex

    SciTech Connect

    Peyton, D.; Sardana, V.; Breslow, E.

    1987-03-24

    Perdeuteriated peptides were synthesized that are capable of binding to the hormone binding site of neurophysin but that differ in the position of aromatic residues. The binding of these peptides to bovine neurophysin I and its des-1-8 derivative was studied by proton nuclear magnetic resonance spectroscopy in order to identify protein residues near the binding site through the observation of differential ring current effects on assignable protein resonances. Phenylalanine in position 3 of bound peptides was shown to induce significant ring current shifts in several resonances assignable to the 1-8 sequence, including those of Leu-3 and/or Leu-5, but was without effect on Tyr-49 ring protons. The magnitude of these shifts was dependent on the identify of peptide residue 1. By contrast, the sole demonstrable direct effect of an aromatic residue in position 1 was a downfield shift in Tyr-49 ring protons. Study of peptide binding to des-1-8-neurophysin demonstrated similar conformations of native and des-1-8 complexes except for the environment of Tyr-49, confirmed the peptide-induced ring current shift assignments in native neurophysin, and indicated an effect of binding on Thr-9. These observations are integrated with other results to provide a partial model of neurophysin-peptide complexes that places the ring of Tyr-49 at a distance 5-10 A from residue 1 of bound peptide and that places both the 1-8 sequence and the protein backbone region containing Tyr-49 proximal to each other and to peptide residue 3. The peptide-protein topographical relationships deduced from the ring current shift data support and extend the preliminary model suggested by spin-label data and indicate that systematically introduced ring current shifts can be employed to provide a qualitative picture of protein topography.

  11. Gas-Phase Amidation of Carboxylic Acids with Woodward's Reagent K Ions

    NASA Astrophysics Data System (ADS)

    Peng, Zhou; Pilo, Alice L.; Luongo, Carl A.; McLuckey, Scott A.

    2015-06-01

    Gas-phase amidation of carboxylic acids in multiply-charged peptides is demonstrated via ion/ion reactions with Woodward's reagent K (wrk) in both positive and negative mode. Woodward's reagent K, N-ethyl-3-phenylisoxazolium-3'-sulfonate, is a commonly used reagent that activates carboxylates to form amide bonds with amines in solution. Here, we demonstrate that the analogous gas-phase chemistry occurs upon reaction of the wrk ions and doubly protonated (or doubly deprotonated) peptide ions containing the carboxylic acid functionality. The reaction involves the formation of the enol ester intermediate in the electrostatic complex. Upon collisional activation, the ethyl amine on the reagent is transferred to the activated carbonyl carbon on the peptide, resulting in the formation of an ethyl amide (addition of 27 Da to the peptide) with loss of a neutral ketene derivative. Further collision-induced dissociation (CID) of the products and comparison with solution-phase amidation product confirms the structure of the ethyl amide.

  12. Investigation of condensed and early stage gas phase hypergolic reactions

    NASA Astrophysics Data System (ADS)

    Dennis, Jacob Daniel

    Traditional hypergolic propellant combinations, such as those used on the space shuttle orbital maneuvering system first flown in 1981, feature hydrazine based fuels and nitrogen tetroxide (NTO) based oxidizers. Despite the long history of hypergolic propellant implementation, the processes that govern hypergolic ignition are not well understood. In order to achieve ignition, condensed phase fuel and oxidizer must undergo simultaneous physical mixing and chemical reaction. This process generates heat, intermediate condensed phase species, and gas phase species, which then may continue to react and generate more heat until ignition is achieved. The process is not well understood because condensed and gas phase reactions occur rapidly, typically in less than 200 μs, on much faster timescales than traditional diagnostic methods can observe. A detailed understanding of even the gas phase chemistry is lacking, but is critical for model development. Initial research has provided confidence that a study of condensed phase hypergolic reactions is useful and possible. Results obtained using an impinging jet apparatus have shown a critical residence time of 0.3 ms is required for the reaction between monomethylhydrazine (MMH) and red fuming nitric acid (RFNA, ~85% HNO3 + 15% N2O4) to achieve conditions favorable for ignition. This critical residence time spans the time required for liquid phase reactions to occur at the fuel/oxidizer interface and can give some insight into the reaction rates for this propellant combination. Experiments performed in a forced mixing constant volume reactor have demonstrated that the chamber pressurization rate for MMH/RFNA can be significantly reduced by diluting the MMH with deionized water. This result indicates that propellant dilution can slow the chemical reaction rates to occur over observable time scales. The research described in this document consists of two efforts that contribute knowledge to the propulsion community regarding the

  13. Gas-phase basicity of 2-furaldehyde.

    PubMed

    Ricci, Andreina; Piccolella, Simona; Pepi, Federico; Patsilinakos, Alexandros; Ragno, Rino; Garzoli, Stefania; Giacomello, Pierluigi

    2012-11-01

    2-Furaldehyde (2-FA), also known as furfural or 2-furancarboxaldehyde, is an heterocyclic aldehyde that can be obtained from the thermal dehydration of pentose monosaccharides. This molecule can be considered as an important sustainable intermediate for the preparation of a great variety of chemicals, pharmaceuticals and furan-based polymers. Despite the great importance of this molecule, its gas-phase basicity (GB) has never been measured. In this work, the GB of 2-FA was determined by the extended Cooks's kinetic method from electrospray ionization triple quadrupole tandem mass spectrometric experiments along with theoretical calculations. As expected, computational results identify the aldehydic oxygen atom of 2-FA as the preferred protonation site. The geometries of O-O-cis and O-O-trans 2-FA and of their six different protomers were calculated at the B3LYP/aug-TZV(d,p) level of theory; proton affinity (PA) values were also calculated at the G3(MP2, CCSD(T)) level of theory. The experimental PA was estimated to be 847.9 ± 3.8 kJ mol(-1), the protonation entropy 115.1 ± 5.03 J mol(-1) K(-1) and the GB 813.6 ± 4.08 kJ mol(-1) at 298 K. From the PA value, a ΔH°(f) of 533.0 ± 12.4 kJ mol(-1) for protonated 2-FA was derived. PMID:23147827

  14. Transferring pharmaceuticals into the gas phase

    NASA Astrophysics Data System (ADS)

    Christen, Wolfgang; Krause, Tim; Rademann, Klaus

    2008-11-01

    The dissolution of molecules of biological interest in supercritical carbon dioxide is investigated using pulsed molecular beam mass spectrometry. Due to the mild processing temperatures of most supercritical fluids, their adiabatic expansion into vacuum permits to transfer even thermally very sensitive substances into the gas phase, which is particularly attractive for pharmaceutical and biomedical applications. In addition, supercritical CO2constitutes a chemically inert solvent that is compatible with hydrocarbon-free ultrahigh vacuum conditions. Here, we report on the dissolution and pulsed supersonic jet expansion of caffeine (C8H10N4O2), the provitamin menadione (C11H8O2), and the amino acid derivative l-phenylalanine tert-butyl ester hydrochloride (C6H5CH2CH(NH2)COOC(CH3)3[dot operator]HCl), into vacuum. An on-axis residual gas analyzer is used to monitor the relative amounts of solute and solvent in the molecular beam as a function of solvent densityE The excellent selectivity and sensitivity provided by mass spectrometry permits to probe even trace amounts of solutes. The strong density variation of CO2 close to the critical point results in a pronounced pressure dependence of the relative ion currents of solute and solvent molecules, reflecting a substantial change in solubility.

  15. Hydrocarbon radical thermochemistry: Gas-phase ion chemistry techniques

    SciTech Connect

    Ervin, Kent M.

    2014-03-21

    Final Scientific/Technical Report for the project "Hydrocarbon Radical Thermochemistry: Gas-Phase Ion Chemistry Techniques." The objective of this project is to exploit gas-phase ion chemistry techniques for determination of thermochemical values for neutral hydrocarbon radicals of importance in combustion kinetics.

  16. Pressure Dependence of Gas-Phase Reaction Rates

    ERIC Educational Resources Information Center

    De Persis, Stephanie; Dollet, Alain; Teyssandier, Francis

    2004-01-01

    It is presented that only simple concepts, mainly taken from activated-complex or transition-state theory, are required to explain and analytically describe the influence of pressure on gas-phase reaction kinetics. The simplest kind of elementary gas-phase reaction is a unimolecular decomposition reaction.

  17. Cryogenic Ion Mobility-Mass Spectrometry: Tracking Ion Structure from Solution to the Gas Phase.

    PubMed

    Servage, Kelly A; Silveira, Joshua A; Fort, Kyle L; Russell, David H

    2016-07-19

    Electrospray ionization (ESI) combined with ion mobility-mass spectrometry (IM-MS) is adding new dimensions, that is, structure and dynamics, to the field of biological mass spectrometry. There is increasing evidence that gas-phase ions produced by ESI can closely resemble their solution-phase structures, but correlating these structures can be complicated owing to the number of competing effects contributing to structural preferences, including both inter- and intramolecular interactions. Ions encounter unique hydration environments during the transition from solution to the gas phase that will likely affect their structure(s), but many of these structural changes will go undetected because ESI-IM-MS analysis is typically performed on solvent-free ions. Cryogenic ion mobility-mass spectrometry (cryo-IM-MS) takes advantage of the freeze-drying capabilities of ESI and a cryogenically cooled IM drift cell (80 K) to preserve extensively solvated ions of the type [M + xH](x+)(H2O)n, where n can vary from zero to several hundred. This affords an experimental approach for tracking the structural evolution of hydrated biomolecules en route to forming solvent-free gas-phase ions. The studies highlighted in this Account illustrate the varying extent to which dehydration can alter ion structure and the overall impact of cryo-IM-MS on structural studies of hydrated biomolecules. Studies of small ions, including protonated water clusters and alkyl diammonium cations, reveal structural transitions associated with the development of the H-bond network of water molecules surrounding the charge carrier(s). For peptide ions, results show that water networks are highly dependent on the charge-carrying species within the cluster. Specifically, hydrated peptide ions containing lysine display specific hydration behavior around the ammonium ion, that is, magic number clusters with enhanced stability, whereas peptides containing arginine do not display specific hydration around the

  18. VUV action spectroscopy of protonated leucine-enkephalin peptide in the 6-14 eV range

    DOE PAGESBeta

    Ranković, M. Lj.; Canon, F.; Nahon, L.; Giuliani, A.; Milosavljević, A. R.

    2015-12-29

    We have studied the VUV photodissociation of gas-phase protonated leucine-enkephalin peptide ion in the 5.7 to 14 eV photon energy range by coupling a linear quadrupole ion trap with a synchrotron radiation source. We report VUV activation tandem mass spectra at 6.7, 8.4 and 12.8 eV photon energies and photodissociation yields for a number of selected fragments. The obtained results provide insights into both near VUV radiation damage and electronic properties of a model peptide. We could distinguish several absorption bands and assign them to particular electronic transitions, according to previous theoretical studies. Furthermore, the photodissociation yields appear to bemore » very different for the various observed fragmentation channels, depending both on the type of fragments and their position along the peptide backbone. The present results are discussed in light of recent gas-phase spectroscopic data on peptides.« less

  19. VUV action spectroscopy of protonated leucine-enkephalin peptide in the 6-14 eV range

    SciTech Connect

    Ranković, M. Lj.; Canon, F.; Nahon, L.; Giuliani, A.; Milosavljević, A. R.

    2015-12-29

    We have studied the VUV photodissociation of gas-phase protonated leucine-enkephalin peptide ion in the 5.7 to 14 eV photon energy range by coupling a linear quadrupole ion trap with a synchrotron radiation source. We report VUV activation tandem mass spectra at 6.7, 8.4 and 12.8 eV photon energies and photodissociation yields for a number of selected fragments. The obtained results provide insights into both near VUV radiation damage and electronic properties of a model peptide. We could distinguish several absorption bands and assign them to particular electronic transitions, according to previous theoretical studies. Furthermore, the photodissociation yields appear to be very different for the various observed fragmentation channels, depending both on the type of fragments and their position along the peptide backbone. The present results are discussed in light of recent gas-phase spectroscopic data on peptides.

  20. VUV action spectroscopy of protonated leucine-enkephalin peptide in the 6-14 eV range

    SciTech Connect

    Ranković, M. Lj.; Canon, F.; Nahon, L.; Giuliani, A.; Milosavljević, A. R.

    2015-12-28

    We have studied the Vacuum Ultraviolet (VUV) photodissociation of gas-phase protonated leucine-enkephalin peptide ion in the 5.7 to 14 eV photon energy range by coupling a linear quadrupole ion trap with a synchrotron radiation source. We report VUV activation tandem mass spectra at 6.7, 8.4, and 12.8 eV photon energies and photodissociation yields for a number of selected fragments. The obtained results provide insight into both near VUV radiation damage and electronic properties of a model peptide. We could distinguish several absorption bands and assign them to particular electronic transitions, according to previous theoretical studies. The photodissociation yields appear to be very different for the various observed fragmentation channels, depending on both the types of fragments and their position along the peptide backbone. The present results are discussed in light of recent gas-phase spectroscopic data on peptides.

  1. Chemistry inside molecular containers in the gas phase

    NASA Astrophysics Data System (ADS)

    Lee, Tung-Chun; Kalenius, Elina; Lazar, Alexandra I.; Assaf, Khaleel I.; Kuhnert, Nikolai; Grün, Christian H.; Jänis, Janne; Scherman, Oren A.; Nau, Werner M.

    2013-05-01

    Inner-phase chemical reactions of guest molecules encapsulated in a macromolecular cavity give fundamental insight into the relative stabilization of transition states by the surrounding walls of the host, thereby modelling the situation of substrates in enzymatic binding pockets. Although in solution several examples of inner-phase reactions are known, the use of cucurbiturils as macrocyclic hosts and bicyclic azoalkanes as guests has now enabled a systematic mass spectrometric investigation of inner-phase reactions in the gas phase, where typically the supply of thermal energy results in dissociation of the supramolecular host-guest assembly. The results reveal a sensitive interplay in which attractive and repulsive van der Waals interactions between the differently sized hosts and guests need to be balanced with a constrictive binding to allow thermally activated chemical reactions to compete with dissociation. The results are important for the understanding of supramolecular reactivity and have implications for catalysis.

  2. Gas-phase interaction of protonated lysine with water

    NASA Astrophysics Data System (ADS)

    Rozman, Marko; Srzic, Dunja; Klasinc, Leo

    2006-07-01

    Gas-phase interaction of LysH+ with D2O has been investigated in order to elucidate the H/D exchange reaction mechanism and possibility of water assisted ion-zwitterion structure formation. The proceed of the interaction is modeled by DFT calculations. Potential energy profiles for: the perturbation from ion-molecule to ion-zwitterion structure, the "flip-flop" and the "bridging" mechanism are presented. Analysis of H/D exchange kinetics results for LysH+ with D2O and CD3OD measured in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer agree with ion-molecule structure of LysH+. Both experimental and theoretical findings suggest that during interaction of LysH+ with D2O isotopic exchange is favored over the water assisted conformational change from ion-molecule into ion-zwitterion structure.

  3. Regenerable Air Purification System for Gas-Phase Contaminant Control

    NASA Technical Reports Server (NTRS)

    Constantinescu, Ileana C.; Qi, Nan; LeVan, M. Douglas; Finn, Cory K.; Finn, John E.; Luna, Bernadette (Technical Monitor)

    2000-01-01

    A regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an. adsorbent column into a closed oxidation loop is under development through cooperative R&D between Vanderbilt University and NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. Recent work has focused on fabrication and operation of a RAPS breadboard at NASA Ames, and on measurement of adsorption isotherm data for several important organic compounds at Vanderbilt. These activities support the use and validation of RAPS modeling software also under development at Vanderbilt, which will in turn be used to construct a prototype system later in the project.

  4. A Phosphohistidine Proteomics Strategy Based on Elucidation of a Unique Gas-Phase Phosphopeptide Fragmentation Mechanism

    PubMed Central

    2015-01-01

    Protein histidine phosphorylation is increasingly recognized as a critical posttranslational modification (PTM) in central metabolism and cell signaling. Still, the detection of phosphohistidine (pHis) in the proteome has remained difficult due to the scarcity of tools to enrich and identify this labile PTM. To address this, we report the first global proteomic analysis of pHis proteins, combining selective immunoenrichment of pHis peptides and a bioinformatic strategy based on mechanistic insight into pHis peptide gas-phase fragmentation during LC–MS/MS. We show that collision-induced dissociation (CID) of pHis peptides produces prominent characteristic neutral losses of 98, 80, and 116 Da. Using isotopic labeling studies, we also demonstrate that the 98 Da neutral loss occurs via gas-phase phosphoryl transfer from pHis to the peptide C-terminal α-carboxylate or to Glu/Asp side chain residues if present. To exploit this property, we developed a software tool that screens LC–MS/MS spectra for potential matches to pHis-containing peptides based on their neutral loss pattern. This tool was integrated into a proteomics workflow for the identification of endogenous pHis-containing proteins in cellular lysates. As an illustration of this strategy, we analyzed pHis peptides from glycerol-fed and mannitol-fed Escherichia coli cells. We identified known and a number of previously speculative pHis sites inferred by homology, predominantly in the phosphoenolpyruvate:sugar transferase system (PTS). Furthermore, we identified two new sites of histidine phosphorylation on aldehyde-alcohol dehydrogenase (AdhE) and pyruvate kinase (PykF) enzymes, previously not known to bear this modification. This study lays the groundwork for future pHis proteomics studies in bacteria and other organisms. PMID:25156620

  5. Gas-phase protonation thermochemistry of arginine.

    PubMed

    Bouchoux, Guy; Desaphy, Sylvain; Bourcier, Sophie; Malosse, Christian; Bimbong, Rosa Ngo Biboum

    2008-03-20

    The gas-phase basicity (GB), proton affinity (PA), and protonation entropy (DeltapS degrees (M)=S degrees (MH+)-S degrees (M)) of arginine (Arg) have been experimentally determined by the extended kinetic method using an electrospray ionization quadrupole time-of-flight (ESI-Q-TOF) mass spectrometer. This method provides GB(Arg)=1004.3+/-2.2 (4.9) kJ.mol(-1) (indicated errors are standard deviations, and in parentheses, 95% confidence limits are given). Consideration of previous experimental data using a fast atom bombardment ionization tandem sector mass spectrometer slightly modifies these estimates since GB(Arg)=1005.9+/-3.1 (6.6) kJ.mol(-1). Lower limits of the proton affinity, PA(Arg)=1046+/-4 (7) kJ.mol(-1), and of the "protonation entropy", DeltapS degrees (Arg)=S degrees (ArgH+)-S degrees (Arg)=-27+/-7 (15) J.mol(-1).K(-1), are also provided by the experiments. Theoretical calculations conducted at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) level, including 298 K enthalpy correction, predict a proton affinity value of ca. 1053 kJ.mol-1 after consideration of isodesmic proton-transfer reactions with guanidine as the reference base. Computations including explicit treatment of hindered rotations and mixing of conformers confirm that a noticeable entropy loss does occur upon protonation, which leads to a theoretical DeltapS degrees (Arg) term of ca. -45 J.mol(-1).K(-1). The following evaluated thermochemical parameter values are proposed: GB(Arg)=1005+/-3 kJ.mol(-1); PA(Arg)=1051+/-5 kJ.mol(-1), and DeltapS degrees (Arg)=-45+/-12 J.mol(-1).K(-1). PMID:18288831

  6. Selective transport of amino acids into the gas phase: driving forces for amino acid solubilization in gas-phase reverse micelles.

    PubMed

    Fang, Yigang; Bennett, Andrew; Liu, Jianbo

    2011-01-28

    We report a study on encapsulation of various amino acids into gas-phase sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) reverse micelles, using electrospray ionization guided-ion-beam tandem mass spectrometry. Collision-induced dissociation of mass-selected reverse micellar ions with Xe was performed to probe structures of gas-phase micellar assemblies, identify solute-surfactant interactions, and determine preferential incorporation sites of amino acids. Integration into gas-phase reverse micelles depends upon amino acid hydrophobicity and charge state. For examples, glycine and protonated amino acids (such as protonated tryptophan) are encapsulated within the micellar core via electrostatic interactions; while neutral tryptophan is adsorbed in the surfactant layer. As verified using model polar hydrophobic compounds, the hydrophobic effect and solute-interface hydrogen-bonding do not provide sufficient driving force needed for interfacial solubilization of neutral tryptophan. Neutral tryptophan, with a zwitterionic structure, is intercalated at the micellar interface between surfactant molecules through complementary effects of electrostatic interactions between tryptophan backbone and AOT polar heads, and hydrophobic interactions between tryptophan side chain and AOT alkyl tails. Protonation of tryptophan could significantly improve its incorporation capacity into gas-phase reverse micelles, and displace its incorporation site from the micellar interfacial zone to the core; protonation of glycine, on the other hand, has little effect on its encapsulation capacity. Another interesting observation is that amino acids of different isoelectric points could be selectively encapsulated into, and transported by, reverse micelles from solution to the gas phase, based upon their competition for protonation and subsequent encapsulation within the micellar core. PMID:21140022

  7. Gas-phase basicities for ions from bradykinin and its des-arginine analogues.

    PubMed

    Ewing, N P; Pallante, G A; Zhang, X; Cassady, C J

    2001-08-01

    Apparent gas-phase basicities (GB(app)s) for [M + H]+ of bradykinin, des-Arg1-bradykinin and des-Arg9-bradykinin have been assigned by deprotonation reactions of [M + 2H]2+ in a Fourier transform ion cyclotron resonance mass spectrometer. With a GB(app) of 225.8 +/- 4.2 kcal x mol(-1), bradykinin [M + H]+ is the most basic of the ions studied. Ions from des-Arg1-bradykinin and des-Arg9-bradykinin have GB(app) values of 222.8 +/- 4.3 kcal x mol(-1) and 214.9 +/- 2.3 kcal x mol(-1), respectively. One purpose of this work was to determine a suitable reaction efficiency 'break point' for assigning GB(app) values to peptide ions using the bracketing method. An efficiency value of 0.1 (i.e. approximately 10% of all collisions resulting in a deprotonation reaction) was used to assign GB(app)s. Support for this criterion is provided by the fact that our GB(app) values for des-Arg1-bradykinin and des-Arg9-bradykinin are identical, within experimental error, to literature values obtained using a modified kinetic method. However, the GB(app)s for bradykinin ions from the two studies differ by 10.3 kcal x mol(-1). The reason for this is not clear, but may involve conformation differences produced by experimental conditions. The results may be influenced by salt-bridge conformers and/or by conformational changes caused by the use of a proton-bound heterodimer in the kinetic method. Factors affecting the basicities of these peptide ions are also discussed, and molecular modeling is used to provide information on protonation sites and conformations. The presence of two highly basic arginine residues on bradykinin results in its high GB(app), while the basicity of des-Arg1-bradykinin ions is increased by the presence of two proline residues at the N-terminus. The proline residue in the second position folds the peptide chain in a manner that increases intramolecular hydrogen bonding to the protonated N-terminal amino group of the proline at the first position. PMID:11523086

  8. Gas phase atomic and molecular processes

    NASA Astrophysics Data System (ADS)

    Zhu, Cheng

    . that in interstellar clouds HF is the major form of gas phase fluorine.

  9. Probing aerosol formation by comprehensive measurements of gas phase oxidation products

    NASA Astrophysics Data System (ADS)

    Ehn, Mikael; Kleist, Einhard; Junninen, Heikki; Sipilä, Mikko; Petäjä, Tuukka; Pullinen, Iida; Springer, Monika; Andres, Stefanie; Rissanen, Matti; Kontkanen, Jenni; Schobesberger, Siegfried; Rubach, Florian; Tillman, Ralf; Lee, Ben H.; Lopez-Hilfiker, Felipe; Kerminen, Veli-Matti; Kulmala, Markku; Worsnop, Douglas R.; Thornton, Joel; Wildt, Jürgen; Mentel, Thomas F.

    2013-05-01

    A comprehensive suite of chemical ionization mass spectrometers (CIMS) were deployed for chamber studies of monoterpene oxidation. The CIMS instruments were able to detect several different groups of compounds ranging from volatile to practically non-volatile. The compound groups showed very different behavior and correlations with aerosol number and mass. Results suggest that major gas phase contributors are not considered in current models.

  10. Gas phase regioselectivity in the deprotonation of p-cresol radical cation

    NASA Astrophysics Data System (ADS)

    Chiavarino, B.; Crestoni, M. E.; Fornarini, S.

    2003-04-01

    The deprotonation of the radical cation of p-cresol, a model of tyrosine residues, has been studied kinetically in the gas phase. The reaction has revealed the operation of competitive deprotonation sites depending on the strength of the base, as shown by an FT-ICR study using d-labelling.

  11. Gas-phase reaction study of disilane pyrolysis: Applications to low pressure chemical vapor deposition

    SciTech Connect

    Johannes, J.E.; Ekerdt, J.G. . Dept. of Chemical Engineering)

    1994-08-01

    The gas-phase thermal reactions during disilane decomposition at low pressure chemical vapor deposition conditions were studied from 300 to 1,000 K using resonance enhanced multiphoton ionization (REMPI) and multiphoton ionization (MPI). REMPI of gas-phase Si, mass 28, was detected from 640 to 840 K and 1 to 10 Torr, with a maximum signal intensity between 700 to 720 K. During disilane decomposition, no SiH (427.8 nm), SiH[sub 2] (494-515 nm), or SiH[sub 3] (419.0 nm) was detected. MPI of higher silanes, silenes, and silylenes were detected through mass fragments 2, 32, and 60; these species reached a maximum signal intensity 20 degrees prior to the mass-28 maximum. Modeling studies that included a detailed low pressure gas-phase kinetic scheme predict relative gas-phase partial pressures generated during disilane pyrolysis. The model predicted experimental trends in the Si partial pressure and the higher silane, silene, and silylene partial pressures.

  12. Prediction of Antimicrobial Activity of Synthetic Peptides by a Decision Tree Model

    PubMed Central

    Lira, Felipe; Perez, Pedro S.; Baranauskas, José A.

    2013-01-01

    Antimicrobial resistance is a persistent problem in the public health sphere. However, recent attempts to find effective substitutes to combat infections have been directed at identifying natural antimicrobial peptides in order to circumvent resistance to commercial antibiotics. This study describes the development of synthetic peptides with antimicrobial activity, created in silico by site-directed mutation modeling using wild-type peptides as scaffolds for these mutations. Fragments of antimicrobial peptides were used for modeling with molecular modeling computational tools. To analyze these peptides, a decision tree model, which indicated the action range of peptides on the types of microorganisms on which they can exercise biological activity, was created. The decision tree model was processed using physicochemistry properties from known antimicrobial peptides available at the Antimicrobial Peptide Database (APD). The two most promising peptides were synthesized, and antimicrobial assays showed inhibitory activity against Gram-positive and Gram-negative bacteria. Colossomin C and colossomin D were the most inhibitory peptides at 5 μg/ml against Staphylococcus aureus and Escherichia coli. The methods described in this work and the results obtained are useful for the identification and development of new compounds with antimicrobial activity through the use of computational tools. PMID:23455341

  13. A computational model for predicting fusion peptide of retroviruses.

    PubMed

    Wu, Sijia; Han, Jiuqiang; Liu, Ruiling; Liu, Jun; Lv, Hongqiang

    2016-04-01

    As a pivotal domain within envelope protein, fusion peptide (FP) plays a crucial role in pathogenicity and therapeutic intervention. Taken into account the limited FP annotations in NCBI database and absence of FP prediction software, it is urgent and desirable to develop a bioinformatics tool to predict new putative FPs (np-FPs) in retroviruses. In this work, a sequence-based FP model was proposed by combining Hidden Markov Method with similarity comparison. The classification accuracies are 91.97% and 92.31% corresponding to 10-fold and leave-one-out cross-validation. After scanning sequences without FP annotations, this model discovered 53,946 np-FPs. The statistical results on FPs or np-FPs reveal that FP is a conserved and hydrophobic domain. The FP software programmed for windows environment is available at https://sourceforge.net/projects/fptool/files/?source=navbar. PMID:26963379

  14. Atomic and molecular physics in the gas phase

    SciTech Connect

    Toburen, L.H.

    1990-09-01

    The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets.

  15. Lattice models of peptide aggregation: evaluation of conformational search algorithms.

    PubMed

    Oakley, Mark T; Garibaldi, Jonathan M; Hirst, Jonathan D

    2005-11-30

    We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems. PMID:16170797

  16. A model of random sequences for de novo peptide sequencing

    SciTech Connect

    Jarman, Kenneth D.; Cannon, William R.; Jarman, Kristin H.; Heredia-Langner, Alejandro

    2003-04-15

    We present a model for the probability of random sequences appearing in product ion spectra obtained from tandem mass spectrometry experiments using collision-induced dissociation. We demonstrate the use of these probabilities for ranking candidate peptide sequences obtained using a de novo algorithm. Sequence candidates are obtained from a spectrum graph that is greatly reduced in size from those in previous graph-theoretical de novo approaches. Evidence of multiple instances of subsequences of each candidate, due to different fragment ion type series as well as isotopic peaks, is incorporated in a hierarchical scoring scheme. This approach is shown to be useful for confirming results from database search and as a first step towards a statistically rigorous de novo algorithm.

  17. Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns.

    PubMed

    Huang, Yingying; Triscari, Joseph M; Tseng, George C; Pasa-Tolic, Ljiljana; Lipton, Mary S; Smith, Richard D; Wysocki, Vicki H

    2005-09-15

    Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from singly charged peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s) in multiply protonated peptides. Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and may be useful in algorithm development that employs

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

    PubMed Central

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

    2009-01-01

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

  19. Interaction of peptides with cell membranes: insights from molecular modeling

    NASA Astrophysics Data System (ADS)

    Li, Zhen-lu; Ding, Hong-ming; Ma, Yu-qiang

    2016-03-01

    The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.

  20. ENGINE EXHAUST PARTICULATE AND GAS PHASE CONTRIBUTIONS TO VASCULAR TOXICITY

    PubMed Central

    Campen, Matthew; Robertson, Sarah; Lund, Amie; Lucero, Joann; McDonald, Jacob

    2014-01-01

    Cardiovascular health effects of near-roadway pollution appear more substantial than other sources of air pollution. The underlying cause of this phenomenon may simply be concentration-related, but the possibility remains that gases and particulate matter (PM) may physically interact and further enhance systemic vascular toxicity. To test this, we utilized a common hypercholesterolemic mouse model (Apolipoprotein E-null) exposed to mixed vehicular emissions (MVE; combined gasoline and diesel exhausts) for 6 h/d × 50 days, with additional permutations of removing PM by filtration and also removing gaseous species from PM by denudation. Several vascular bioassays, including matrix metalloproteinase 9 (MMP9) protein, 3-nitrotyrosine, and plasma-induced vasodilatory impairments, highlighted that the whole emissions, containing both particulate and gaseous components, was collectively more potent than MVE-derived PM or gas mixtures, alone. Thus, we conclude that inhalation of fresh whole emissions induce greater systemic vascular toxicity than either the particulate or gas phase alone. These findings lend credence to the hypothesis that the near-roadway environment may have a more focused public health impact due to gas-particle interactions. PMID:24730681

  1. Engine exhaust particulate and gas phase contributions to vascular toxicity.

    PubMed

    Campen, Matthew; Robertson, Sarah; Lund, Amie; Lucero, Joann; McDonald, Jacob

    2014-05-01

    Cardiovascular health effects of near-roadway pollution appear more substantial than other sources of air pollution. The underlying cause of this phenomenon may simply be concentration-related, but the possibility remains that gases and particulate matter (PM) may physically interact and further enhance systemic vascular toxicity. To test this, we utilized a common hypercholesterolemic mouse model (Apolipoprotein E-null) exposed to mixed vehicle emission (MVE; combined gasoline and diesel exhausts) for 6 h/d × 50 d, with additional permutations of removing PM by filtration and also removing gaseous species from PM by denudation. Several vascular bioassays, including matrix metalloproteinase-9 protein, 3-nitrotyrosine and plasma-induced vasodilatory impairments, highlighted that the whole emissions, containing both particulate and gaseous components, was collectively more potent than MVE-derived PM or gas mixtures, alone. Thus, we conclude that inhalation of fresh whole emissions induce greater systemic vascular toxicity than either the particulate or gas phase alone. These findings lend credence to the hypothesis that the near-roadway environment may have a more focused public health impact due to gas-particle interactions. PMID:24730681

  2. Surface plasmon sensing of gas phase contaminants using optical fiber.

    SciTech Connect

    Thornberg, Steven Michael; White, Michael I.; Rumpf, Arthur Norman; Pfeifer, Kent Bryant

    2009-10-01

    Fiber-optic gas phase surface plasmon resonance (SPR) detection of several contaminant gases of interest to state-of-health monitoring in high-consequence sealed systems has been demonstrated. These contaminant gases include H{sub 2}, H{sub 2}S, and moisture using a single-ended optical fiber mode. Data demonstrate that results can be obtained and sensitivity is adequate in a dosimetric mode that allows periodic monitoring of system atmospheres. Modeling studies were performed to direct the design of the sensor probe for optimized dimensions and to allow simultaneous monitoring of several constituents with a single sensor fiber. Testing of the system demonstrates the ability to detect 70mTorr partial pressures of H{sub 2} using this technique and <280 {micro}Torr partial pressures of H{sub 2}S. In addition, a multiple sensor fiber has been demonstrated that allows a single fiber to measure H{sub 2}, H{sub 2}S, and H{sub 2}O without changing the fiber or the analytical system.

  3. A many-body model to study proteins. II. Incidence of many-body polarization effects on the interaction of the calmodulin protein with four Ca2+ dications and with a target enzyme peptide

    NASA Astrophysics Data System (ADS)

    Cuniasse, Philippe; Masella, Michel

    2003-07-01

    The origin of the interactions occurring in the calmodulin protein interacting with one of its target peptide and counterions, and binding four calcium dications, has been investigated in the gas phase, using the many-body model presented in Paper I [Masella and Cuniasse, J. Chem. Phys. 119, 1866 (2003)] and a classical pairwise force field. As compared to the latter force field, the many-body model is shown to provide a geometrical description of the calmodulin/target peptide structure in better agreement with the x-ray experimental one, and a better description of the Ca2+ binding sites (as compared to "small molecule" structures reported in the Cambridge Structural Database). Regarding the energy, both models provide qualitatively a similar description of the interactions occurring in the calmodulin/target peptide system. However, quantitatively, the pairwise model predicts interaction energies greater by about 25% as compared to the many-body one in the case of calmodulin/Ca2+ interactions. This is due to the inability of pairwise force fields to account for the strong anticooperative effects predicted to occur in [Ca,(carboxylate)n]2-n systems by both the many-body model and quantum computations. Hence, the new many-body model appears to be well suited for describing proteinic systems interacting with cations, both in terms of geometry and energy.

  4. HomoSAR: bridging comparative protein modeling with quantitative structural activity relationship to design new peptides.

    PubMed

    Borkar, Mahesh R; Pissurlenkar, Raghuvir R S; Coutinho, Evans C

    2013-11-15

    Peptides play significant roles in the biological world. To optimize activity for a specific therapeutic target, peptide library synthesis is inevitable; which is a time consuming and expensive. Computational approaches provide a promising way to simply elucidate the structural basis in the design of new peptides. Earlier, we proposed a novel methodology termed HomoSAR to gain insight into the structure activity relationships underlying peptides. Based on an integrated approach, HomoSAR uses the principles of homology modeling in conjunction with the quantitative structural activity relationship formalism to predict and design new peptide sequences with the optimum activity. In the present study, we establish that the HomoSAR methodology can be universally applied to all classes of peptides irrespective of sequence length by studying HomoSAR on three peptide datasets viz., angiotensin-converting enzyme inhibitory peptides, CAMEL-s antibiotic peptides, and hAmphiphysin-1 SH3 domain binding peptides, using a set of descriptors related to the hydrophobic, steric, and electronic properties of the 20 natural amino acids. Models generated for all three datasets have statistically significant correlation coefficients (r(2)) and predictive r2 (r(pred)2) and cross validated coefficient ( q(LOO)2). The daintiness of this technique lies in its simplicity and ability to extract all the information contained in the peptides to elucidate the underlying structure activity relationships. The difficulties of correlating both sequence diversity and variation in length of the peptides with their biological activity can be addressed. The study has been able to identify the preferred or detrimental nature of amino acids at specific positions in the peptide sequences. PMID:24105965

  5. Negative ion gas-phase chemistry of arenes.

    PubMed

    Danikiewicz, Witold; Zimnicka, Magdalena

    2016-01-01

    Reactions of aromatic and heteroaromatic compounds involving anions are of great importance in organic synthesis. Some of these reactions have been studied in the gas phase and are occasionally mentioned in reviews devoted to gas-phase negative ion chemistry, but no reviews exist that collect all existing information about these reactions. This work is intended to fill this gap. In the first part of this review, methods for generating arene anions in the gas phase and studying their physicochemical properties and fragmentation reactions are presented. The main topics in this part are as follows: processes in which gas-phase arene anions are formed, measurements and calculations of the proton affinities of arene anions, proton exchange reactions, and fragmentation processes of substituted arene anions, especially phenide ions. The second part is devoted to gas-phase reactions of arene anions. The most important of these are reactions with electrophiles such as carbonyl compounds and α,β-unsaturated carbonyl and related compounds (Michael acceptors). Other reactions including oxidation of arene anions and halogenophilic reactions are also presented. In the last part of the review, reactions of electrophilic arenes with nucleophiles are discussed. The best known of these is the aromatic nucleophilic substitution (SN Ar) reaction; however, other processes that lead to the substitution of a hydrogen atom in the aromatic ring are also very important. Aromatic substrates in these reactions are usually but not always nitroarenes bearing other substituents in the ring. The first step in these reactions is the formation of an anionic σ-adduct, which, depending on the substituents in the aromatic ring and the structure of the attacking nucleophile, is either an intermediate or a transition state in the reaction path. In the present review, we attempted to collect the results of both experimental and computational studies of the aforementioned reactions conducted since the

  6. Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling.

    PubMed

    Rand, Kasper D; Zehl, Martin; Jørgensen, Thomas J D

    2014-10-21

    acidic conditions where the amide hydrogen exchange rate is slowed by many orders of magnitude). The ability to localize the individual deuterated residues (the spatial resolution) is determined by the size (typically ∼7-15 residues) and the number of peptic peptides. These peptides provide a relatively coarse-grained picture of the protein dynamics. A fundamental understanding of the relationship between protein function/dysfunction and conformational dynamics requires in many cases higher resolution and ultimately single-residue resolution. In this Account, we summarize our efforts to achieve single-residue deuterium levels in proteins by electron-based or laser-induced gas-phase fragmentation methods. A crucial analytical requirement for this approach is that the pattern of deuterium labeling from solution is retained in the gas-phase fragment ions. It is therefore essential to control and minimize any occurrence of gas-phase randomization of the solution deuterium label (H/D scrambling) during the MS experiment. For this purpose, we have developed model peptide probes to accurately measure the onset and extent of H/D scrambling. Our analytical procedures to control the occurrence of H/D scrambling are detailed along with the physical parameters that induce it during MS analysis. In light of the growing use of gas-phase dissociation experiments to measure the HDX of proteins in order to obtain a detailed characterization and understanding of the dynamic conformations and interactions of proteins at the molecular level, we discuss the perspectives and challenges of future high-resolution HDX-MS methodology. PMID:25171396

  7. MOLECULAR SPECTROSCPY AND REACTIONS OF ACTINIDES IN THE GAS PHASE AND CRYOGENIC MATRICES

    SciTech Connect

    Heaven, Michael C.; Gibson, John K.; Marcalo, Joaquim

    2009-02-01

    In this chapter we review the spectroscopic data for actinide molecules and the reaction dynamics for atomic and molecular actinides that have been examined in the gas phase or in inert cryogenic matrices. The motivation for this type of investigation is that physical properties and reactions can be studied in the absence of external perturbations (gas phase) or under minimally perturbing conditions (cryogenic matrices). This information can be compared directly with the results from high-level theoretical models. The interplay between experiment and theory is critically important for advancing our understanding of actinide chemistry. For example, elucidation of the role of the 5f electrons in bonding and reactivity can only be achieved through the application of experimentally verified theoretical models. Theoretical calculations for the actinides are challenging due the large numbers of electrons that must be treated explicitly and the presence of strong relativistic effects. This topic has been reviewed in depth in Chapter 17 of this series. One of the goals of the experimental work described in this chapter has been to provide benchmark data that can be used to evaluate both empirical and ab initio theoretical models. While gas-phase data are the most suitable for comparison with theoretical calculations, there are technical difficulties entailed in generating workable densities of gas-phase actinide molecules that have limited the range of species that have been characterized. Many of the compounds of interest are refractory, and problems associated with the use of high temperature vapors have complicated measurements of spectra, ionization energies, and reactions. One approach that has proved to be especially valuable in overcoming this difficulty has been the use of pulsed laser ablation to generate plumes of vapor from refractory actinide-containing materials. The vapor is entrained in an inert gas, which can be used to cool the actinide species to room

  8. Gas phase acetaldehyde production in a continuous bioreactor

    SciTech Connect

    Hwang, Soon Ook . Dept. of Chemical Engineering); Trantolo, D.J. . Center for Biotechnology Engineering); Wise, D.L. . Dept. of Chemical Engineering Northeastern Univ., Boston, MA . Center for Biotechnology Engineering)

    1993-08-20

    The gas phase continuous production of acetaldehyde was studied with particular emphasis on the development of biocatalyst (alcohol oxidase on solid phase support materials) for a fixed bed reactor. Based on the experimental results in a batch bioreactor, the biocatalysts were prepared by immobilization of alcohol oxidase on Amberlite IRA-400, packed into a column, and the continuous acetaldehyde production in the gas phase by alcohol oxidase was performed. The effects of the reaction temperature, flow rates of gaseous stream, and ethanol vapor concentration on the performance of the continuous bioreactor were investigated.

  9. Gas phase radiative effects in diffusion flames

    NASA Astrophysics Data System (ADS)

    Bedir, Hasan

    Several radiation models are evaluated for a stagnation point diffusion flame of a solid fuel in terms of accuracy and computational time. Narrowband, wideband, spectral line weighted sum of gray gases (SLWSGG), and gray gas models are included in the comparison. Radiative heat flux predictions by the nongray narrowband, wideband, and SLWSGG models are found to be in good agreement with each other, whereas the gray gas models are found to be inaccurate. The narrowband model, the most complex among the models evaluated, is then applied first to a solid fuel and second to a pure gaseous diffusion flame. A polymethylmethacrylate (PMMA) diffusion flame in a stagnation point geometry is solved with the narrowband model with COsb2, Hsb2O, and MMA vapor included in participating species. A detailed account of the emission and absorption from these species as well as the radiative heat fluxes are given as a function of the stretch rate. It is found that at low stretch rate the importance of radiation is increased due to an increase in the optical thickness, and a decrease in the conductive heat flux. Results show that COsb2 is the biggest emitter and absorber in the flame, MMA vapor is the second and Hsb2O is the least important. A pure gaseous flame in an opposed jet configuration is solved with the narrowband radiation model with CO as the fuel, and Osb2 as the oxidizer. Detailed. chemical kinetics and transport are incorporated into the combustion model with the use of the CHEMKIN and TRANSPORT software packages. The governing equations are solved with a modified version of the OPPDIF code. Dry and wet CO flames as well as COsb2 dilution are studied. Comparison of the results with and without the consideration of radiation reveals that the radiation is important for the whole flammable range of dry CO flames and for the low stretch rates of wet flames. Without the consideration of radiation the temperature and the species mole fractions (especially of minor species

  10. An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

    PubMed

    Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

    2015-07-30

    Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation. PMID:26196065

  11. Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns

    SciTech Connect

    Huang, Yingying; Triscari, Joseph M.; Tseng, George C.; Pasa-Tolic, Ljiljana; Lipton, Mary S.; Smith, Richard D.; Wysocki, Vicki H.

    2005-09-01

    Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion

  12. The Decomposition of Hydrazine in the Gas Phase and over an Iridium Catalyst

    SciTech Connect

    Schmidt, Michael W.; Gordon, Mark S.

    2013-09-30

    Hydrazine is an important rocket fuel, used as both a monopropellant and a bipropellant. This paper presents theoretical results to complement the extensive experimental studies of the gas phase and Ir catalyzed decompositions involved in the monopropellant applications of hydrazine. Gas phase electronic structure theory calculations that include electron correlation predict that numerous molecular and free radical reactions occur within the same energy range as the basic free radical pathways: NN bond breaking around 65 kcal/mol and NH bond breaking around 81 kcal/mol. The data suggest that a revision to existing kinetics modeling is desirable, based on the energetics and the new elementary steps reported herein. A supported Ir-6 octahedron model for the Shell 405 Iridium catalyst used in thrusters was developed. Self-Consistent Field and electron correlation calculations (with core potentials and associated basis sets) find a rich chemistry for hydrazine on this catalyst model. The model catalyst provides dramatically lower NN and NH bond cleavage energies and an even smaller barrier to breaking the NH bond by NH2 abstractions. Thus, the low temperature decomposition over the catalyst is interpreted in terms of consecutive NH2 abstractions to produce ammonia and nitrogen. The higher temperature channel, which has hydrogen and nitrogen products, may be due to a mixture of two mechanisms. These two mechanisms are successive NH cleavages with surface H + H recombinations, and the same type of assisted H-2 eliminations found to occur in the gas phase part of this study.

  13. Gas-phase chemistry in dense interstellar clouds including grain surface molecular depletion and desorption

    NASA Technical Reports Server (NTRS)

    Bergin, E. A.; Langer, W. D.; Goldsmith, P. F.

    1995-01-01

    We present time-dependent models of the chemical evolution of molecular clouds which include depletion of atoms and molecules onto grain surfaces and desorption, as well as gas-phase interactions. We have included three mechanisms to remove species from the grain mantles: thermal evaporation, cosmic-ray-induced heating, and photodesorption. A wide range of parameter space has been explored to examine the abundance of species present both on the grain mantles and in the gas phase as a function of both position in the cloud (visual extinction) and of evolutionary state (time). The dominant mechanism that removes molecules from the grain mantles is cosmic-ray desorption. At times greater than the depletion timescale, the abundances of some simple species agree with abundances observed in the cold dark cloud TMC-1. Even though cosmic-ray desorption preserves the gas-phase chemistry at late times, molecules do show significant depletions from the gas phase. Examination of the dependence of depletion as a function of density shows that when the density increases from 10(exp 3)/cc to 10(exp 5)/cc several species including HCO(+), HCN, and CN show gas-phase abundance reductions of over an order of magnitude. The CO: H2O ratio in the grain mantles for our standard model is on the order of 10:1, in reasonable agreement with observations of nonpolar CO ice features in rho Ophiuchus and Serpens. We have also examined the interdependence of CO depletion with the space density of molecular hydrogen and binding energy to the grain surface. We find that the observed depletion of CO in Taurus in inconsistent with CO bonding in an H2O rich mantle, in agreement with observations. We suggest that if interstellar grains consist of an outer layer of CO ice, then the binding energies for many species to the grain mantle may be lower than commonly used, and a significant portion of molecular material may be maintained in the gas phase.

  14. Long-time-scale interaction dynamics between a model antimicrobial peptide and giant unilamellar vesicles.

    PubMed

    Burton, Matthew G; Huang, Qi M; Hossain, Mohammed A; Wade, John D; Clayton, Andrew H A; Gee, Michelle L

    2013-11-26

    The interaction dynamics between a lytic peptide and a biomembrane was studied using time-lapse fluorescence lifetime imaging microscopy. The model membrane was 1,2-dipalmitoyl-sn-glycero-3-phosphochloine giant unilamellar vesicles (GUVs), and the peptide was the K14 derivative of melittin, to which the polarity-sensitive fluorescent probe AlexaFluor 430 was grafted. The interaction of the peptide with the GUVs resulted in a progressive quenching of the fluorescence lifetime over a period of minutes. From previous photophysics characterization of the peptide, we were able to deconvolve the contribution of three distinct peptide states to the lifetime trajectory and use this data to develop a kinetics model for the interaction process. It was found that the peptide-membrane interaction was well described by a two-step mechanism: peptide monomer adsorption followed by membrane surface migration, assembly, and insertion to form membrane pores. There was an equilibrium exchange between pore and surface monomers at all lipid/peptide (L/P) concentration ratios, suggesting that the fully inserted phase was reached, even at low peptide concentrations. In contrast to previous studies, there was no evidence of critical behavior; irrespective of L/P ratio, lytic pores were the dominant peptide state at equilibrium and were formed even at very low peptide concentrations. We suggest that this behavior is seen in GUVs because their low curvature means low Laplace pressure. Membrane elasticity is therefore relatively ineffective at damping the thermal fluctuations of lipid molecules that lead to random molecular-level lipid protrusions and membrane undulations. The transient local membrane deformations that result from these thermal fluctuations create the conditions necessary for facile peptide insertion. PMID:24168523

  15. Numerical analysis of an impinging jet reactor for the CVD and gas-phase nucleation of titania

    NASA Astrophysics Data System (ADS)

    Gokoglu, Suleyman A.; Stewart, Gregory D.; Collins, Joshua; Rosner, Daniel E.

    1994-06-01

    We model a cold-wall atmospheric pressure impinging jet reactor to study the CVD and gas-phase nucleation of TiO2 from a titanium tetra-iso-propoxide (TTIP)/oxygen dilute source gas mixture in nitrogen. The mathematical model uses the computational code FIDAP and complements our recent asymptotic theory for high activation energy gas-phase reactions in thin chemically reacting sublayers. The numerical predictions highlight deviations from ideality in various regions inside the experimental reactor. Model predictions of deposition rates and the onset of gas-phase nucleation compare favorably with experiments. Although variable property effects on deposition rates are not significant (approximately 11 percent at 1000 K), the reduction rates due to Soret transport is substantial (approximately 75 percent at 1000 K).

  16. Numerical Analysis of an Impinging Jet Reactor for the CVD and Gas-Phase Nucleation of Titania

    NASA Technical Reports Server (NTRS)

    Gokoglu, Suleyman A.; Stewart, Gregory D.; Collins, Joshua; Rosner, Daniel E.

    1994-01-01

    We model a cold-wall atmospheric pressure impinging jet reactor to study the CVD and gas-phase nucleation of TiO2 from a titanium tetra-iso-propoxide (TTIP)/oxygen dilute source gas mixture in nitrogen. The mathematical model uses the computational code FIDAP and complements our recent asymptotic theory for high activation energy gas-phase reactions in thin chemically reacting sublayers. The numerical predictions highlight deviations from ideality in various regions inside the experimental reactor. Model predictions of deposition rates and the onset of gas-phase nucleation compare favorably with experiments. Although variable property effects on deposition rates are not significant (approximately 11 percent at 1000 K), the reduction rates due to Soret transport is substantial (approximately 75 percent at 1000 K).

  17. Apparatus for the premixed gas phase combustion of liquid fuels

    SciTech Connect

    Roffe, G.A.; Trucco, H.A.

    1981-04-21

    This invention relates to improvements in the art of liquid fuel combustion and, more particularly, concerns a method and apparatus for the controlled gasification of liquid fuels, the thorough premixing of the then gasified fuel with air and the subsequent gas-phase combustion of the mixture to produce a flame substantially free of soot, carbon monoxide, nitric oxide and unburned fuel.

  18. INVESTIGATION OF GAS-PHASE OZONE AS A POTENTIAL BIOCIDE

    EPA Science Inventory

    The paper presents data on the effect of ozone on both vegetative and spore-forming fungi as well as on spore-forming bacteria. (NOTE: Despite the wide use of ozone generators in indoor air cleaning, there is little research data on ozone's biocidal activity in the gas phase.) Dr...

  19. Can the ordinary chondrites have condensed from a gas phase

    NASA Technical Reports Server (NTRS)

    Herndon, J. M.; Suess, H. E.

    1977-01-01

    The conditions under which ordinary chondrites containing iron in three different chemical states can form in thermodynamic equilibrium with a gas phase are calculated. Hydrogen depletion factors of 100-1000 are obtained and the formation of liquid condensates from residual gases occurs at pressures (prior to hydrogen depletion) of roughly equal to or greater than 1 atm.

  20. Statistical and Microscopic Approach to Gas Phase Chemical Kinetics.

    ERIC Educational Resources Information Center

    Perez, J. M.; Quereda, R.

    1983-01-01

    Describes advanced undergraduate laboratory exercise examining the dependence of the rate constants and the instantaneous concentrations with the nature and energy content in a gas-phase complex reaction. Computer program (with instructions and computation flow charts) used with the exercise is available from the author. (Author/JN)

  1. Ion-Molecule Reactions in Gas Phase Radiation Chemistry.

    ERIC Educational Resources Information Center

    Willis, Clive

    1981-01-01

    Discusses some aspects of the radiation chemistry of gases, focusing on the ion-molecule and charge neutralization reactions which set study of the gas phase apart. Uses three examples that illustrate radiolysis, describing the radiolysis of (1) oxygen, (2) carbon dioxide, and (3) acetylene. (CS)

  2. Sulfur doping of diamond films: Spectroscopic, electronic, and gas-phase studies

    NASA Astrophysics Data System (ADS)

    Petherbridge, James R.; May, Paul W.; Fuge, Gareth M.; Robertson, Giles F.; Rosser, Keith N.; Ashfold, Michael N. R.

    2002-03-01

    Chemical vapor deposition (CVD) has been used to grow sulfur doped diamond films on undoped Si and single crystal HPHT diamond as substrates, using a 1% CH4/H2 gas mixture with various levels of H2S addition (100-5000 ppm), using both microwave (MW) plasma enhanced CVD and hot filament (HF) CVD. The two deposition techniques yield very different results. HFCVD produces diamond films containing only trace amounts of S (as analyzed by x-ray photoelectron spectroscopy), the film crystallinity is virtually unaffected by gas phase H2S concentration, and the films remain highly resistive. In contrast, MWCVD produces diamond films with S incorporated at levels of up to 0.2%, and the amount of S incorporation is directly proportional to the H2S concentration in the gas phase. Secondary electron microscopy observations show that the crystal quality of these films reduces with increasing S incorporation. Four point probe measurements gave the room temperature resistivities of these S-doped and MW grown films as ˜200 Ω cm, which makes them ˜3 times more conductive than undoped diamond grown under similar conditions. Molecular beam mass spectrometry has been used to measure simultaneously the concentrations of the dominant gas phase species present during growth, for H2S doping levels (1000-10 000 ppm in the gas phase) in 1% CH4/H2 mixtures, and for 1% CS2/H2 gas mixtures, for both MW and HF activation. CS2 and CS have both been detected in significant concentrations in all of the MW plasmas that yield S-doped diamond films, whereas CS was not detected in the gas phase during HF growth. This suggests that CS may be an important intermediary facilitating S incorporation into diamond. Furthermore, deposition of yellow S was observed on the cold chamber walls when using H2S concentrations >5000 ppm in the MW system, but very little S deposition was observed for the HF system under similar conditions. All of these results are rationalized by a model of the important gas phase

  3. Gas-Phase Theoretical Kinetics for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Klippenstein, Stephen

    2013-05-01

    We will survey a number of our applications of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. For low temperature interstellar chemistry, careful consideration of the long-range expansion of the potential allows for quantitative predictions of the kinetics. Our recent calculations for the reactions of H3+ with O(3P) and with CO suggest an increase of the predicted destruction rate of H3+ by a factor of 2.5 to 3.0 for temperatures that are typical of dense clouds. Further consideration of the interplay between spin-orbit and multipole terms for open-shell atomic fragments allows us to predict the kinetics for a number of the reactions that have been listed as important reactions for interstellar chemical modeling [V. Wakelam, I. W. M. Smith, E. Herbst, J. Troe, W. Geppert, et al. Space Science Rev., 156, 13-72, 2010]. Our calculations for Titan's atmosphere demonstrate the importance of radiative emission as a stabilization process in the low-pressure environment of Titan's upper atmosphere. Theory has also helped to illuminate the role of various reactions in both Titan's atmosphere and in extrasolar planetary atmospheres. Comparisons between theory and experiment have provided a more detail understanding of the kinetics of PAH dimerization. High level predictions of thermochemical properties are remarkably accurate, and allow us to provide important data for studying P chemistry in planetary atmospheres. Finally, our study of O(3P) + C3 provides an example of a case where theory provides suggestive but not definitive results, and further experiments are clearly needed.

  4. Gas Phase Theoretical Kinetics for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Klippenstein, Stephen J.; Georgievskii, Y.; Harding, L. B.

    2012-05-01

    We will survey a number of our applications of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan’s atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. For low temperature interstellar chemistry, careful consideration of the long-range expansion of the potential allows for quantitative predictions of the kinetics. Our recent calculations for the reactions of H3+ with O(3P) and with CO suggest an increase of the predicted destruction rate of H3+ by a factor of 2.5 to 3.0 for temperatures that are typical of dense clouds. Further consideration of the interplay between spin-orbit and multipole terms for open-shell atomic fragments allows us to predict the kinetics for a number of the reactions that have been listed as important reactions for interstellar chemical modeling [V. Wakelam, I. W. M. Smith, E. Herbst, J. Troe, W. Geppert, et al. Space Science Rev., 156, 13-72, 2010]. Our calculations for Titan’s atmosphere demonstrate the importance of radiative emission as a stabilization process in the low-pressure environment of Titan’s upper atmosphere. Theory has also helped to illuminate the role of various reactions in both Titan’s atmosphere and in extrasolar planetary atmospheres. Comparisons between theory and experiment have provided a more detail understanding of the kinetics of PAH dimerization. High level predictions of thermochemical properties are remarkably accurate, and allow us to provide important data for studying P chemistry in planetary atmospheres. Finally, our study of O(3P) + C3 provides an example of a case where theory provides suggestive but not definitive results, and further experiments are clearly needed.

  5. Fluorescence probe of polypeptide conformational dynamics in gas phase and in solution

    NASA Astrophysics Data System (ADS)

    Iavarone, Anthony T.; Meinen, Jan; Schulze, Susanne; Parks, Joel H.

    2006-07-01

    Fluorescence measurements of polypeptides derivatized with the fluorescent dye BODIPY TMR have been used to probe the polypeptide conformational dynamics as a function of temperature and charge state. Measurements of (BODIPY TMR)-[Pro]n-Arg-Trp and (BODIPY TMR)-[Gly-Ser]m-Arg-Trp have been performed for charge states 1+ and 2+ of n = 4 and 10 and m = 2 and 5. The 2+ charge states of both of these polypeptides exhibit similar temperature dependences for equal chain lengths (n = 4, m = 2 and n = 10, m = 5) and suggest conformations dominated by Coulomb repulsion. In the absence of such Coulomb repulsion, the 1+ charge state conformations appear to be characterized by the flexibility of the polypeptide chain for which [Gly-Ser]m > [Pro]n. Comparisons of these gas phase polypeptide measurements with corresponding measurements in solution provide a direct measure of the effects of solvent on the conformational dynamics. The change in fluorescence as a function of temperature in the gas phase is two orders of magnitude greater than that in solution, a dramatic result we attribute to the restrictions on intramolecular dynamics imposed by diffusion-limited kinetics and the lack of shielding by solvent. Measurements were also made of unsolvated Pron peptides without the tryptophan (Trp) residue to isolate the interaction of the fluorescent dye with charges.

  6. Structure and orientation study of Ebola fusion peptide inserted in lipid membrane models.

    PubMed

    Agopian, Audrey; Castano, Sabine

    2014-01-01

    The fusion peptide of Ebola virus comprises a highly hydrophobic sequence located downstream from the N-terminus of the glycoprotein GP2 responsible for virus-host membrane fusion. The internal fusion peptide of GP2 inserts into membranes of infected cell to mediate the viral and the host cell membrane fusion. Since the sequence length of Ebola fusion peptide is still not clear, we study in the present work the behavior of two fusion peptides of different lengths which were named EBO17 and EBO24 referring to their amino acid length. The secondary structure and orientation of both peptides in lipid model systems made of DMPC:DMPG:cholesterol:DMPE (6:2:5:3) were investigated using PMIRRAS and polarized ATR spectroscopy coupled with Brewster angle microscopy. The infrared results showed a structural flexibility of both fusion peptides which are able to transit reversibly from an α-helix to antiparallel β-sheets. Ellipsometry results corroborate together with isotherm measurements that EBO peptides interacting with lipid monolayer highly affected the lipid organization. When interacting with a single lipid bilayer, at low peptide content, EBO peptides insert as mostly α-helices mainly perpendicular into the lipid membrane thus tend to organize the lipid acyl chains. Inserted in multilamellar vesicles at higher peptide content, EBO peptides are mostly in β-sheet structures and induce a disorganization of the lipid chain order. In this paper, we show that the secondary structure of the Ebola fusion peptide is reversibly flexible between α-helical and β-sheet conformations, this feature being dependent on its concentration in lipids, eventually inducing membrane fusion. PMID:24055820

  7. Poly-arginine and arginine-rich peptides are neuroprotective in stroke models

    PubMed Central

    Meloni, Bruno P; Brookes, Laura M; Clark, Vince W; Cross, Jane L; Edwards, Adam B; Anderton, Ryan S; Hopkins, Richard M; Hoffmann, Katrin; Knuckey, Neville W

    2015-01-01

    Using cortical neuronal cultures and glutamic acid excitotoxicity and oxygen-glucose deprivation (OGD) stroke models, we demonstrated that poly-arginine and arginine-rich cell-penetrating peptides (CPPs), are highly neuroprotective, with efficacy increasing with increasing arginine content, have the capacity to reduce glutamic acid-induced neuronal calcium influx and require heparan sulfate preotoglycan-mediated endocytosis to induce a neuroprotective effect. Furthermore, neuroprotection could be induced with immediate peptide treatment or treatment up to 2 to 4 hours before glutamic acid excitotoxicity or OGD, and with poly-arginine-9 (R9) when administered intravenously after stroke onset in a rat model. In contrast, the JNKI-1 peptide when fused to the (non-arginine) kFGF CPP, which does not rely on endocytosis for uptake, was not neuroprotective in the glutamic acid model; the kFGF peptide was also ineffective. Similarly, positively charged poly-lysine-10 (K10) and R9 fused to the negatively charged poly-glutamic acid-9 (E9) peptide (R9/E9) displayed minimal neuroprotection after excitotoxicity. These results indicate that peptide positive charge and arginine residues are critical for neuroprotection, and have led us to hypothesize that peptide-induced endocytic internalization of ion channels is a potential mechanism of action. The findings also question the mode of action of different neuroprotective peptides fused to arginine-rich CPPs. PMID:25669902

  8. Poly-arginine and arginine-rich peptides are neuroprotective in stroke models.

    PubMed

    Meloni, Bruno P; Brookes, Laura M; Clark, Vince W; Cross, Jane L; Edwards, Adam B; Anderton, Ryan S; Hopkins, Richard M; Hoffmann, Katrin; Knuckey, Neville W

    2015-06-01

    Using cortical neuronal cultures and glutamic acid excitotoxicity and oxygen-glucose deprivation (OGD) stroke models, we demonstrated that poly-arginine and arginine-rich cell-penetrating peptides (CPPs), are highly neuroprotective, with efficacy increasing with increasing arginine content, have the capacity to reduce glutamic acid-induced neuronal calcium influx and require heparan sulfate preotoglycan-mediated endocytosis to induce a neuroprotective effect. Furthermore, neuroprotection could be induced with immediate peptide treatment or treatment up to 2 to 4 hours before glutamic acid excitotoxicity or OGD, and with poly-arginine-9 (R9) when administered intravenously after stroke onset in a rat model. In contrast, the JNKI-1 peptide when fused to the (non-arginine) kFGF CPP, which does not rely on endocytosis for uptake, was not neuroprotective in the glutamic acid model; the kFGF peptide was also ineffective. Similarly, positively charged poly-lysine-10 (K10) and R9 fused to the negatively charged poly-glutamic acid-9 (E9) peptide (R9/E9) displayed minimal neuroprotection after excitotoxicity. These results indicate that peptide positive charge and arginine residues are critical for neuroprotection, and have led us to hypothesize that peptide-induced endocytic internalization of ion channels is a potential mechanism of action. The findings also question the mode of action of different neuroprotective peptides fused to arginine-rich CPPs. PMID:25669902

  9. Effect of duty-cycles on the air plasma gas-phase of dielectric barrier discharges

    NASA Astrophysics Data System (ADS)

    Barni, R.; Biganzoli, I.; Dell'Orto, E. C.; Riccardi, C.

    2015-10-01

    An experimental investigation concerning the effects of a duty-cycle in the supply of a dielectric barrier discharge in atmospheric pressure air has been performed. Electrical characteristics of the discharge have been measured, focusing mainly on the statistical properties of the current filaments and on dielectric surface charging, both affected by the frequent repetition of breakdown imposed by the duty-cycle. Information on the gas-phase composition was gathered too. In particular, a strong enhancement in the ozone formation rate is observed when suitable long pauses separate the active discharge phases. A simulation of the chemical kinetics in the gas-phase, based on a simplified discharge modeling, is briefly described in order to shed light on the observed increase in ozone production. The effect of a duty-cycle on surface modification of polymeric films in order to increase their wettability has been investigated too.

  10. The Gas-Phase Deuterium Fractionation of Formaldehyde

    NASA Astrophysics Data System (ADS)

    Osamura, Yoshihiro; Roberts, Helen; Herbst, Eric

    2005-03-01

    The dominant mechanism for the deuteration of formaldehyde in the gas phase of low-temperature interstellar cloud cores occurs via reaction with the deuterating ions H2D+, HD+2, and D+3. Until now, it has been assumed that deuteration leads to an ion that, on recombination with electrons, can produce a deuterated neutral species with a statistical branching fraction. Quantum chemical calculations reported here, however, show an entirely different picture, in which the deuteration of formaldehyde leads to the molecular ion H2COD+, where the deuterium binds only on the oxygen side of the molecule. The structure is quite stable, while an alternative structure, H2DCO+, cannot be produced in a straightforward manner. Dissociative recombination of H2COD+ to reproduce a formaldehyde structure then removes the deuteration if the dissociation is direct, i.e., it occurs without change of structure. There are several possible indirect mechanisms by which dissociative recombination can lead to HDCO, however. For example, if the direct products are HCOD+H, it is possible that subsequent isomerization to HDCO can occur, although this involved process is unlikely. Another possibility is isomerization during the actual dissociation of the H2COD intermediate. Models of deuterium fractionation in which dissociative recombination is predominantly direct are presented, and it is found that the deuterium fractionation of formaldehyde to form both HDCO and D2CO can still occur via other mechanisms, although with less efficiency than previously obtained. If the dissociative recombination is half indirect, however, then we can recover the previously calculated efficiency.

  11. Gas-Phase Combustion Synthesis of Nonoxide Nanoparticles in Microgravity

    NASA Technical Reports Server (NTRS)

    Axelbaum, R. L.; Kumfer, B. M.; Sun, Z.; Chao, B. H.

    2001-01-01

    Gas-phase combustion synthesis is a promising process for creating nanoparticles for the growing nanostructure materials industry. The challenges that must be addressed are controlling particle size, preventing hard agglomerates, maintaining purity, and, if nonoxides are synthesized, protecting the particles from oxidation and/or hydrolysis during post-processing. Sodium-halide Flame Encapsulation (SFE) is a unique methodology for producing nonoxide nanoparticles that addresses these challenges. This flame synthesis process incorporates sodium and metal-halide chemistry, resulting in nanoparticles that are encapsulated in salt during the early stages of their growth in the flame. Salt encapsulation has been shown to allow control of particle size and morphology, while serving as an effective protective coating for preserving the purity of the core particles. Metals and compounds that have been produced using this technology include Al, W, Ti, TiB2, AlN, and composites of W-Ti and Al-AlN. Oxygen content in SFE synthesized nano- AlN has been measured by neutron activation analysis to be as low as 0.54wt.%, as compared to over 5wt.% for unprotected AlN of comparable size. The overall objective of this work is to study the SFE process and nano-encapsulation so that they can be used to produce novel and superior materials. SFE experiments in microgravity allow the study of flame and particle dynamics without the influence of buoyancy forces. Spherical sodium-halide flames are produced in microgravity by ejecting the halide from a spherical porous burner into a quiescent atmosphere of sodium vapor and argon. Experiments are performed in the 2.2 sec Drop Tower at the NASA-Glenn Research Center. Numerical models of the flame and particle dynamics were developed and are compared with the experimental results.

  12. Charged supramolecular assemblies of surfactant molecules in gas phase.

    PubMed

    Bongiorno, David; Ceraulo, Leopoldo; Indelicato, Sergio; Turco Liveri, Vincenzo; Indelicato, Serena

    2016-01-01

    The aim of this review is to critically analyze recent literature on charged supramolecular assemblies formed by surfactant molecules in gas phase. Apart our specific interest on this research area, the stimuli to undertake the task arise from the widespread theoretical and applicative benefits emerging from a comprehensive view of this topic. In fact, the study of the formation, stability, and physicochemical peculiarities of non-covalent assemblies of surfactant molecules in gas phase allows to unveil interesting aspects such as the role of attractive, repulsive, and steric intermolecular interactions as driving force of supramolecular organization in absence of interactions with surrounding medium and the size and charge state dependence of aggregate structural and dynamical properties. Other interesting aspects worth to be investigated are joined to the ability of these assemblies to incorporate selected solubilizates molecules as well as to give rise to chemical reactions within a single organized structure. In particular, the incorporation of large molecules such as proteins has been of recent interest with the objective to protect their structure and functionality during the transition from solution to gas phase. Exciting fall-out of the study of gas phase surfactant aggregates includes mass and energy transport in the atmosphere, origin of life and simulation of supramolecular aggregation in the interstellar space. Moreover, supramolecular assemblies of amphiphilic molecules in gas phase could find remarkable applications as atmospheric cleaning agents, nanosolvents and nanoreactors for specialized chemical processes in confined space. Mass spectrometry techniques have proven to be particularly suitable to generate these assemblies and to furnish useful information on their size, size polydispersity, stability, and structural organization. On the other hand molecular dynamics simulations have been very useful to rationalize many experimental findings and to

  13. Mechanical unfolding pathway of a model β-peptide foldamer

    NASA Astrophysics Data System (ADS)

    Uribe, Lalita; Jaschonek, Stefan; Gauss, Jürgen; Diezemann, Gregor

    2015-05-01

    Foldamers constructed from oligomers of β-peptides form stable secondary helix structures already for small chain lengths, which makes them ideal candidates for the investigation of the (un)folding of polypeptides. Here, the results of molecular simulations of the mechanical unfolding of a β-heptapeptide in methanol solvent revealing the detailed unfolding pathway are reported. The unfolding process is shown to proceed via a stable intermediate even for such a small system. This result is arrived at performing non-equilibrium force ramp simulations employing different pulling velocities and also using standard calculations of the potential of mean force, i.e., the free energy as a function of the helix elongation. It is thus demonstrated that even with the rather large pulling velocities employed in the force ramp simulations relevant information about the equilibrium kinetics can be obtained. The smallness of the system allows a detailed analysis of the unfolding pathway, which is characterized by an opening of the terminal loops followed by the unfolding of the center. This sequence is in accord with the configurational preferences of the system that also are responsible for the stability of the 314-helix. From an analysis of the distributions of rupture forces and the force spectra, the kinetic rates for both transitions were determined and common models were used to extract geometric quantities describing the free energy landscape of the system.

  14. "Best Match" Model and Effect of Na+/H+ Exchange on Anion Attachment to Peptides and Stability of Formed Adducts in Negative Ion Electrospray Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Liu, Xiaohua; Cole, Richard B.

    2013-12-01

    The "Best Match" model has been extended to account for the role that Na+/H+ exchange plays on anion attachment in negative ion electrospray. Without any Na+/H+ exchange on (Glu) fibrinopeptide B, the higher basicity anions F- and CH3COO- can hardly form observable adducts; however, after multiple Na+/H+ exchanges, adduct formation is enabled. Moreover, dissociation pathways of CF3COO- adducts with singly deprotonated peptides that have undergone 0 to 3 Na+/H+ exchanges exhibit a shift in CID product ions from losing predominately CF3COOH (case of 0 Na+/H+ exchanges) to losing predominately CF3COO- (case of 3 Na+/H+ exchanges). These phenomena can be rationalized by considering that Na+ cations exchange at, and serve to "block", the most acidic sites, thereby forcing implicated anions to attach to lower acidity protons. In addition to forming ion pairs with carboxylate groups, Na+ also participates in formation of tri-atomic ions of the form ANaA- during adduct dissociation. The fact that low gas-phase basicity (GB) anions preferentially form ANaA- species, even though high GB anions form more stable tri-atomic species, indicates that the monatomic ions were not in close contact in the initial adduct. The propensity for formation of stable anionic adducts is dependent on the degree of matching between anion GBs and GBapp of deprotonated sites on the peptide. The GBapp is raised dramatically as the charge state of the peptide increases via a through-space effect. The presence of Na+ on carboxylate sites substantially decreases the GBapp by neutralizing these sites, while slightly increasing the intrinsic GBs by an inductive effect.

  15. Interaction of the Alzheimer Aβ(25-35) peptide segment with model membranes.

    PubMed

    Cuco, Andreia; Serro, Ana Paula; Farinha, José Paulo; Saramago, Benilde; da Silva, Amélia Gonçalves

    2016-05-01

    Alzheimer's disease is characterized by the presence of amyloid plaques in the brain. The main components of these plaques are the Aβ(1-40) and Aβ(1-42) peptides but the Aβ(25-35) sequence is the most frequently studied fragment because it represents a biologically active region of the longer Aβ peptides. In the present work, the interactions of Aβ(25-35) peptide with model membranes were investigated, taking into consideration the aggregation state of the peptide. Monolayers and liposomes were taken as model membranes with two lipid compositions: the equimolar ternary mixture of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), sphingomyelin (SM), and cholesterol (Chol) and the equimolar POPC/SM binary mixture. The interaction of Aβ(25-35) with the monolayers, investigated at low concentrations (0.25-4μM), suggested a three step mechanism: adsorption-monomers or dimers adsorb at the polar region of the lipid monolayer; nucleation-adsorbed peptides act as nucleation sites for higher aggregates; and penetration-these aggregates insert in the hydrophobic region of the monolayer. Chol slightly enhances the peptide-lipid monolayer interaction. The large aggregates nucleated in the bulk solution evidenced a weak interaction with monolayers. The interaction of Aβ(25-35) with liposomes, followed by a Quartz Crystal Microbalance with Dissipation (QCM-D) in a large range of peptide concentrations (10-80μM), was very small, independently of the peptide concentration. PMID:26816349

  16. Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics.

    PubMed

    Jarnuczak, Andrew F; Lee, Dave C H; Lawless, Craig; Holman, Stephen W; Eyers, Claire E; Hubbard, Simon J

    2016-09-01

    Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from signal intensity alone in the absence of a standard. A deeper understanding of the governing principles of peptide ionization and exploitation of the inherent ionization and detection parameters of individual peptides is thus of great value. Here, using the yeast proteome as a model system, we establish the concept of peptide F-factor as a measure of detectability, closely related to ionization efficiency. F-factor is calculated by normalizing peptide precursor ion intensity by absolute abundance of the parent protein. We investigated F-factor characteristics in different shotgun proteomics experiments, including across multiple ESI-based LC-MS platforms. We show that F-factors mirror previously observed physicochemical predictors as peptide detectability but demonstrate a nonlinear relationship between hydrophobicity and peptide detectability. Similarly, we use F-factors to show how peptide ion coelution adversely affects detectability and ionization. We suggest that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex peptide mixtures, selection of surrogate peptides in targeted MS studies, and for calibration of peptide ion signal in label-free workflows. Data are available via ProteomeXchange with identifier PXD003472. PMID:27454336

  17. A toy model of prebiotic peptide evolution: the possible role of relative amino acid abundances.

    PubMed

    Polanco, Carlos; Buhse, Thomas; Samaniego, José Lino; Castañón González, Jorge Alberto

    2013-01-01

    This paper presents a mathematical-computational toy model based on the assumed dynamic principles of prebiotic peptide evolution. Starting from a pool of amino acid monomers, the model describes in a generalized manner the generation of peptides and their sequential information. The model integrates the intrinsic and dynamic key elements of the initiation of biopolymerization, such as the relative amino acid abundances and polarities, as well as the oligomer reversibility, i.e. fragmentation and recombination, and peptide self-replication. Our modeling results suggest that the relative amino acid abundances, as indicated by Miller-Urey type electric discharge experiments, played a principal role in the early sequential information of peptide profiles. Moreover, the computed profiles display an astonishing similarity to peptide profiles observed in so-called biological common ancestors found in the following three microorganisms; E. coli, M. jannaschii, and S. cereviasiae. The prebiotic peptide fingerprint was obtained by the so-called polarity index method that was earlier reported as a tool for the identification of cationic amphipathic antibacterial short peptides. PMID:23741717

  18. A Gas-phase Formation Route to Interstellar Trans-methyl Formate

    NASA Astrophysics Data System (ADS)

    Cole, Callie A.; Wehres, Nadine; Yang, Zhibo; Thomsen, Ditte L.; Snow, Theodore P.; Bierbaum, Veronica M.

    2012-07-01

    The abundance of methyl formate in the interstellar medium has previously been underpredicted by chemical models. Additionally, grain surface chemistry cannot account for the relative abundance of the cis- and trans-conformers of methyl formate, and the trans-conformer is not even formed at detectable abundance on these surfaces. This highlights the importance of studying formation pathways to methyl formate in the gas phase. The rate constant and branching fractions are reported for the gas-phase reaction between protonated methanol and formic acid to form protonated trans-methyl formate and water as well as adduct ion: Rate constants were experimentally determined using a flowing afterglow-selected ion flow tube apparatus at 300 K and a pressure of 530 mTorr helium. The results indicate a moderate overall rate constant of (3.19 ± 0.39) × 10-10 cm3 s-1 (± 1σ) and an average branching fraction of 0.05 ± 0.04 for protonated trans-methyl formate and 0.95 ± 0.04 for the adduct ion. These experimental results are reinforced by ab initio calculations at the MP2(full)/aug-cc-pVTZ level of theory to examine the reaction coordinate and complement previous density functional theory calculations. This study underscores the need for continued observational studies of trans-methyl formate and for the exploration of other gas-phase formation routes to complex organic molecules.

  19. A GAS-PHASE FORMATION ROUTE TO INTERSTELLAR TRANS-METHYL FORMATE

    SciTech Connect

    Cole, Callie A.; Wehres, Nadine; Yang Zhibo; Thomsen, Ditte L.; Bierbaum, Veronica M.; Snow, Theodore P. E-mail: Nadine.Wehres@colorado.edu E-mail: Veronica.Bierbaum@colorado.edu E-mail: dlt@chem.ku.dk

    2012-07-20

    The abundance of methyl formate in the interstellar medium has previously been underpredicted by chemical models. Additionally, grain surface chemistry cannot account for the relative abundance of the cis- and trans-conformers of methyl formate, and the trans-conformer is not even formed at detectable abundance on these surfaces. This highlights the importance of studying formation pathways to methyl formate in the gas phase. The rate constant and branching fractions are reported for the gas-phase reaction between protonated methanol and formic acid to form protonated trans-methyl formate and water as well as adduct ion: Rate constants were experimentally determined using a flowing afterglow-selected ion flow tube apparatus at 300 K and a pressure of 530 mTorr helium. The results indicate a moderate overall rate constant of (3.19 {+-} 0.39) Multiplication-Sign 10{sup -10} cm{sup 3} s{sup -1} ({+-} 1{sigma}) and an average branching fraction of 0.05 {+-} 0.04 for protonated trans-methyl formate and 0.95 {+-} 0.04 for the adduct ion. These experimental results are reinforced by ab initio calculations at the MP2(full)/aug-cc-pVTZ level of theory to examine the reaction coordinate and complement previous density functional theory calculations. This study underscores the need for continued observational studies of trans-methyl formate and for the exploration of other gas-phase formation routes to complex organic molecules.

  20. Kinetics of gas phase oxygen control system (OCS) for stagnant and flowing Pb-Bi Systems

    NASA Astrophysics Data System (ADS)

    Lefhalm, C. H.; Knebel, J. U.; Mack, K. J.

    2001-07-01

    Pb and Pb-Bi are known to be very corrosive to structural materials at elevated temperatures. In recent studies, the necessity of measurement and control of the oxygen concentration in the liquid metal in order to safely operate a liquid Pb or Pb-Bi loop has been shown. The dynamic behaviour of the gas phase oxygen control system (OCS), which was developed at Forschungszentrum Karlsruhe (FZK), is investigated with respect to diffusion as the limiting process of oxygen exchange between the gas phase and the liquid metal. In this paper the development of a physical model for this diffusion process is described and compared to experimental results of a stagnant liquid Pb-Bi system. The experimental findings are in very good agreement with the theoretical equations describing the thermodynamic and kinetic behaviour of such a system. Recent investigations in a Pb-Bi loop at the Karlsruhe Lead Laboratory (KALLA) indicate that this gas phase OCS is a promising candidate system for an accelerator-driven subcritical system (ADS).

  1. Cathelicidin peptide sheep myeloid antimicrobial peptide-29 prevents endotoxin-induced mortality in rat models of septic shock.

    PubMed

    Giacometti, Andrea; Cirioni, Oscar; Ghiselli, Roberto; Mocchegiani, Federico; D'Amato, Giuseppina; Circo, Raffaella; Orlando, Fiorenza; Skerlavaj, Barbara; Silvestri, Carmela; Saba, Vittorio; Zanetti, Margherita; Scalise, Giorgio

    2004-01-15

    The present study was designed to investigate the antiendotoxin activity and therapeutic efficacy of sheep myeloid antimicrobial peptide (SMAP)-29, a cathelicidin-derived peptide. The in vitro ability of SMAP-29 to bind LPS from Escherichia coli 0111:B4 was determined using a sensitive limulus chromogenic assay. Two rat models of septic shock were performed: (1) rats were injected intraperitoneally with 1 mg E. coli 0111:B4 LPS and (2) intraabdominal sepsis was induced via cecal ligation and single puncture. All animals were randomized to receive parenterally isotonic sodium chloride solution, 1 mg/kg SMAP-29, 1 mg/kg polymyxin B or 20 mg/kg imipenem. The main outcome measures were: abdominal exudate and plasma bacterial growth, plasma endotoxin and tumor necrosis factor-alpha concentrations, and lethality. The in vitro study showed that SMAP-29 completely inhibited the LPS procoagulant activity at approximately 10 microM peptide concentration. The in vivo experiments showed that all compounds reduced the lethality when compared with control animals. SMAP-29 achieved a substantial decrease in endotoxin and tumor necrosis factor-alpha plasma concentrations when compared with imipenem and saline treatment and exhibited a slightly lower antimicrobial activity than imipenem. No statistically significant differences were noted between SMAP-29 and polymyxin B. SMAP-29, because of its double antiendotoxin and antimicrobial activities, could be an interesting compound for septic shock treatment. PMID:14563656

  2. Context-Sensitive Markov Models for Peptide Scoring and Identification from Tandem Mass Spectrometry

    PubMed Central

    Grover, Himanshu; Wallstrom, Garrick; Wu, Christine C.

    2013-01-01

    Abstract Peptide and protein identification via tandem mass spectrometry (MS/MS) lies at the heart of proteomic characterization of biological samples. Several algorithms are able to search, score, and assign peptides to large MS/MS datasets. Most popular methods, however, underutilize the intensity information available in the tandem mass spectrum due to the complex nature of the peptide fragmentation process, thus contributing to loss of potential identifications. We present a novel probabilistic scoring algorithm called Context-Sensitive Peptide Identification (CSPI) based on highly flexible Input-Output Hidden Markov Models (IO-HMM) that capture the influence of peptide physicochemical properties on their observed MS/MS spectra. We use several local and global properties of peptides and their fragment ions from literature. Comparison with two popular algorithms, Crux (re-implementation of SEQUEST) and X!Tandem, on multiple datasets of varying complexity, shows that peptide identification scores from our models are able to achieve greater discrimination between true and false peptides, identifying up to ∼25% more peptides at a False Discovery Rate (FDR) of 1%. We evaluated two alternative normalization schemes for fragment ion-intensities, a global rank-based and a local window-based. Our results indicate the importance of appropriate normalization methods for learning superior models. Further, combining our scores with Crux using a state-of-the-art procedure, Percolator, we demonstrate the utility of using scoring features from intensity-based models, identifying ∼4-8 % additional identifications over Percolator at 1% FDR. IO-HMMs offer a scalable and flexible framework with several modeling choices to learn complex patterns embedded in MS/MS data. PMID:23289783

  3. Dermaseptins as models for the elucidation of membrane-acting helical amphipathic antimicrobial peptides.

    PubMed

    Amiche, Mohamed; Galanth, Cécile

    2011-08-01

    Antimicrobial peptides (AMPs) produced by a wide variety of organisms are major actors of the host defense systems against invading pathogenic microorganisms. These peptides exhibit a broad spectrum of action against bacteria, yeasts, fungi, protozoa and viruses. It is widely believed that a large part of their antimicrobial effect derives from direct interactions with the lipid membrane surrounding the target cells, causing its permeabilization and cell lysis. However, the exact nature of these interactions is presently unclear. The skin of the amphibians has proved to be a remarkably rich storehouse of AMPs that encompass a wide variety of structural motifs. This natural AMP bank is used in combined approaches, based on biophysical and cellular biology methods, to elucidate how these peptides perturb the membrane and whether such membrane perturbations are related to the antimicrobial activity of these peptides. Here we review our current knowledge about the structure and the mechanism of action of the dermaseptin super-family, α-helical amphipathic AMPs isolated from the skin of frogs of the Phyllomedusa genus. Dermaseptins are genetically related, with a remarkable identity in signal sequences and acidic propieces of their preproforms but have clearly diverged to yield several families of microbicidal cationic peptides that are structurally distinct. Particularly, we focused on the orthologous peptides dermaseptin S and B of which the shortening from the carboxy terminal extremity causes a drastic change in their membrane disruption activity. These peptides could be good models to study the membrane-peptide interactions discussed in this review. PMID:21470155

  4. Recent Advances in Computational Models for the Study of Protein-Peptide Interactions.

    PubMed

    Kilburg, D; Gallicchio, E

    2016-01-01

    We review computational models and software tools in current use for the study of protein-peptide interactions. Peptides and peptide derivatives are growing in interest as therapeutic agents to target protein-protein interactions. Protein-protein interactions are pervasive in biological systems and are responsible for the regulation of critical functions within the cell. Mutations or dysregulation of expression can alter the network of interactions among proteins and cause diseases such as cancer. Protein-protein binding interfaces, which are often large, shallow, and relatively feature-less, are difficult to target with small-molecule inhibitors. Peptide derivatives based on the binding motifs present in the target protein complex are increasingly drawing interest as superior alternatives to conventional small-molecule inhibitors. However, the design of peptide-based inhibitors also presents novel challenges. Peptides are more complex and more flexible than standard medicinal compounds. They also tend to form more extended and more complex interactions with their protein targets. Computational modeling is increasingly being employed to supplement synthetic and biochemical work to offer guidance and energetic and structural insights. In this review, we discuss recent in silico structure-based and physics-based approaches currently employed to model protein-peptide interactions with a few examples of their applications. PMID:27567483

  5. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides

    NASA Astrophysics Data System (ADS)

    Tran, Thanh Thuy; Nguyen, Phuong H.; Derreumaux, Philippe

    2016-05-01

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

  6. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides.

    PubMed

    Tran, Thanh Thuy; Nguyen, Phuong H; Derreumaux, Philippe

    2016-05-28

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases. PMID:27250331

  7. Substituent effects on the gas-phase acidity of silane

    SciTech Connect

    Gordon, M.S.; Volk, D.E. ); Gano, D.R. )

    1989-12-20

    In a previous paper, the gas-phase acidities of XH{sub n} compounds (X = C, N, O, F, Si, P, S, Cl) were predicted with ab initio wave functions. At the MP4{sup 2} level of theory with extended basis sets acidities for these species were determined to be within 2 kcal/mol of experimental value. In the present work, with 6-31G(d) geometries and full MP4/MC-311++G{sup 6}(3df,2pd) energies, the effects of CH{sub 3}, NH{sub 2}, OH, F, SiH{sub 3}, PH{sub 2}, SH, and Cl on the gas-phase acidity of silane are examined. Only a few related calculations have been carried out. All calculations were performed with Gaussian86, and all structures were verified as minima by diagonalizing the analytically determined hessians. Only the valence electrons were correlated in the perturbation theory calculations.

  8. Para-Hydrogen-Enhanced Gas-Phase Magnetic Resonance Imaging

    SciTech Connect

    Bouchard, Louis-S.; Kovtunov, Kirill V.; Burt, Scott R.; Anwar,M. Sabieh; Koptyug, Igor V.; Sagdeev, Renad Z.; Pines, Alexander

    2007-02-23

    Herein, we demonstrate magnetic resonance imaging (MRI) inthe gas phase using para-hydrogen (p-H2)-induced polarization. A reactantmixture of H2 enriched in the paraspin state and propylene gas is flowedthrough a reactor cell containing a heterogenized catalyst, Wilkinson'scatalyst immobilized on modified silica gel. The hydrogenation product,propane gas, is transferred to the NMR magnet and is spin-polarized as aresult of the ALTADENA (adiabatic longitudinal transport and dissociationengenders net alignment) effect. A polarization enhancement factor of 300relative to thermally polarized gas was observed in 1D1H NMR spectra.Enhancement was also evident in the magnetic resonance images. This isthe first demonstration of imaging a hyperpolarized gaseous productformed in a hydrogenation reaction catalyzed by a supported catalyst.This result may lead to several important applications, includingflow-through porous materials, gas-phase reaction kinetics and adsorptionstudies, and MRI in low fields, all using catalyst-free polarizedfluids.

  9. Kinetics of gas phase tetramethyldioxetane decomposition and chemiluminescence

    SciTech Connect

    Cannon, B.D.; Crim, F.F.

    1981-11-04

    Pulsed-laser excitation of overtone vibrations or a weak electronic transition in gas-phase tetramethyldioxetane in combination with temporally and spectrally resolved detection of decomposition product luminescence reveals the presence, along with electronically excited acetone, of an additional emitting species which is not observed in solution studies. The emission is at shorter wavelengths than the acetone phosphorescence, and the emitting species has a zero-pressure decay rate of 0.019 +- 0.014 ..mu..s/sup -1/. The rapid collisional quenching which occurs on roughly every other encounter (k/sub q/ = 5.6 ..mu..s/sup -1/ torr/sup -1/) explains the inability of solution measurements to detect this feature of the tetramethyldioxetane decomposition kinetics. This newly observed component is likely to extend the interpretation of gas-phase decomposition experiments using infrared multiphoton absorption or collisions with fast Xe atoms to excite tetramethyldioxetane.

  10. Ionization of vitamin C in gas phase: Theoretical study.

    PubMed

    Abyar, Fatemeh; Farrokhpour, Hossein

    2016-07-01

    In this work, the gas phase ionization energies and photoelectron spectra of four important conformers of vitamin C were calculated. Symmetry adapted cluster/configuration interaction methodology employing the single and double excitation operators (SAC-CI SD-R) along with D95++(d,p) basis set were used for the calculations. Thermochemistry calculations were also performed on all possible conformers of vitamin C to find the relative stability of conformers in the gas phase. The calculated ionization bands of each conformer were assigned by calculating the contribution of natural bonding orbital (NBO) in the calculated canonical molecular orbitals involved in the ionization. SAC-CI calculations showed that the first ionization band of vitamin C is related to the π electrons of CC bond of the ring of molecule although, there is the lone electron pairs of oxygen atoms and π electrons of CO bond in the molecule. PMID:27092998

  11. Gas-phase reactivity of ruthenium carbonyl cluster anions.

    PubMed

    Henderson, Matthew A; Kwok, Samantha; McIndoe, J Scott

    2009-04-01

    Partially-ligated anionic ruthenium carbonyl clusters react with alkenes, arenes, and alkanes in the gas phase; the products undergo extensive C-H activation and lose dihydrogen and carbon monoxide under collision-induced dissociation conditions. Triethylsilane and phenylsilane are also reactive towards the unsaturated clusters, and oxygen was shown to rapidly break down the cluster core by oxidative cleavage of the metal-metal bonds. These qualitative gas-phase reactivity studies were conducted using an easily-installed and inexpensive modification of a commercial electrospray ionization mass spectrometer. Interpretation of the large amounts of data generated in these studies is made relatively straightforward by employing energy-dependent electrospray ionization mass spectrometry (EDESI-MS). PMID:19185511

  12. Gas phase fractionation method using porous ceramic membrane

    DOEpatents

    Peterson, Reid A.; Hill, Jr., Charles G.; Anderson, Marc A.

    1996-01-01

    Flaw-free porous ceramic membranes fabricated from metal sols and coated onto a porous support are advantageously used in gas phase fractionation methods. Mean pore diameters of less than 40 .ANG., preferably 5-20 .ANG. and most preferably about 15 .ANG., are permeable at lower pressures than existing membranes. Condensation of gases in small pores and non-Knudsen membrane transport mechanisms are employed to facilitate and increase membrane permeability and permselectivity.

  13. Development of Monopole Interaction Models for Ionic Compounds. Part I: Estimation of Aqueous Henry’s Law Constants for Ions and Gas Phase pKa Values for Acidic Compounds

    EPA Science Inventory

    The SPARC (SPARC Performs Automated Reasoning in Chemistry) physicochemical mechanistic models for neutral compounds have been extended to estimate Henry’s Law Constant (HLC) for charged species by incorporating ionic electrostatic interaction models. Combinations of absolute aq...

  14. Gas phase decontamination of gaseous diffusion process equipment

    SciTech Connect

    Bundy, R.D.; Munday, E.B.; Simmons, D.W.; Neiswander, D.W.

    1994-03-01

    D&D of the process facilities at the gaseous diffusion plants (GDPs) will be an enormous task. The EBASCO estimate places the cost of D&D of the GDP at the K-25 Site at approximately $7.5 billion. Of this sum, nearly $4 billion is associated with the construction and operation of decontamination facilities and the dismantlement and transport of contaminated process equipment to these facilities. In situ long-term low-temperature (LTLT) gas phase decontamination is being developed and demonstrated at the K-25 site as a technology that has the potential to substantially lower these costs while reducing criticality and safeguards concerns and worker exposure to hazardous and radioactive materials. The objective of gas phase decontamination is to employ a gaseous reagent to fluorinate nonvolatile uranium deposits to form volatile LJF6, which can be recovered by chemical trapping or freezing. The LTLT process permits the decontamination of the inside of gas-tight GDP process equipment at room temperature by substituting a long exposure to subatmospheric C1F for higher reaction rates at higher temperatures. This paper outlines the concept for applying LTLT gas phase decontamination, reports encouraging laboratory experiments, and presents the status of the design of a prototype mobile system. Plans for demonstrating the LTLT process on full-size gaseous diffusion equipment are also outlined briefly.

  15. Group 3 LEA protein model peptides protect enzymes against desiccation stress.

    PubMed

    Furuki, Takao; Sakurai, Minoru

    2016-09-01

    We tested whether model peptides for group 3 late embryogenesis abundant (G3LEA) proteins, which we developed previously, are capable of maintaining the catalytic activities of enzymes dried in their presence. Three different peptides were compared: 1) PvLEA-22, which consists of two tandem repeats of the 11-mer motif found in G3LEA proteins from an African sleeping chironomid; 2) PvLEA-44, which is made of four tandem repeats of the same 11-mer motif; and 3) a peptide whose amino acid composition is the same as that of PvLEA-22, but whose sequence is scrambled. We selected two enzymes, lactate dehydrogenase (LDH) and β-d-galactosidase (BDG), as targets because they have different isoelectric point (pI) values, in the alkaline and acidic range, respectively. While these enzymes were almost inactivated when dried alone, their catalytic activity was preserved at ≥70% of native levels in the presence of any of the above three peptides. This degree of protection is comparable to that conferred by several full-length G3LEA proteins, as reported previously for LDH. Interestingly, the protective activity of the peptides was enhanced slightly when they were mixed with trehalose, especially when the molar content of the peptides was low. On the basis of these results, the G3LEA model peptides show promise as protectants for the dry preservation of enzymes/proteins with a wide range of pI values. PMID:27131872

  16. MALDI imaging mass spectrometry to investigate endogenous peptides in an animal model of Usher's disease.

    PubMed

    Chatterji, Bijon; Dickhut, Clarissa; Mielke, Svenja; Krüger, Jonas; Just, Ingo; Glage, Silke; Meier, Martin; Wedekind, Dirk; Pich, Andreas

    2014-07-01

    Imaging MS (MSI) has emerged as a valuable tool to study the spatial distribution of biomolecules in the brain. Herein, MALDI-MSI was used to determine the distribution of endogenous peptides in a rat model of Usher's disease. This rare disease is considered as a leading cause of deaf-blindness in humans worldwide. Cryosections of brain tissue were analyzed by MALDI-MSI to differentiate between healthy and diseased rats. MSI results were highly reproducible. Tissue-specific peptides were identified by MS/MS using LC-Orbitrap and MALDI-TOF/TOF analyses. These peptides were proposed for histological classification due to their particular spatial distribution in the brain, for example, substantia nigra, corpus callosum, and hippocampus. Several endogenous peptides showed significantly increased ion densities, particularly in the colliculi superiores and in the substantia nigra of diseased rats, including peptides derived from Fsd1, dystrobrevin-β, and ProSAAS. Furthermore, several proteolytic degradation products of the myelin basic protein were identified, of which one peptide is most likely mediated by calpain-2. Our findings contribute to the characterization of this animal model and include possible peptide markers of disease. PMID:24841751

  17. A model-based method for the prediction of the isotopic distribution of peptides.

    PubMed

    Valkenborg, Dirk; Jansen, Ivy; Burzykowski, Tomasz

    2008-05-01

    The process of monoisotopic mass determination, i.e., nomination of the correct peak of an isotopically resolved group of peptide peaks as a monoisotopic peak, requires prior information about the isotopic distribution of the peptide. This points immediately to the difficulty of monoisotopic mass determination, whereas a single mass spectrum does not contain information about the atomic composition of a peptide and therefore the isotopic distribution of the peptide remains unknown. To solve this problem a technique is required, which is able to estimate the isotopic distribution given the information of a single mass spectrum. Senko et al. calculated the average isotopic distribution for any mass peptide via the multinomial expansion (Yergey 1983), using a scaled version of the average amino acid Averagine (Senko et al. 1995). Another method, introduced by Breen et al., approximates the result of the multinomial expansion by a Poisson model (Breen et al. 2000). Although both methods perform well, they have their specific limitations. In this manuscript, we propose an alternative method for the prediction of the isotopic distribution based on a model for consecutive ratios of peaks from the isotopic distribution, similar in spirit to the approach introduced by Gay et al. (1999). The presented method is computationally simple and accurate in predicting the expected isotopic distribution. Further, we extend our method to estimate the isotopic distribution of sulphur-containing peptides. This is important because the naturally occurring isotopes of sulphur have an impact on the isotopic distribution of a peptide. PMID:18325782

  18. A computer model for one-dimensional mass and energy transport in and around chemically reacting particles, including complex gas-phase chemistry, multicomponent molecular diffusion, surface evaporation, and heterogeneous reaction

    NASA Technical Reports Server (NTRS)

    Cho, S. Y.; Yetter, R. A.; Dryer, F. L.

    1992-01-01

    Various chemically reacting flow problems highlighting chemical and physical fundamentals rather than flow geometry are presently investigated by means of a comprehensive mathematical model that incorporates multicomponent molecular diffusion, complex chemistry, and heterogeneous processes, in the interest of obtaining sensitivity-related information. The sensitivity equations were decoupled from those of the model, and then integrated one time-step behind the integration of the model equations, and analytical Jacobian matrices were applied to improve the accuracy of sensitivity coefficients that are calculated together with model solutions.

  19. KL4 Peptide Induces Reversible Collapse Structures on Multiple Length Scales in Model Lung Surfactant

    PubMed Central

    Holten-Andersen, Niels; Michael Henderson, J.; Walther, Frans J.; Waring, Alan J.; Ruchala, Piotr; Notter, Robert H.; Lee, Ka Yee C.

    2011-01-01

    We investigated the effects of KL4, a 21-residue amphipathic peptide approximating the overall ratio of positively charged to hydrophobic amino acids in surfactant protein B (SP-B), on the structure and collapse of dipalmitoylphosphatidylcholine and palmitoyl-oleoyl-phosphatidylglycerol monolayers. As reported in prior work on model lung surfactant phospholipid films containing SP-B and SP-B peptides, our experiments show that KL4 improves surfactant film reversibility during repetitive interfacial cycling in association with the formation of reversible collapse structures on multiple length scales. Emphasis is on exploring a general mechanistic connection between peptide-induced nano- and microscale reversible collapse structures (silos and folds). PMID:22208194

  20. Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes

    NASA Technical Reports Server (NTRS)

    Rodriquez-Gomez, D.; Darve, E.; Pohorille, A.

    2006-01-01

    Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

  1. Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy

    PubMed Central

    Lee, Jieun; Ju, Soomi; Kim, In Tae; Jung, Sun-Hwa; Min, Sun-Joon; Kim, Chulki; Sim, Sang Jun; Kim, Sang Kyung

    2015-01-01

    Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction. PMID:26690165

  2. Probing the Lipid-Protein Interface Using Model Transmembrane Peptides with a Covalently Linked Acyl Chain

    PubMed Central

    Nyholm, Thomas K.M.; van Duyl, Bianca; Rijkers, Dirk T.S.; Liskamp, Rob M.J.; Killian, J. Antoinette

    2011-01-01

    The aim of this study was to gain insight into how interactions between proteins and lipids in membranes are sensed at the protein-lipid interface. As a probe to analyze this interface, we used deuterium-labeled acyl chains that were covalently linked to a model transmembrane peptide. First, a perdeuterated palmitoyl chain was coupled to the Trp-flanked peptide WALP23 (Ac-CGWW(LA)8LWWA-NH2), and the deuterium NMR spectrum was analyzed in di-C18:1-phosphatidylcholine (PC) bilayers. We found that the chain order of this peptide-linked chain is rather similar to that of a noncovalently coupled perdeuterated palmitoyl chain, except that it exhibits a slightly lower order. Similar results were obtained when site-specific deuterium labels were used and when the palmitoyl chain was attached to the more-hydrophobic model peptide WLP23 (Ac-CGWWL17WWA-NH2) or to the Lys-flanked peptide KALP23 (Ac-CGKK(LA)8LKKA-NH2). The experiments showed that the order of both the peptide-linked chains and the noncovalently coupled palmitoyl chains in the phospholipid bilayer increases in the order KALP23 < WALP23 < WLP23. Furthermore, changes in the bulk lipid bilayer thickness caused by varying the lipid composition from di-C14:1-PC to di-C18:1-PC or by including cholesterol were sensed rather similarly by the covalently coupled chain and the noncovalently coupled palmitoyl chains. The results indicate that the properties of lipids adjacent to transmembrane peptides mostly reflect the properties of the surrounding lipid bilayer, and hence that (at least for the single-span model peptides used in this study) annular lipids do not play a highly specific role in protein-lipid interactions. PMID:22004750

  3. Membrane topology of a 14-mer model amphipathic peptide: a solid-state NMR spectroscopy study.

    PubMed

    Ouellet, Marise; Doucet, Jean-Daniel; Voyer, Normand; Auger, Michèle

    2007-06-01

    We have investigated the interaction between a synthetic amphipathic 14-mer peptide and model membranes by solid-state NMR. The 14-mer peptide is composed of leucines and phenylalanines modified by the addition of crown ethers and forms a helical amphipathic structure in solution and bound to lipid membranes. To shed light on its membrane topology, 31P, 2H, 15N solid-state NMR experiments have been performed on the 14-mer peptide in interaction with mechanically oriented bilayers of dilauroylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), and dipalmitoylphosphatidylcholine (DPPC). The 31P, 2H, and 15N NMR results indicate that the 14-mer peptide remains at the surface of the DLPC, DMPC, and DPPC bilayers stacked between glass plates and perturbs the lipid orientation relative to the magnetic field direction. Its membrane topology is similar in DLPC and DMPC bilayers, whereas the peptide seems to be more deeply inserted in DPPC bilayers, as revealed by the greater orientational and motional disorder of the DPPC lipid headgroup and acyl chains. 15N{31P} rotational echo double resonance experiments have also been used to measure the intermolecular dipole-dipole interaction between the 14-mer peptide and the phospholipid headgroup of DMPC multilamellar vesicles, and the results indicate that the 14-mer peptide is in contact with the polar region of the DMPC lipids. On the basis of these studies, the mechanism of membrane perturbation of the 14-mer peptide is associated to the induction of a positive curvature strain induced by the peptide lying on the bilayer surface and seems to be independent of the bilayer hydrophobic thickness. PMID:17487978

  4. Fluorescence Spectroscopy of Gas-phase Polycyclic Aromatic Hydrocarbons

    NASA Technical Reports Server (NTRS)

    Thomas, J. D.; Witt, A. N.

    2006-01-01

    The purpose of this investigation was to produce fluorescence spectra of polycyclic aromatic hydrocarbon (PAH) molecules in the gas-phase for comparison with blue luminescence (BL) emission observed in astrophysical sources Vijh et al. (2004, 2005a,b). The BL occurs roughly from 350 to 450 nm, with a sharp peak near 380 nm. PAHs with three to four rings, e.g. anthracene and pyrene, were found to produce luminescence in the appropriate spectral region, based on existing studies. Relatively few studies of the gas-phase fluorescence of PAHs exist; those that do exist have dealt primarily with the same samples commonly available for purchase such as pyrene and anthracene. In an attempt to understand the chemistry of the nebular environment we also obtained several nitrogen substituted PAHs from our colleagues at NASA Ames. In order to simulate the astrophysical environment we also took spectra by heating the PAHs in a flame. The flame environment counteracts the formation of eximers and permits the spectroscopy of free-flying neutral molecules. Experiments with coal tar demonstrate that fluorescence spectroscopy reveals primarily the presence of the smallest molecules, which are most abundant and which possess the highest fluorescence efficiencies. One gas-phase PAH that seems to fit the BL spectrum most closely is phenanthridine. In view of the results from the spectroscopy of coal tar, a compound containing a mixture of PAHs ranging from small to very large PAH molecules, we can not preclude the presence of larger PAHs in interstellar sources exhibiting BL.

  5. Gas-phase chemiluminescent reactions of ozone with monoterpenes

    NASA Astrophysics Data System (ADS)

    Arora, P. K.; Chatha, J. P. S.; Vohra, K. G.

    1983-08-01

    Chemiluminescent reactions of ozone with monoterpenes such as linallol, geraniol, d-limonene and α-pinene have been studied in the gas phase at low pressures. Methylglyoxal phosphorescence has been observed in the first two reactions. Emissions from HCHO( 1A 2) and glyoxal ( 3A u) are observed in the reaction of ozone with d-limonene and formation of excited glyoxal is found to be first order in ozone. The reaction of ozone with β-pinene gives rise to emission from a α-dicarbonyl compound and this is found to be first order in ozone. The mechanisms for the formation of excited species are proposed.

  6. The solar system/interstellar medium connection - Gas phase abundances

    NASA Technical Reports Server (NTRS)

    Lutz, Barry L.

    1987-01-01

    Gas-phase abundances in the outer solar system are presented as diagnostics of the interstellar medium at the time of the solar system formation, some 4.55 billion years ago. Possible influences of the thermal and chemical histories of the primitive solar nebula and of the processes which led to the formation and evolution of the outer planets and comets on the elemental and molecular composition of the primordial matter are outlined. The major components of the atmospheres of the outer planets and of the comae of comets are identified, and the cosmogonical and cosmological implications are discussed.

  7. Neurotransmitters in the Gas Phase: La-Mb Studies

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

    LA-MB-FTMW spectroscopy combines laser ablation with Fourier transform microwave spectroscopy in supersonic jets overcoming the problems of thermal decomposition associated with conventional heating methods. We present here the results on LA-MB-FTMW studies of some neurotransmitters. Six conformers of dopamine, four of adrenaline, five of noradrenaline and three conformers of serotonin have been characterized in the gas phase. The rotational and nuclear quadrupole coupling constants extracted from the analysis of the rotational spectrum are directly compared with those predicted by ab initio methods to achieve the conclusive identification of different conformers and the experimental characterization of the intramolecular forces at play which control conformational preferences.

  8. Gas Phase Chemical Detection with an Integrated Chemical Analysis System

    SciTech Connect

    Baca, Albert G.; Casalnuovo, Stephen A.; Frye-Mason, Gregory C.; Heller, Edwin J.; Hietala, Susan L.; Hietala, Vincent M.; Kottenstette, Richard J.; Lewis, Patrick R.; Manginell, Ronald P.; Matzke, Carloyn M.; Reno, John L.; Sasaki, Darryl Y.; Schubert, W. Kent

    1999-07-08

    Microfabrication technology has been applied to the development of a miniature, multi-channel gas phase chemical laboratory that provides fast response, small size, and enhanced versatility and chemical discrimination. Each analysis channel includes a sample concentrator followed by a gas chromatographic separator and a chemically selective surface acoustic wave detector array to achieve high sensitivity and selectivity. The performance of the components, individually and collectively, is described. The design and performance of novel micromachined acoustic wave devices, with the potential for improved chemical sensitivity, are also described.

  9. Development of small molecule non-peptide formyl peptide receptor (FPR) ligands and molecular modeling of their recognition.

    PubMed

    Schepetkin, I A; Khlebnikov, A I; Giovannoni, M P; Kirpotina, L N; Cilibrizzi, A; Quinn, M T

    2014-01-01

    Formyl peptide receptors (FPRs) are G protein-coupled receptors (GPCRs) expressed on a variety of cell types. These receptors play an important role in the regulation of inflammatory reactions and sensing cellular damage. They have also been implicated in the pathogenesis of various diseases, including neurodegenerative diseases, cataract formation, and atherogenesis. Thus, FPR ligands, both agonists and antagonists, may represent novel therapeutics for modulating host defense and innate immunity. A variety of molecules have been identified as receptor subtype-selective and mixed FPR agonists with potential therapeutic value during last decade. This review describes our efforts along with recent advances in the identification, optimization, biological evaluation, and structure-activity relationship (SAR) analysis of small molecule non-peptide FPR agonists and antagonists, including chiral molecules. Questions regarding the interaction at the molecular level of benzimidazoles, pyrazolones, pyridazin-3(2H)-ones, N-phenylureas and other derivatives with FPR1 and FPR2 are discussed. Application of computational models for virtual screening and design of FPR ligands is also considered. PMID:24350845

  10. Role of the transmembrane domain in SNARE protein mediated membrane fusion: peptide nucleic acid/peptide model systems.

    PubMed

    Wehland, Jan-Dirk; Lygina, Antonina S; Kumar, Pawan; Guha, Samit; Hubrich, Barbara E; Jahn, Reinhard; Diederichsen, Ulf

    2016-08-16

    Fusion of synaptic vesicles with the presynaptic plasma membrane is mediated by Soluble NSF (N-ethylmaleimide-sensitive factor) Attachment Protein Receptor proteins also known as SNAREs. The backbone of this essential process is the assembly of SNAREs from opposite membranes into tight four helix bundles forcing membranes in close proximity. With model systems resembling SNAREs with reduced complexity we aim to understand how these proteins work at the molecular level. Here, peptide nucleic acids (PNAs) are used as excellent candidates for mimicking the SNARE recognition motif by forming well-characterized duplex structures. Hybridization between complementary PNA strands anchored in liposomes through native transmembrane domains (TMDs) induces the merger of the outer leaflets of the participating vesicles but not of the inner leaflets. A series of PNA/peptide hybrids differing in the length of TMDs and charges at the C-terminal end is presented. Interestingly, mixing of both outer and inner leaflets is seen for TMDs containing an amide in place of the natural carboxylic acid at the C-terminal end. Charged side chains at the C-terminal end of the TMDs are shown to have a negative impact on the mixing of liposomes. The length of the TMDs is vital for fusion as with the use of shortened TMDs, fusion was completely prevented. PMID:27345759

  11. Prediction of (L)-methionine VCD spectra in the gas phase and water solution.

    PubMed

    Rode, Joanna E; Dobrowolski, Jan Cz; Sadlej, Joanna

    2013-11-21

    In this paper we provide a computational study of the l-methionine conformational landscape and VCD spectra in the gas phase and a water environment simulated by implicit PCM and the hybrid model, i.e., a combination of explicit "microsolvation" and implicit models. In the gas phase, two groups of conformers differing in H-bonding, i.e., OH···NH2 and NH···O═C, could be distinguished based solely on the IR ν(OH) and ν(NH) stretching vibrations range. On the other hand, VCD better reflected chain differences. The most stable OH···NH2 conformer was predicted to be easily detected, and the presence of two out of four NH···O═C conformers could be confirmed. Three zwitterionic methionine conformers were shown to dominate in water. Their VCD spectra, simulated within the hybrid model at the B3LYP-IEF-PCM/aug-cc-pVDZ level of theory, indicated that they could be recognized in the mixture. Use of the hybrid model is crucial for good reproduction of the hydrogen bonding pattern in the VCD spectra of methionine in water solution. However, the 1300-800 cm(-1) region of the skeleton vibrations of methionine appeared to be relatively insensitive to the model of the solvent. PMID:24195697

  12. Critical temperature for the nuclear liquid-gas phase transition (from multifragmentation and fission)

    SciTech Connect

    Karnaukhov, V. A.; Oeschler, H.; Budzanowski, A.; Avdeyev, S. P.; Botvina, A. S.; Cherepanov, E. A.; Karcz, W.; Kirakosyan, V. V.; Rukoyatkin, P. A.; Skwirczynska, I.; Norbeck, E.

    2008-12-15

    Critical temperature T{sub c} for the nuclear liquid-gas phase transition is estimated from both the multifragmentation and fission data. In the first case, the critical temperature is obtained by analysis of the intermediate-mass-fragment yields in p(8.1 GeV) + Au collisions within the statistical model of multifragmentation. In the second case, the experimental fission probability for excited {sup 188}Os is compared with the calculated one with T{sub c} as a free parameter. It is concluded for both cases that the critical temperature is higher than 15 MeV.

  13. Tuning a High Transmission Ion Guide to Prevent Gas-Phase Proton Exchange During H/D Exchange MS Analysis.

    PubMed

    Guttman, Miklos; Wales, Thomas E; Whittington, Dale; Engen, John R; Brown, Jeffery M; Lee, Kelly K

    2016-04-01

    Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for protein structural analysis has been adopted for many purposes, including biopharmaceutical development. One of the benefits of examining amide proton exchange by mass spectrometry is that it can readily resolve different exchange regimes, as evidenced by either binomial or bimodal isotope patterns. By careful analysis of the isotope pattern during exchange, more insight can be obtained on protein behavior in solution. However, one must be sure that any observed bimodal isotope patterns are not artifacts of analysis and are reflective of the true behavior in solution. Sample carryover and certain stationary phases are known as potential sources of bimodal artifacts. Here, we describe an additional undocumented source of deuterium loss resulting in artificial bimodal patterns for certain highly charged peptides. We demonstrate that this phenomenon is predominantly due to gas-phase proton exchange between peptides and bulk solvent within the initial stages of high-transmission conjoined ion guides. Minor adjustments of the ion guide settings, as reported here, eliminate the phenomenon without sacrificing signal intensity. Such gas-phase deuterium loss should be appreciated for all HDX-MS studies using such ion optics, even for routine studies not focused on interpreting bimodal spectra. Graphical Abstract ᅟ. PMID:26810432

  14. Tuning a High Transmission Ion Guide to Prevent Gas-Phase Proton Exchange During H/D Exchange MS Analysis

    NASA Astrophysics Data System (ADS)

    Guttman, Miklos; Wales, Thomas E.; Whittington, Dale; Engen, John R.; Brown, Jeffery M.; Lee, Kelly K.

    2016-04-01

    Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for protein structural analysis has been adopted for many purposes, including biopharmaceutical development. One of the benefits of examining amide proton exchange by mass spectrometry is that it can readily resolve different exchange regimes, as evidenced by either binomial or bimodal isotope patterns. By careful analysis of the isotope pattern during exchange, more insight can be obtained on protein behavior in solution. However, one must be sure that any observed bimodal isotope patterns are not artifacts of analysis and are reflective of the true behavior in solution. Sample carryover and certain stationary phases are known as potential sources of bimodal artifacts. Here, we describe an additional undocumented source of deuterium loss resulting in artificial bimodal patterns for certain highly charged peptides. We demonstrate that this phenomenon is predominantly due to gas-phase proton exchange between peptides and bulk solvent within the initial stages of high-transmission conjoined ion guides. Minor adjustments of the ion guide settings, as reported here, eliminate the phenomenon without sacrificing signal intensity. Such gas-phase deuterium loss should be appreciated for all HDX-MS studies using such ion optics, even for routine studies not focused on interpreting bimodal spectra.

  15. Reactive uptake of ozone by proxies for organic aerosols: Surface-bound and gas-phase products

    NASA Astrophysics Data System (ADS)

    Thomas, Elan R.; Frost, Gregory J.; Rudich, Yinon

    2001-02-01

    Gas-phase and surface-bound products were determined for the reaction of ozone with self assembled monolayers of alkanes and terminal alkenes serving as proxies for atmospheric organic aerosols. The organic surfaces were characterized using infrared (IR) spectroscopy (direct absorption and attenuated total reflection) as well as contact angle measurements with water before and after the reaction with ozone. The contact angle of the organic surfaces was reduced by ˜20° owing to the reaction. Following the reaction, IR absorption due to the presence of carbonyls and carboxylic acids was observed on the surface. Gas-phase products were determined using infrared spectroscopy immediately above the reaction surface. Under dry conditions, gas-phase formaldehyde yields of 0.5±0.1 for organic monolayers of allyltrichlorosilane (C3=) and octenyltrichlorosilane (C8=) terminal alkenes were observed, in good agreement with the yields observed for gas phase ozonolysis of terminal alkenes. Surfaces of n-octane (C8) as well as processed alkene surfaces were nonreactive toward ozone. The reaction mechanism of ozone with the surface alkenes is discussed. Finally, the possible implications for the chemistry of organic aerosols are discussed and studied using a box model and realistic atmospheric scenarios.

  16. Preconceptual design of the gas-phase decontamination demonstration cart

    SciTech Connect

    Munday, E.B.

    1993-12-01

    Removal of uranium deposits from the interior surfaces of gaseous diffusion equipment will be a major portion of the overall multibillion dollar effort to decontaminate and decommission the gaseous diffusion plants. Long-term low-temperature (LTLT) gas-phase decontamination is being developed at the K-25 Site as an in situ decontamination process that is expected to significantly lower the decontamination costs, reduce worker exposure to radioactive materials, and reduce safeguard concerns. This report documents the preconceptual design of the process equipment that is necessary to conduct a full-scale demonstration of the LTLT method in accordance with the process steps listed above. The process equipment and method proposed in this report are not intended to represent a full-scale production campaign design and operation, since the gas evacuation, gas charging, and off-gas handling systems that would be cost effective in a production campaign are not cost effective for a first-time demonstration. However, the design presented here is expected to be applicable to special decontamination projects beyond the demonstration, which could include the Deposit Recovery Program. The equipment will therefore be sized to a 200 ft size 1 converter (plus a substantial conservative design margin), which is the largest item of interest for gas phase decontamination in the Deposit Recovery Program. The decontamination equipment will allow recovery of the UF{sub 6}, which is generated from the reaction of ClF{sub 3} with the uranium deposits, by use of NaF traps.

  17. Gas-phase reactions of cyclopropenylidene with protonated alkyl amines.

    PubMed

    Lin, Ziqing; Tan, Lei; Yang, Yang; Dai, Mingji; Tureček, František; Ouyang, Zheng; Xia, Yu

    2016-04-21

    Vinylidene carbenes (C3H2) are of high interest to interstellar, combustion, and organic chemistry. Due to their high instability, the direct experimental investigation of their chemical reactivity has rarely been achieved. Herein, we report a first study on the reactions of cyclopropenylidene (c-C3H2) with protonated alkyl amines in the gas phase using a home-built ion trap mass spectrometer. The high gas-phase basicity (GB) of ((1)A1) c-C3H2 (calculated as 920 kJ mol(-1)) facilitates the formation of a proton-bound dimer with protonated amines as the first step in the reaction. The dimer can stay as it is or rearrange to a covalent product. The formation of the covalent complex is highly exothermic and its yield is affected by the GB of alkyl amines. The highest yield (82%) was achieved when the GB of the amine was slightly lower but comparable to that of c-C3H2. Our results demonstrate a new reaction pathway of c-C3H2, which has long been considered as a "dead end" in interstellar carbon chemistry. PMID:26978226

  18. Gas phase oxidation downstream of a catalytic combustor

    NASA Technical Reports Server (NTRS)

    Tien, J. S.; Anderson, D. N.

    1979-01-01

    Effect of the length available for gas-phase reactions downstream of the catalytic reactor on the emission of CO and unburned hydrocarbons was investigated. A premixed, prevaporized propane/air feed to a 12/cm/diameter catalytic/reactor test section was used. The catalytic reactor was made of four 2.5 cm long monolithic catalyst elements. Four water cooled gas sampling probes were located at positions between 0 and 22 cm downstream of the catalytic reactor. Measurements of unburned hydrocarbon, CO, and CO2 were made. Tests were performed with an inlet air temperature of 800 K, a reference velocity of 10 m/s, pressures of 3 and 600,000 Pa, and fuel air equivalence ratios of 0.14 to 0.24. For very lean mixtures, hydrocarbon emissions were high and CO continued to be formed downstream of the catalytic reactor. At the highest equivalence ratios tested, hydrocarbon levels were much lower and CO was oxidized to CO2 in the gas phase downstream. To achieve acceptable emissions, a downstream region several times longer than the catalytic reactor could be required.

  19. Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids

    NASA Astrophysics Data System (ADS)

    Bonacci, Gustavo; Asciutto, Eliana K.; Woodcock, Steven R.; Salvatore, Sonia R.; Freeman, Bruce A.; Schopfer, Francisco J.

    2011-09-01

    Nitro-fatty acids are electrophilic signaling mediators formed in increased amounts during inflammation by nitric oxide and nitrite-dependent redox reactions. A more rigorous characterization of endogenously-generated species requires additional understanding of their gas-phase induced fragmentation. Thus, collision induced dissociation (CID) of nitroalkane and nitroalkene groups in fatty acids were studied in the negative ion mode to provide mass spectrometric tools for their structural characterization. Fragmentation of nitroalkanes occurred mainly through loss of the NO{2/-} anion or neutral loss of HNO2. The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional γ or δ unsaturation occurred through a multiple step cyclization reaction process, leading to 5 and 6 member ring heterocyclic products and carbon chain fragmentation. Cyclization products were not obtained during nitroalkane fragmentation, highlighting the role of double bond π electrons during NO{2/-} rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of 13C and 15N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples.

  20. Gas phase contributions to topochemical hydride reduction reactions

    SciTech Connect

    Kobayashi, Yoji; Li, Zhaofei; Hirai, Kei; Tassel, Cédric; Loyer, François; Ichikawa, Noriya; Abe, Naoyuki; Yamamoto, Takafumi; Shimakawa, Yuichi; and others

    2013-11-15

    Alkali and alkali earth hydrides have been used as solid state reductants recently to yield many interesting new oxygen-deficient transition metal oxides. These reactions have tacitly been assumed to be a solid phase reaction between the reductant and parent oxide. We have conducted a number of experiments with physical separation between the reductant and oxides, and find that in some cases reduction proceeds even when the reagents are physically separated, implying reactions with in-situ generated H{sub 2} and, to a lesser extent, getter mechanisms. Our findings change our understanding of these topochemical reactions, and should enhance the synthesis of additional new oxides and nanostructures. - Graphical abstract: Topochemical reductions with hydrides: Solid state or gas phase reaction? Display Omitted - Highlights: • SrFeO{sub 2} and LaNiO{sub 2} were prepared by topochemical reduction of oxides. • Separating the reducing agent (CaH{sub 2}, Mg metal) from the oxide still results in reduction. • Such topochemical reactions can occur in the gas phase.

  1. Gas-phase reactivity of novel Ziegler-Natta catalysts

    SciTech Connect

    Alameddin, N.G.; Eyler, J.R.; Richardson, D.E.

    1994-12-31

    The discovery of soluble group 4 metallocene-based catalysts for the Ziegler-Natta polymerization of olefins has generated considerable interest in the field. In particular, the versatility of the Cp (cyclopentadienyl) ligand has made practical the development of a host of novel catalysts which can produce extremely regiospecific and stereospecific polymers. With further improvements in activity and stability, these catalysts are expected to make a major impact on the polymerization industry. Presently, catalyst design is driven by using the steric and electronic properties of the ligands to guide the monomer addition. However, since these ligands have considerable steric bulk, the choice of solvent will significantly affect their catalytic properties. Therefore, an understanding of the intrinsic reactivity of these catalysts independent of a solvent is one of the first steps to building a better catalyst. The work in progress is a study of the reactivity of zircononene-based catalysts in the gas phase. The authors are in the process of studying the rates of reaction of a series of these compounds with H{sub 2} as well as with a number of olefins. In the gas phase, the intrinsic reactivity of these catalysts is revealed and their chemistry can be studied in detail.

  2. Gas-Phase Acidities of Phosphorylated Amino Acids.

    PubMed

    Stover, Michele L; Plummer, Chelsea E; Miller, Sean R; Cassady, Carolyn J; Dixon, David A

    2015-11-19

    Gas-phase acidities and heats of formation have been predicted at the G3(MP2)/SCRF-COSMO level of theory for 10 phosphorylated amino acids and their corresponding amides, including phospho-serine (pSer), -threonine (pThr), and -tyrosine (pTyr), providing the first reliable set of these values. The gas-phase acidities (GAs) of the three named phosphorylated amino acids and their amides have been determined using proton transfer reactions in a Fourier transform ion cyclotron mass spectrometer. Excellent agreement was found between the experimental and predicted GAs. The phosphate group is the deprotonation site for pSer and pThr and deprotonation from the carboxylic acid generated the lowest energy anion for pTyr. The infrared spectra were calculated for six low energy anions of pSer, pThr, and pTyr. For deprotonated pSer and pThr, good agreement is found between the experimental IRMPD spectra and the calculated spectra for our lowest energy anion structure. For pTyr, the IR spectra for a higher energy phosphate deprotonated structure is in good agreement with experiment. Additional experiments tested electrospray ionization (ESI) conditions for pTyr and determined that variations in solvent, temperature, and voltage can result in a different experimental GA value, indicating that ESI conditions affect the conformation of the pTyr anion. PMID:26492552

  3. Modeling the structure of bound peptide ligands to major histocompatibility complex

    PubMed Central

    Tong, Joo Chuan; Tan, Tin Wee; Ranganathan, Shoba

    2004-01-01

    In this article, we present a new technique for the rapid and precise docking of peptides to MHC class I and class II receptors. Our docking procedure consists of three steps: (1) peptide residues near the ends of the binding groove are docked by using an efficient pseudo-Brownian rigid body docking procedure followed by (2) loop closure of the intervening backbone structure by satisfaction of spatial constraints, and subsequently, (3) the refinement of the entire backbone and ligand interacting side chains and receptor side chains experiencing atomic clash at the MHC receptor–peptide interface. The method was tested by remodeling of 40 nonredundant complexes of at least 3.00 Å resolution for which three-dimensional structural information is available and independently for docking peptides derived from 15 nonredundant complexes into a single template structure. In the first test, 33 out of 40 MHC class I and class II peptides and in the second test, 11 out of 15 MHC–peptide complexes were modeled with a Cα RMSD < 1.00 Å. PMID:15322290

  4. Interactions of calmodulin with death-associated protein kinase peptides: experimental and modeling studies.

    PubMed

    Kuczera, Krzysztof; Kursula, Petri

    2012-01-01

    We have studied the interactions between calmodulin (CaM) and three target peptides from the death-associated protein kinase (DAPK) protein family using both experimental and modeling methods, aimed at determining the details of the underlying biological regulation mechanisms. Experimentally, calorimetric binding free energies were determined for the complexes of CaM with peptides representing the DAPK2 wild-type and S308D mutant, as well as DAPK1. The observed affinity of CaM was very similar for all three studied peptides. The DAPK2 and DAPK1 peptides differ significantly in sequence and total charge, while the DAPK2 S308D mutant is designed to model the effects of DAPK2 Ser308 phosphorylation. The crystal structure of the CaM-DAPK2 S308D mutant peptide is also reported. The structures of CaM-DAPK peptide complexes present a mode of CaM-kinase interaction, in which bulky hydrophobic residues at positions 10 and 14 are both bound to the same hydrophobic cleft. To explain the microscopic effects underlying these interactions, we performed free energy calculations based on the approximate MM-PBSA approach. For these highly charged systems, standard MM-PBSA calculations did not yield satisfactory results. We proposed a rational modification of the approach which led to reasonable predictions of binding free energies. All three complexes are strongly stabilized by two effects: electrostatic interactions and buried surface area. The strong favorable interactions are to a large part compensated by unfavorable entropic terms, in which vibrational entropy is the largest contributor. The electrostatic component of the binding free energy followed the trend of the overall peptide charge, with strongest interactions for DAPK1 and weakest for the DAPK2 mutant. The electrostatics was dominated by interactions of the positively charged residues of the peptide with the negatively charged residues of CaM. The nonpolar binding free energy was comparable for all three peptides, the

  5. Position for determining gas phase volatile organic compound concentrations in transuranic waste containers

    SciTech Connect

    Connolly, M.J.; Liekhus, K.J.; Djordjevic, S.M.; Loehr, C.A. Spangler, L.R.

    1995-12-01

    In the conditional no-migration determination (NMD) for the test phase of the Waste isolation Pilot Plant (WIPP), the US Environmental Protection Agency (EPA) imposed certain conditions on the US Department of Energy (DOE) regarding gas phase volatile organic compound (VOC) concentrations in the void space of transuranic (TRU) waste containers. The EPA required the DOE to ensure that each waste container has no layer of confinement that contains flammable mixtures of gases or mixtures of gases that could become flammable when mixed with air. The EPA also required that sampling of the headspace of waste containers outside inner layers of confinement be representative of the entire void space of the container. The EPA stated that all layers of confinement in a container would have to be sampled until DOE can demonstrate to the EPA that sampling of all layers is unnecessary. A test program was conducted to demonstrate that the gas phase VOC concentration in the void space of each layer of confinement in vented drums can be estimated from measured drum headspace using a theoretical transport model and that sampling of each layer of confinement is unnecessary. This report summarizes the studies performed in the INEL test program and extends them for the purpose of developing a methodology for determining gas phase VOC concentrations in both vented and unvented TRU waste containers. The methodology specifies conditions under which waste drum headspace gases can be said to be representative of drum gases as a whole and describes a method for predicting drum concentrations in situations where the headspace concentration is not representative.

  6. 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.

  7. Position for determining gas-phase volatile organic compound concentrations in transuranic waste containers. Revision 2

    SciTech Connect

    Connolly, M.J.; Liekhus, K.J.; Djordjevic, S.M.; Loehr, C.A.; Spangler, L.R.

    1998-06-01

    In the conditional no-migration determination (NMD) for the test phase of the Waste Isolation Pilot Plant (WIPP), the US Environmental Protection Agency (EPA) imposed certain conditions on the US Department of Energy (DOE) regarding gas phase volatile organic compound (VOC) concentrations in the void space of transuranic (TRU) waste containers. Specifically, the EPA required the DOE to ensure that each waste container has no layer of confinement that contains flammable mixtures of gases or mixtures of gases that could become flammable when mixed with air. The EPA also required that sampling of the headspace of waste containers outside inner layers of confinement be representative of the entire void space of the container. The EPA stated that all layers of confinement in a container would have to be sampled until DOE can demonstrate to the EPA that sampling of all layers is either unnecessary or can be safely reduced. A test program was conducted at the Idaho National Engineering and Environmental Laboratory (INEEL) to demonstrate that the gas phase VOC concentration in the void space of each layer of confinement in vented drums can be estimated from measured drum headspace using a theoretical transport model and that sampling of each layer of confinement is unnecessary. This report summarizes the studies performed in the INEEL test program and extends them for the purpose of developing a methodology for determining gas phase VOC concentrations in both vented and unvented TRU waste containers. The methodology specifies conditions under which waste drum headspace gases can be said to be representative of drum gases as a whole and describes a method for predicting drum concentrations in situations where the headspace concentration is not representative. The methodology addresses the approach for determining the drum VOC gas content for two purposes: operational period drum handling and operational period no-migration calculations.

  8. Position for determining gas phase volatile organic compound concentrations in transuranic waste containers. Revision 1

    SciTech Connect

    Connolly, M.J.; Liekhus, K.J.; Djordjevic, S.M.; Loehr, C.A.; Spangler, L.R.

    1995-08-01

    In the conditional no-migration determination (NMD) for the test phase of the Waste Isolation Pilot Plant (WIPP), the US Environmental Protection Agency (EPA) imposed certain conditions on the US Department of Energy (DOE) regarding gas phase volatile organic compound (VOC) concentrations in the void space of transuranic (TRU) waste containers. Specifically, the EPA required the DOE to ensure that each waste container has no layer of confinement that contains flammable mixtures of gases or mixtures of gases that could become flammable when mixed with air. The EPA also required that sampling of the headspace of waste containers outside inner layers of confinement be representative of the entire void space of the container. The EPA stated that all layers of confinement in a container would have to be sampled until DOE can demonstrate to the EPA that sampling of all layers is either unnecessary or can be safely reduced. A test program was conducted at the Idaho National Engineering Laboratory (INEL) to demonstrate that the gas phase VOC concentration in the void space of each layer of confinement in vented drums can be estimated from measured drum headspace using a theoretical transport model and that sampling of each layer of confinement is unnecessary. This report summarizes the studies performed in the INEL test program and extends them for the purpose of developing a methodology for determining gas phase VOC concentrations in both vented and unvented TRU waste containers. The methodology specifies conditions under which waste drum headspace gases can be said to be representative of drum gases as a whole and describes a method for predicting drum concentrations in situations where the headspace concentration is not representative. The methodology addresses the approach for determining the drum VOC gas content for two purposes: operational period drum handling and operational period no-migration calculations.

  9. Valorization of cruor slaughterhouse by-product by enzymatic hydrolysis for the production of antibacterial peptides: focus on α 1-32 family peptides mechanism and kinetics modeling.

    PubMed

    Hedhili, K; Dimitrov, K; Vauchel, P; Sila, A; Chataigné, G; Dhulster, P; Nedjar, N

    2015-10-01

    Bovine hemoglobin is the major component of the cruor (slaughterhouse by-product) and can be considered as an important source of active peptides that could be obtained by pepsic hydrolysis. The kinetics of appearance and disappearance of several antibacterial peptides from α 1-32 family during hydrolysis of synthesized α 1-32 peptide, of purified bovine hemoglobin and of cruor was studied, and reaction scheme for the hydrolysis of α 1-32 family peptides from these three sources was determined. On this basis, a mathematical model was proposed to predict the concentration of each peptide of interest of this family depending on hydrolysis time, and also on temperature (in the range 15-37 °C), pH (in the range 3.5-5.5) and enzyme to substrate ratio (in the range 1/50-1/200 for the synthesized peptide and 1/5-1/20 for purified bovine hemoglobin and cruor). Apparent rate constants of reactions were determined by applying the model on a set of experimental data and it was shown that they depended on the temperature according to Arrhenius's law, that their dependence on the pH was linear, and that enzyme to substrate ratio influence was limited (in the studied range). PMID:26099509

  10. Gas Phase Chromatography of some Group 4, 5, and 6 Halides

    SciTech Connect

    Sylwester, Eric Robert

    1998-10-01

    Gas phase chromatography using The Heavy Element Volatility Instrument (HEVI) and the On Line Gas Apparatus (OLGA III) was used to determine volatilities of ZrBr{sub 4}, HfBr{sub 4}, RfBr{sub 4}, NbBr{sub 5}, TaOBr{sub 3}, HaCl{sub 5}, WBr{sub 6}, FrBr, and BiBr{sub 3}. Short-lived isotopes of Zr, Hf, Rf, Nb, Ta, Ha, W, and Bi were produced via compound nucleus reactions at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory and transported to the experimental apparatus using a He gas transport system. The isotopes were halogenated, separated from the other reaction products, and their volatilities determined by isothermal gas phase chromatography. Adsorption Enthalpy ({Delta}H{sub a}) values for these compounds were calculated using a Monte Carlo simulation program modeling the gas phase chromatography column. All bromides showed lower volatility than molecules of similar molecular structures formed as chlorides, but followed similar trends by central element. Tantalum was observed to form the oxybromide, analogous to the formation of the oxychloride under the same conditions. For the group 4 elements, the following order in volatility and {Delta}H{sub a} was observed: RfBr{sub 4} > ZrBr{sub 4} > HfBr{sub 4}. The {Delta}H{sub a} values determined for the group 4, 5, and 6 halides are in general agreement with other experimental data and theoretical predictions. Preliminary experiments were performed on Me-bromides. A new measurement of the half-life of {sup 261}Rf was performed. {sup 261}Rf was produced via the {sup 248}Cm({sup 18}O, 5n) reaction and observed with a half-life of 74{sub -6}{sup +7} seconds, in excellent agreement with the previous measurement of 78{sub -6}{sup +11} seconds. We recommend a new half-life of 75{+-}7 seconds for {sup 261}Rf based on these two measurements. Preliminary studies in transforming HEVI from an isothermal (constant temperature) gas phase chromatography instrument to a thermochromatographic (variable temperature