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Sample records for model gas-phase peptide

  1. Spectroscopic Investigation of H Atom Transfer in a Gas-phase Dissociation Reaction: McLafferty Rearrangement of Model Gas-phase Peptide Ions

    SciTech Connect

    Michael J. Van Stipdonk; Dale R. Kersetter; Christopher M. Leavitt; Gary S. Groenewold; Jeffrey Steill; Jos Oomens

    2008-07-01

    Wavelength-selective infrared multiple-photon photodissociation (WS-IRMPD) was used to study isotopically-labeled ions generated by McLafferty rearrangement of nicotinyl-glycine-tert-butyl ester and betaine-glycine-tert-butyl ester. The tert-butyl esters were incubated in a mixture of D2O and CH3OD to induce solution-phase hydrogen-deuterium exchange and then converted to gas-phase ions using electrospray ionization. McLafferty rearrangement was used to generate the free-acid forms of the respective model peptides through transfer of an H atom and elimination of butene. The specific aim was to use vibrational spectra generated by WS-IRMPD technique to determine whether the H atom remains at the acid group, or migrates to one or more of the other exchangeable sites. Comparison of the IRMPD results in the region from 1200-1900 cm-1 to theoretical spectra for different isotopically-labeled isomers clearly shows that the H atom is situated at the C-terminal acid group and migration to amide positions is negligible on the time scale of the experiment. The results of this study suggest that use of the McLafferty rearrangement for peptide esters could be an effective approach for generation of H-atom isotope tracers, in-situ, for subsequent investigation of intra-molecular proton migration during peptide fragmentation studies.

  2. Amide-I and -II vibrations of the cyclic beta-sheet model peptide gramicidin S in the gas phase.

    PubMed

    Kupser, Peter; Pagel, Kevin; Oomens, Jos; Polfer, Nick; Koksch, Beate; Meijer, Gerard; von Helden, Gert

    2010-02-17

    In the condensed phase, the peptide gramicidin S is often considered as a model system for a beta-sheet structure. Here, we investigate gramicidin S free of any influences of the environment by measuring the mid-IR spectra of doubly protonated (deuterated) gramicidin S in the gas phase. In the amide I (i.e., C=O stretch) region, the spectra show a broad split peak between 1580 and 1720 cm(-1). To deduce structural information, the conformational space has been searched using molecular dynamics methods and several structural candidates have been further investigated at the density functional level. The calculations show the importance of the interactions of the charged side-chains with the backbone, which is responsible for the lower frequency part of the amide I peak. When this interaction is inhibited via complexation with two 18-crown-6 molecules, the amide I peak narrows and shows two maxima at 1653 and 1680 cm(-1). A comparison to calculations shows that for this complexed ion, four C=O groups are in an antiparallel beta-sheet arrangement. Surprisingly, an analysis of the calculated spectra shows that these beta-sheet C=O groups give rise to the vibrations near 1680 cm(-1). This is in sharp contrast to expectations based on values for the condensed phase, where resonances of beta-sheet sections are thought to occur near 1630 cm(-1). The difference between those values might be caused by interactions with the environment, as the condensed phase value is mostly deduced for beta-sheet sections that are embedded in larger proteins, that interact strongly with solvent or that are part of partially aggregated species.

  3. 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.

  4. 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

  5. Gas Phase Hydration of Model Peptide Chains: Far/mid Infrared Signature of Water Intermolecular Motions in the Monohydrate

    NASA Astrophysics Data System (ADS)

    Cirtog, M.; Loquais, Y.; Brenner, V.; Tardivel, B.; Mons, M.; Gloaguen, E.; Rijs, A. M.

    2012-06-01

    The far/mid infrared region (100 - 800 cm-1) of two hydrated conformations of the model peptide chain N-acetyl-phenylalanine-amide (Ac-Phe-NH_2) have been investigated in a supersonic jet expansion by conformational selective double-resonance IR/UV spectroscopy, using the free electron laser FELIX for the far IR tunability. The two folded conformations (identified in a previous work share the same H-bonding network, with the water molecule bridging the peptide ends as a donor and acceptor but differ by the orientation of the free hydrogen. By comparison with the isolated peptide, hydration gives rise to new spectroscopic features locate in three different spectral regions namely around 160, 400 and 600 cm-1. The analysis of a series of quantum chemical harmonic frequency calculations using various approaches (DFT and DFT-D) suggests that this spectral region constitutes a real challenge to the theory. As expected, the low frequency modes present a strong anharmonicity and sensitivity to the position of the water molecule. It has nevertheless allowed us to assign the new experimental signatures to a direct excitation of normal modes widely involving intermolecular libration and wagging motions of the water molecule in the complex, and revealed an extended coupling with the peptide backbone deformation motions. H.S. Biswal, Y. Loquais, B. Tardivel, E. Gloaguen and M. Mons, J. Am. Chem. Soc. 133, 3931 (2011). S. Jaeqx, M. Schmit, W.J. van der Zande, and A.M. Rijs, manuscript in preparation

  6. 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

  7. 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.

  8. Gas-Phase Dissociation Pathways of Multiply Charged Peptide Clusters

    PubMed Central

    Jurchen, John C.; Garcia, David E.; Williams, Evan R.

    2005-01-01

    Numerous studies of cluster formation and dissociation have been conducted to determine properties of matter in the transition from the condensed phase to the gas phase using materials as diverse as atomic nuclei, noble gasses, metal clusters, and amino acids. Here, electrospray ionization is used to extend the study of cluster dissociation to peptides including leucine enkephalin with 7–19 monomer units and 2–5 protons, and somatostatin with 5 monomer units and 4 protons under conditions where its intramolecular disulfide bond is either oxidized or reduced. Evaporation of neutral monomers and charge separation by cluster fission are the competing dissociation pathways of both peptides. The dominant fission product for all leucine enkephalin clusters studied is a proton-bound dimer, presumably due to the high gas-phase stability of this species. The branching ratio of the fission and evaporation processes for leucine enkephalin clusters appears to be determined by the value of z2/n for the cluster where z is the charge and n the number of monomer units in the cluster. Clusters with low and high values of z2/n dissociate primarily by evaporation and cluster fission respectively, with a sharp transition between dissociation primarily by evaporation and primarily by fission measured at a z2/n value of ~0.5. The dependence of the dissociation pathway of a cluster on z2/n is similar to the dissociation of atomic nuclei and multiply charged metal clusters indicating that leucine enkephalin peptide clusters exist in a state that is more disordered, and possibly fluid, rather than highly structured in the dissociative transition state. The branching ratio, but not the dissociation pathway of [somatostatin5 + 4H]4+ is altered by the reduction of its internal disulfide bond indicating that monomer conformational flexibility plays a role in peptide cluster dissociation. PMID:14652186

  9. Is it biologically relevant to measure the structures of small peptides in the gas-phase?

    NASA Astrophysics Data System (ADS)

    Barran, Perdita E.; Polfer, Nick C.; Campopiano, Dominic J.; Clarke, David J.; Langridge-Smith, Patrick R. R.; Langley, Ross J.; Govan, John R. W.; Maxwell, Alison; Dorin, Julia R.; Millar, Robert P.; Bowers, Michael T.

    2005-02-01

    Recent developments in sample introduction of biologically relevant molecules have heralded a new era for gas-phase methods of structural determination. One of the biggest challenges is to relate gas-phase structures, often measured in the absence of water and counter ions, with in vivo biologically active structures. An advantage of gas-phase based techniques is that a given peptide can be analysed in a variety of different forms, for example, as a function of charge state, or with additional water molecules. Molecular modelling can provide insight into experimental findings and help elucidate the differences between structural forms. Combining experiment and theory provides a thorough interrogation of candidate conformations. Here two important naturally occurring peptide systems have been examined in detail and results are assessed in terms of their biological significance. The first of these is gonadotropin-releasing hormone (GnRH), a decapeptide which is the central regulator of the reproductive system in vertebrates. We have examined several naturally occurring variants of this peptide using Ion Mobility Mass Spectrometry and Electron Capture Dissociation (ECD) in conjunction with Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR-MS). Candidate conformations are modelled using the AMBER force field. Single amino acid changes, for example Gly6 --> Ala6, or Ala6 --> D-Ala6, have observable effects on the gas phase structure of GnRH. It has been shown that evolutionary primary sequence variations are key to the biological activity of GnRH, and it is thought that this is due to different binding affinities at target receptors. This work provides strong evidence that this activity is structurally based. The second system examined is the relationship between the quaternary structure and activity of two novel [beta]-defensins. FT-ICR mass spectrometry has been employed to characterize di-sulphide bridging and dissociation based experiments utilised to

  10. Gas-phase peptide fragmentation: how understanding the fundamentals provides a springboard to developing new chemistry and novel proteomic tools.

    PubMed

    Barlow, Christopher K; O'Hair, Richard A J

    2008-10-01

    This tutorial provides an overview of the evolution of some of the key concepts in the gas-phase fragmentation of different classes of peptide ions under various conditions [e.g. collision-induced dissociation (CID) and electron transfer dissociation (ETD)], and then demonstrates how these concepts can be used to develop new methods. For example, an understanding of the role of the mobile proton and neighboring group interactions in the fragmentation reactions of protonated peptides has led to the design of the 'SELECT' method. For ETD, a model based on the Landau-Zener theory reveals the role of both thermodynamic and geometric effects in the electron transfer from polyatomic reagent anions to multiply protonated peptides, and this predictive model has facilitated the design of a new strategy to form ETD reagent anions from precursors generated via ESI. Finally, two promising, emerging areas of gas-phase ion chemistry of peptides are also described: (1) the design of new gas-phase radical chemistry to probe peptide structure, and (2) selective cleavage of disulfide bonds of peptides in the gas phase via various physicochemical approaches.

  11. 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.

  12. Gas-phase ion isomer analysis reveals the mechanism of peptide sequence scrambling.

    PubMed

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

    2014-03-18

    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 → (c)b) pathway is less energetically (or kinetically) favored.

  13. Conformations of Gly(n)H+ and Ala(n)H+ peptides in the gas phase.

    PubMed Central

    Hudgins, R R; Mao, Y; Ratner, M A; Jarrold, M F

    1999-01-01

    High-resolution ion mobility measurements and molecular dynamics simulations have been used to probe the conformations of protonated polyglycine and polyalanine (Gly(n)H and Ala(n)H+, n = 3-20) in the gas phase. The measured collision integrals for both the polyglycine and the polyalanine peptides are consistent with a self-solvated globule conformation, where the peptide chain wraps around and solvates the charge located on the terminal amine. The conformations of the small peptides are governed entirely by self-solvation, whereas the larger ones have additional backbone hydrogen bonds. Helical conformations, which are stable for neutral Alan peptides, were not observed in the experiments. Molecular dynamics simulations for Ala(n)H+ peptides suggest that the charge destabilizes the helix, although several of the low energy conformations found in the simulations for the larger Ala(n)H+ peptides have small helical regions. PMID:10049339

  14. 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.

  15. 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.

  16. 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

  17. Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons.

    PubMed

    Bythell, Benjamin J; Suhai, Sándor; Somogyi, Arpád; Paizs, Béla

    2009-10-01

    The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.

  18. Modeling Gas-Phase Chemistry in Cometary Atmospheres

    NASA Astrophysics Data System (ADS)

    Boice, D. C.

    Gas-phase chemistry is central to understand the physics and chemistry of comets. Photochemistry is a major source of ions and electrons that further initiate key gas-phase reactions, leading to the plethora of molecules and atoms seen in cometary atmospheres. The relevant physico-chemical processes are identified within a modeling framework to understand observations and in situ measurements of comets (e.g., Halley, Borrelly, Hyakutake, Hale-Bopp, Tempel 1, Wild 2) and to provide valuable insights into the intrinsic properties of their nuclei. Details of these processes are presented, from the collision-dominated inner coma to the solar wind interaction region. This extensive modeling effort to investigate these important cometary processes is highly relevant to ground-based observations of comets and past, on going, and future spacecraft missions to these primitive objects.Gas-phase chemistry is central to understand the physics and chemistry of comets. Photochemistry is a major source of ions and electrons that further initiate key gas-phase reactions, leading to the plethora of molecules and atoms seen in cometary atmospheres. The relevant physico-chemical processes are identified within a modeling framework to understand observations and in situ measurements of comets (e.g., Halley, Borrelly, Hyakutake, Hale-Bopp, Tempel 1, Wild 2) and to provide valuable insights into the intrinsic properties of their nuclei. Details of these processes are presented, from the collision-dominated inner coma to the solar wind interaction region. This extensive modeling effort to investigate these important cometary processes is highly relevant to ground-based observations of comets and past, on going, and future spacecraft missions to these primitive objects.

  19. 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.

  20. 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

  1. Reagent Cluster Anions for Multiple Gas-Phase Covalent Modifications of Peptide and Protein Cations

    NASA Astrophysics Data System (ADS)

    Prentice, Boone M.; Stutzman, John R.; McLuckey, Scott A.

    2013-07-01

    Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the `cost' of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K10 + 3H]3+ and the reagent cluster [5R5Na - Na]-). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.

  2. Secondary structures of short peptide chains in the gas phase: Double resonance spectroscopy of protected dipeptides

    NASA Astrophysics Data System (ADS)

    Chin, Wutharath; Dognon, Jean-Pierre; Canuel, Clélia; Piuzzi, François; Dimicoli, Iliana; Mons, Michel; Compagnon, Isabelle; von Helden, Gert; Meijer, Gerard

    2005-02-01

    The conformational structure of short peptide chains in the gas phase is studied by laser spectroscopy of a series of protected dipeptides, Ac-Xxx-Phe-NH2, Xxx=Gly, Ala, and Val. The combination of laser desorption with supersonic expansion enables us to vaporize the peptide molecules and cool them internally; IR/UV double resonance spectroscopy in comparison to density functional theory calculations on Ac-Gly-Phe-NH2 permits us to identify and characterize the conformers populated in the supersonic expansion. Two main conformations, corresponding to secondary structures of proteins, are found to compete in the present experiments. One is composed of a doubly γ-fold corresponding to the 27 ribbon structure. Topologically, this motif is very close to a β-strand backbone conformation. The second conformation observed is the β-turn, responsible for the chain reversal in proteins. It is characterized by a relatively weak hydrogen bond linking remote NH and CO groups of the molecule and leading to a ten-membered ring. The present gas phase experiment illustrates the intrinsic folding properties of the peptide chain and the robustness of the β-turn structure, even in the absence of a solvent. The β-turn population is found to vary significantly with the residues within the sequence; the Ac-Val-Phe-NH2 peptide, with its two bulky side chains, exhibits the largest β-turn population. This suggests that the intrinsic stabilities of the 27 ribbon and the β-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.

  3. 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

  4. Far-Ir Spectroscopy of Neutral Gas Phase Peptides: Signatures from Combined Experiments and Simulations

    NASA Astrophysics Data System (ADS)

    Mahé, Jérôme; Gaigeot, Marie-Pierre; Bakker, Daniël; Jaeqx, Sander; Rijs, Anouk

    2016-06-01

    Within the past two decades, action vibrational spectroscopy has become an almost routine experimental method to probe the structures of molecules and clusters in the gas phase (neutral and ions). Such experiments are mainly performed in the 1000-4000 wn fingerprint regions. Though successful in many respects, these spectral domains can be however restrictive in the information provided, and sometimes reach limitations for unravelling structures without ambiguity. In a collaborative work with the group of Dr A.M. Rijs (FELIX laboratory, Radbout University, The Netherlands) we have launched a new strategy where the far-IR/Tera-Hertz domain (100-800 wn domain) is experimentally probed for neutral gas phase molecules. Our group in Paris apply finite temperature DFT-based molecular dynamics (DFT-MD) simulations in order to unravel the complex signatures arising in the far-IR domain, and provide an unambiguous assignment both of the structural conformation of the gas phase molecules (taking into account the experimental conditions) and an understanding of the spectral signatures/fingerprints. We will discuss our experimental and theoretical investigations on two neutral peptides in the 100-800 wn far-IR spectral domain, i.e. Z-Ala6 and PheGly dipeptide, that represent two systems which definitive conformational assignment was not possible without the far IR signatures. We will also present our very recent results on the Phe-X peptide series, where X stands for Gly, Ala, Pro, Val, Ser, Cys, combining experiments and DFT-MD simulations, providing a detailed understanding of the vibrational fingerprints in the far-IR domain. In all exemples, we will show how DFT-MD simulations is the proper theoretical tool to account for vibrational anharmonicities and mode couplings, of prime importance in the far-IR domain. References : J. Mahé, S. Jaeqx, A.M. Rijs, M.P. Gaigeot, Phys. Chem. Chem. Phys., 17 :25905 (2015) S. Jaeqx, J. Oomens, A. Cimas, M.P. Gaigeot, A.M. Rijs, Angew

  5. Probing secondary structures of peptide chains using gas phase laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Mons, Michel

    2006-03-01

    A bottom-up approach involving conformer-specific IR studies of short peptide sequences enables us to map the intramolecular interactions that shape the peptide backbone, in particular those H-bonds that are responsible for stability and formation of secondary structures in proteins, like turns or helices. The combination of laser-desorption of solid samples coupled to the efficient cooling in a supersonic expansion makes it possible to isolate in the gas phase the lowest conformations of the energy landscape of small flexible biomolecules. The low temperature achieved enables spectroscopists to record UV spectra in which the contribution of each conformer populated can be distinguished and the corresponding conformation identified using IR/UV double resonance spectroscopy. Data collected are directly comparable to the best quantum chemistry calculations on these species and therefore constitute a severe test for the theoretical methods used. It will be shown how investigation of sequences with an increasing number of building blocks permits to deduce the robust structural trends of a peptide backbone: i) local conformational preference of the backbone in one-residue chains, ii) in capped dipeptides, the competition between a succession of local conformational preferences and overall folded structures, in which a different type of H-bonding scheme, involving distant H-bonding sites along the backbone, takes place: in particular beta-turns, the secondary structure responsible for chain reversals, and finally iii) evidence for the spontaneous helical folding (short 3-10 helix) of three-residue chains will be presented, illustrating the relative weakness of the H-bonding in these molecular assemblies.

  6. An empirical model for gas phase acidity and basicity estimation.

    PubMed

    You, H; Kim, G E; Na, C H; Lee, S; Lee, C J; Cho, K-H; Akiyama, Y; Ishida, T; No, K T

    2014-01-01

    Gas phase acidity and basicity estimation models have been developed for acidic and basic functional groups of amino acid side-chains and also for a number of small organic molecules. The acidic functional groups include aliphatic and aromatic alcohol, and aliphatic and aromatic carboxylic acid, and the basic functional groups include aliphatic, aromatic and hetero-aromatic amines, and also pyridino-, pyrazolo- and imidazolo-groupings. The models are described in terms of a linear combination of descriptors that highly influence reactivity at the reaction centres of the functional groups. In order to describe the chemical environments of the deprotonating and protonating sites, atomic descriptors such as the effective atomic electronegativity and effective atomic polarizability of the atoms in the reaction field and the electrostatic potentials at the reaction sites have been introduced. The coefficient of determination (r(2)) of each model is above 0.8, apart from the imidazole model. The models are readily applicable, ranging from simple organic molecules to proteins.

  7. Gas-Phase Hydrogen-Deuterium Exchange Labeling of Select Peptide Ion Conformer Types: a Per-Residue Kinetics Analysis

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H]4+ ions exhibit two major conformer types with collision cross sections of 418 Å2 and 446 Å2; the [M + 3H]3+ ions also yield two different conformer types having collision cross sections of 340 Å2 and 367 Å2. Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H]3+ ions show faster HDX rate contributions compared with [M + 4H]4+ ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H]4+ ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS).

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

    PubMed

    Prentice, Boone M; McLuckey, Scott A

    2013-02-01

    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.

  9. Infrared Spectroscopy with ab initio molecular dynamics simulations : gas phase floppy peptides of increasing size and complexity, in relation with IR-MPD experiments

    NASA Astrophysics Data System (ADS)

    Gaigeot, Marie-Pierre

    2009-03-01

    We present finite temperature DFT-based Car-Parrinello molecular dynamics (MD) simulations for the calculation of infrared spectra of complex molecular systems, either in the gas phase or in the condensed phase. We will review the fundamentals of the method, as well as the applicability and originality of finite temperature MD simulations for the purpose of modeling infrared spectra. Illustrations are taken from the infrared spectroscopy of alanine peptides of increasing size and complexity (from dipeptides to an octo-peptide) in the gas phase, in relation with IR-MPD (Infrared Multi Photon Dissociation) experiments : 300-400 K gas-phase action spectroscopy as devised on the CLIO platform at the University of Orsay-France or on the platform developed in the group of L. Snoek at Oxford-UK. A special emphasis on vibrational anharmonicities and how they can be extracted from molecular dynamics simulations will be put forward. Furthermore, band assignments in terms of atomic movements from MD is challenging and we have introduced a general method for obtaining effective normal modes of molecular systems from MD simulations.

  10. Intra- and Inter-Molecular Cross-Linking of Peptide Ions in the Gas Phase: Reagents and Conditions

    NASA Astrophysics Data System (ADS)

    Mentinova, Marija; McLuckey, Scott A.

    2011-05-01

    Intra-molecular and inter-molecular cross-linking of protonated polypeptide ions in the gas phase via ion/ion reactions have been demonstrated using N-hydroxysulfosuccinimide (sulfo-NHS)- based reagent anions. The initial step in the ion/ion reaction involves the formation of a long-lived complex between the peptide and reagent, which is a prerequisite for the covalent bioconjugation chemistry. The sulfonate groups on the NHS rings of the homo-bifunctional cross-linking reagents have high affinity for the protonated sites in the peptide and, therefore, facilitate the long-lived complex formation. In addition to the formation of a long-lived chemical complex, intra-molecular cross-linking also requires two unprotonated primary amine sites within a molecule where the covalent modification takes place. Alternatively, inter-molecular cross-linking demands the availability of one neutral primary amine site in each of the two peptides that are being cross-linked. Nucleophilic displacement of two sulfo-NHS groups by the amine functionalities in the peptide is a signature of the covalent cross-linking chemistry in the gas phase. Upon removal of the two sulfo-NHS groups, two amide bonds are formed between an unprotonated, primary amine group of a lysine side chain in the peptide and the carboxyl group in the reagent.

  11. Formation of gas-phase peptide ions and their dissociation in MALDI: insights from kinetic and ion yield studies.

    PubMed

    Moon, Jeong Hee; Yoon, Sohee; Bae, Yong Jin; Kim, Myung Soo

    2015-01-01

    Insights on mechanisms for the generation of gas-phase peptide ions and their dissociation in matrix-assisted laser desorption ionization (MALDI) gained from the kinetic and ion yield studies are presented. Even though the time-resolved photodissociation technique was initially used to determine the dissociation kinetics of peptide ions and their effective temperature, it was replaced by a simpler method utilizing dissociation yields from in-source decay (ISD) and post-source decay (PSD). The ion yields for a matrix and a peptide were measured by repeatedly irradiating a region on a sample and collecting ion signals until the sample in the region was completely depleted. Matrix- and peptide-derived gas-phase cations were found to be generated by pre-formed ion emission or by ion-pair emission followed by anion loss, but not by laser-induced ionization. The total number of ions, that is, matrix plus peptide, was found to be equal to the number of ions emitted from a pure matrix. A matrix plume was found to cool as it expanded, from around 800-1,000 K to 400-500 K. Dissociation of peptide ions along b/y channels was found to occur statistically, that is, following RRKM behavior. Small critical energy (E0  = 0.6-0.7 eV) and highly negative critical entropy (ΔS(‡)  = -30 to -25 eu) suggested that the transition structure was stabilized by multiple intramolecular interactions.

  12. Matrix-assisted laser desorption mass spectrometry of gas-phase peptide-metal complexes

    NASA Astrophysics Data System (ADS)

    Hortal, Ana R.; Hurtado, Paola; Martínez-Haya, Bruno

    2008-12-01

    Cation attachment to a model peptide has been investigated in matrix-assisted laser desorption experiments. Angiotensin I (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu) is chosen as a system for study, and Cu2+ and K+ salts are used as cationizing agents. Three fundamentally different types of samples are investigated: (1) a crystalline sample of Ang I, metal salt and MALDI matrix, prepared with the conventional dried droplet method; (2) a solvent-free fine powder mixture of the same three compounds, and (3) a solution of the angiotensin and the metal salt in an ionic liquid matrix (a molten organic salt that acts as a MALDI active solvent). Effective protonation and cationization of the peptide are achieved with the three methods. The transition metal systematically provides more efficient cationization than the alkali metal. At sufficiently high concentration of the salt, the attachment of up to four copper cations to the angiotensin is observed in the MALDI spectrum. In contrast, only one K+ cation is efficiently bound to the peptide. For a given salt concentration, the highest degree of cationization is obtained in the laser desorption from the ionic liquid matrix. This is attributed to the efficient transfer of free metal cations to the desorption plume, where the complexation takes place.

  13. 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.

  14. Gas-phase tyrosine-to-cysteine radical migration in model systems.

    PubMed

    Lesslie, Michael; Osburn, Sandra; van Stipdonk, Michael J; Ryzhov, Victor

    2015-01-01

    Radical migration, both intramolecular and intermolecular, from the tyrosine phenoxyl radical Tyr(O(∙)) to the cysteine radical Cys(S(∙)) in model peptide systems was observed in the gas phase. Ion-molecule reactions (IMRs) between the radical cation of homotyrosine and propyl thiol resulted in a fast hydrogen atom transfer. In addition, radical cations of the peptide LysTyrCys were formed via two different methods, affording regiospecific production of Tyr(O(∙)) or Cys(S(∙)) radicals. Collision-induced dissociation of these isomeric species displayed evidence of radical migration from the oxygen to sulfur, but not for the reverse process. This was supported by theoretical calculations, which showed the Cys(S(∙)) radical slightly lower in energy than the Tyr(O(∙)) isomer. IMRs of the LysTyrCys radical cation with allyl iodide further confirmed these findings. A mechanism for radical migration involving a proton shuttle by the C-terminal carboxylic group is proposed. PMID:26307738

  15. Steady deflagration of HMX with simple kinetics: A gas phase chain reaction model

    SciTech Connect

    Ward, M.J.; Brewster, M.Q.; Son, S.F.

    1998-08-01

    A new approach is presented for modeling steady combustion of energetic solids, in particular HMX. A simplified, global, gas phase chain reaction kinetic mechanism is employed. Specifically, a zero-order, high activation energy thermal decomposition initiation reaction in the condensed phase followed by a second-order, low activation energy chain reaction in the gas phase is assumed. A closed-form solution is obtained, which is based on the activation energy asymptotics analysis of Lengelle in the condensed phase and the assumption of zero activation energy in the gas phase. Comparisons between the model and a variety of experimental observations over a wide range of pressures and initial temperatures are presented and demonstrate the validity of the approach. The model provides excellent agreement with burning rate data (including sensitivity to pressure and initial temperature) and temperature profile data (in particular the gas phase). This suggests that in the realm of simplified, approximate kinetics modeling of energetic solids, the low gas phase activation energy limit is a more appropriate model than the classical high activation energy limit or heuristic flame sheet models. The model also indicates that the condensed phase reaction zone plays an important role in determining the deflagration rate of HMX, underscoring the need for better understanding of the chemistry in this zone.

  16. 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

  17. Are gas-phase models of interstellar chemistry tenable? The case of methanol.

    PubMed

    Garrod, Robin; Park, In Hee; Caselli, Paola; Herbst, Eric

    2006-01-01

    We consider the case of methanol production in cold dark clouds, also known as quiescent cores, for which recent work shows that a purely gas-phase synthesis is unlikely to produce a sufficient amount to explain the observational fractional abundance of approximately 10(-9). Moreover, recent experiments appear to confirm a previous hypothesis that methanol can be formed on cold grain surfaces by the hydrogenation of CO via successive reactions with hydrogen atoms. In this paper we consider two ways of including the surface formation of methanol into chemical models of cold dark clouds. First, we use a gas-phase model and artificially include the surface formation of methanol in the same manner that the formation of molecular hydrogen is included. Secondly, we utilize a gas-grain code with a new mechanism for desorption following exothermic chemical reactions on grain surfaces. The latter method can reproduce the observed fractional abundance of gas-phase methanol and many other gas-phase species in the well-studied cold dark cloud TMC1-CP but the best fit to the observational data occurs at times significantly later than at ages estimated from gas-phase models.

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    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 S1 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.

  19. 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.

  20. 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)

  1. Secondary structures of Val-Phe and Val-Tyr(Me) peptide chains in the gas phase: effect of the nature of the protecting groups

    NASA Astrophysics Data System (ADS)

    Chin, Wutharath; Dognon, Jean-Pierre; Piuzzi, François; Dimicoli, Iliana; Mons, Michel

    Recent experimental gas-phase studies of very similar peptide chain models (Ac-Val-Tyr(Me)-NHMe and Ac-Val-Phe-NH2) have led to different assignments for the secondary structures adopted: β-strand and β-turn, respectively. We present a discussion of the possible causes for such different behaviour in the light of quantum chemistry calculations. The consistent set of data presently obtained (relative energies and IR calculated spectra) leads us to propose the same structural assignment for the experimentally observed Val-Tyr(Me) and Val-Phe peptide chains, i.e. a β-turn conformation. In addition, calculations also suggest that the nature of the chemical protection on the C-terminal (-NHMe vs. -NH2) of the chain model does not affect its conformational preference, nor its structure or its energetics, which suggests the less simple, but more informative, -NH2-protected models for the determination of the intrinsic structural properties of a peptide chain.

  2. 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.

  3. Gas phase IR spectra of tri-peptide Z-Pro-Leu-Gly: Effect of C-terminal amide capping on secondary structure

    NASA Astrophysics Data System (ADS)

    Chakraborty, Shamik; Yamada, Kohei; Ishiuchi, Shun-ichi; Fujii, Masaaki

    2012-04-01

    Three-residue peptides capped with benzyloxycarbonyl (Z-) group, Z-Pro-Leu-Gly-NH2 and Z-Pro-Leu-Gly-OH, are investigated by infrared (IR) spectroscopy, using supersonic-jet laser desorption technique, in the N-H and O-H stretching frequency ranges. The IR spectra show clear evidence of the formation of different hydrogen-bonding network in the two peptides. The possible gas phase structure is proposed from density functional theory calculations using cc-pVDZ basis set. The Z-Pro-Leu-Gly-OH in the gas phase forms successive γ-turn structure with free C-terminal carboxyl group whereas main structural element in Z-Pro-Leu-Gly-NH2 is β-turn with C-terminal sbnd NH2 group forming hydrogen bond. Structural information is employed to predict their binding capability in gas phase.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Peptide salt bridge stability: from gas phase via microhydration to bulk water simulations.

    PubMed

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

    2012-11-14

    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.

  11. Modeling the effects of gas phase CO2 intrusion on the biogeochemistry of variably saturated soils

    NASA Astrophysics Data System (ADS)

    Altevogt, Andrew S.; Jaffe, Peter R.

    2005-09-01

    The transport of gas phase carbon dioxide through unsaturated soils has the potential to significantly alter the soil biogeochemistry. Leakage of CO2 from deep reservoirs, either naturally occurring or anthropogenically emplaced, may displace oxygen in the soil gas and hence radically alter the redox conditions of a soil. Furthermore, the formation of carbonic acid in the aqueous phase will alter the pH of the soil system. A two-dimensional numerical model has been developed to explore the effects of gaseous CO2 leakage on the biogeochemistry of a variably saturated porous media. The model describes the sequential degradation of organic carbon by microorganisms using a series of terminal electron acceptors. Gas phase CO2 intrusion results in changes in redox conditions and pH of the soil water, both of which lead to alteration of the biogeochemistry of the soil. Alteration of the biogeochemical profile of a representative field site is explored with the numerical model.

  12. Effect of the basic residue on the energetics, dynamics, and mechanisms of gas-phase fragmentation of protonated peptides.

    PubMed

    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-resolved and collision energy-resolved surface-induced dissociation (SID) of singly protonated peptides with the N-terminal arginine residue and their analogues, in which arginine is replaced with less basic lysine and histidine residues, was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). SID experiments demonstrated 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 Rice-Ramsperger-Kassel-Marcus (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. Because pathways involving SB intermediates are characterized by low threshold energies, they efficiently compete with classical oxazolone and imine/enol pathways of arginine-containing peptides on a long time scale of the FTICR instrument. In contrast, fragmentation of histidine- and lysine-containing peptides is largely determined by canonical 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 analogues.

  13. Gas-phase reactivity of peptide thiyl (RS•), perthiyl (RSS•), and sulfinyl (RSO•) radical ions formed from atmospheric pressure ion/radical reactions.

    PubMed

    Tan, Lei; Xia, Yu

    2013-04-01

    In this study, we demonstrated the formation of gas-phase peptide perthiyl (RSS•) and thiyl (RS•) radical ions besides sulfinyl radical (RSO•) ions from atmospheric pressure (AP) ion/radical reactions of peptides containing inter-chain disulfide bonds. The identity of perthiyl radical was verified from characteristic 65 Da (•SSH) loss in collision-induced dissociation (CID). This signature loss was further used to assess the purity of peptide perthiyl radical ions formed from AP ion/radical reactions. Ion/molecule reactions combined with CID were carried out to confirm the formation of thiyl radical. Transmission mode ion/molecule reactions in collision cell (q2) were developed as a fast means to estimate the population of peptide thiyl radical ions. The reactivity of peptide thiyl, perthiyl, and sulfinyl radical ions was evaluated based on ion/molecule reactions toward organic disulfides, allyl iodide, organic thiol, and oxygen, which followed in order of thiyl (RS•) > perthiyl (RSS•) > sulfinyl (RSO•). The gas-phase reactivity of these three types of sulfur-based radicals is consistent with literature reports from solution studies.

  14. Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

    PubMed Central

    KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

    2014-01-01

    We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

  15. Gas-phase spectroscopy and anharmonic vibrational analysis of the 3-residue peptide Z-Pro-Leu-Gly-NH2 by the laser desorption supersonic jet technique

    NASA Astrophysics Data System (ADS)

    Ishiuchi, Shun-ichi; Yamada, Kohei; Chakraborty, Shamik; Yagi, Kiyoshi; Fujii, Masaaki

    2013-06-01

    The electronic excitation and infrared (IR) spectra of a capped tri-peptide, Z-PLG-NH2 (Z = benzyloxycarbonyl, P = Pro, L = Leu, G = Gly), were measured in the gas phase by using the laser desorption supersonic jet technique. By measuring an ultraviolet-ultraviolet hole burning spectrum, it was found that Z-PLG-NH2 has the maximum three conformers in the gas phase, but that the population is mainly distributed to a single conformation. Molecular dynamics simulations and density functional theory calculations well-reproduced the observed IR spectrum, except for splitting of the NH stretching bands by a β-turn structure that corresponds to a global minimum structure. Anharmonic vibrational analysis by vibrational quasi-degenerate perturbation theory (VQDPT) successfully reproduced the anharmonic splitting, and confirmed the assignments.

  16. Accurate Characterization of the Peptide Linkage in the Gas Phase: A Joint Quantum-Chemical and Rotational Spectroscopy Study of the Glycine Dipeptide Analogue.

    PubMed

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Largo, Laura; Peña, Isabel; Cabezas, Carlos; Alonso, José Luis

    2014-02-01

    Accurate structures of aminoacids in the gas phase have been obtained by joint microwave and quantum-chemical investigations. However, the structure and conformational behavior of α-aminoacids once incorporated into peptide chains are completely different and have not yet been characterized with the same accuracy. To fill this gap, we present here an accurate characterization of the simplest dipeptide analogue (N-acetyl-glycinamide) involving peptidic bonds. State-of-the-art quantum-chemical computations are complemented by a comprehensive study of the rotational spectrum using a combination of Fourier transform microwave spectroscopy with laser ablation. The coexistence of the C7 and C5 conformers has been proved and energetically as well as spectroscopically characterized. This joint theoretical-experimental investigation demonstrated the feasibility of obtaining accurate structures for flexible small biomolecules, thus paving the route to the elucidation of the inherent behavior of peptides.

  17. 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)

  18. 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.

  19. Transition metals as electron traps. I. Structures, energetics, electron capture, and electron-transfer-induced dissociations of ternary copper-peptide complexes in the gas phase.

    PubMed

    Turecek, Frantisek; Jones, Jace W; Holm, Anne I S; Panja, Subhasis; Nielsen, Steen Brøndsted; Hvelplund, Preben

    2009-05-01

    Electron-induced dissociations of gas-phase ternary copper-2,2'-bipyridine complexes of Gly-Gly-Gly and Gly-Gly-Leu were studied on a time scale ranging from 130 ns to several milliseconds using a combination of charge-reversal ((+)CR(-)) and electron-capture-induced dissociation (ECID) measured on a beam instrument and electron capture dissociation (ECD) measured in a Penning trap. Charge-reduced intermediates were observed on the short time scale in the (+)CR(-) and ECID experiments but not in ECD. Ion dissociations following electron transfer or capture mostly occurred by competitive bpy or peptide ligand loss, whereas peptide backbone fragmentations were suppressed in the presence of the ligated metal ion. Extensive electron structure theory calculations using density functional theory and large basis sets provided optimized structures and energies for the precursor ions, charge-reduced intermediates, and dissociation products. The Cu complexes underwent substantial structure changes upon electron capture. Cu was calculated to be pentacoordinated in the most stable singly charged complexes of the [Cu(peptide-H)bpy](+*) type where it carried a approximately +1 atomic charge. Cu coordination in charge-reduced [Cu(peptide-H)bpy] intermediates depended on the spin state. The themodynamically more stable singlet states had tricoordinated Cu, whereas triplet states had a tetracoordinated Cu. Cu was tricoordinated in stable [Cu(peptide-H)bpy](-*) products of electron transfer. [Cu(peptide)bpy](2+*) complexes contained the peptide ligand in a zwitterionic form while Cu was tetracoordinated. Upon electron capture, Cu was tri- or tetracoordinated in the [Cu(peptide)bpy](+) charge-reduced analogs and the peptide ligands underwent prototropic isomerization to canonical forms. The role of excited singlet and triplet electronic states is assessed. PMID:19132713

  20. Development and evaluation of the aerosol dynamics and gas phase chemistry model ADCHEM

    NASA Astrophysics Data System (ADS)

    Roldin, P.; Swietlicki, E.; Schurgers, G.; Arneth, A.; Lehtinen, K. E. J.; Boy, M.; Kulmala, M.

    2011-06-01

    The aim of this work was to develop a model suited for detailed studies of aerosol dynamics, gas and particle phase chemistry within urban plumes, from local scale (1 × 1 km2) to regional scale. This article describes and evaluates the trajectory model for Aerosol Dynamics, gas and particle phase CHEMistry and radiative transfer (ADCHEM). The model treats both vertical and horizontal dispersion perpendicular to an air mass trajectory (2-space dimensions). The Lagrangian approach enables a more detailed representation of the aerosol dynamics, gas and particle phase chemistry and a finer spatial and temporal resolution compared to that of available regional 3D-CTMs. These features make it among others well suited for urban plume studies. The aerosol dynamics model includes Brownian coagulation, dry deposition, wet deposition, in-cloud processing, condensation, evaporation, primary particle emissions and homogeneous nucleation. The organic mass partitioning was either modeled with a 2-dimensional volatility basis set (2D-VBS) or with the traditional two-product model approach. In ADCHEM these models consider the diffusion limited and particle size dependent condensation and evaporation of 110 and 40 different organic compounds respectively. The gas phase chemistry model calculates the gas phase concentrations of 61 different species, using 130 different chemical reactions. Daily isoprene and monoterpene emissions from European forests were simulated separately with the vegetation model LPJ-GUESS, and included as input to ADCHEM. ADCHEM was used to simulate the ageing of the urban plumes from the city of Malmö in southern Sweden (280 000 inhabitants). Several sensitivity tests were performed concerning the number of size bins, size structure method, aerosol dynamic processes, vertical and horizontal mixing, coupled or uncoupled condensation and the secondary organic aerosol formation. The simulations show that the full-stationary size structure gives accurate results

  1. Development and evaluation of the aerosol dynamic and gas phase chemistry model ADCHEM

    NASA Astrophysics Data System (ADS)

    Roldin, P.; Swietlicki, E.; Schurgers, G.; Arneth, A.; Lehtinen, K. E. J.; Boy, M.; Kulmala, M.

    2010-08-01

    The aim of this work was to develop a model ideally suited for detailed studies on aerosol dynamics, gas and particle phase chemistry within urban plumes, from local scale (1×1 km2) to regional or global scale. This article describes and evaluates the trajectory model for Aerosol Dynamics, gas and particle phase CHEMistry and radiative transfer (ADCHEM), which has been developed and used at Lund University since 2007. The model treats both vertical and horizontal dispersion perpendicular to an air mass trajectory (2-space dimensions), which is not treated in Lagrangian box-models (0-space dimensions). The Lagrangian approach enables a more detailed representation of the aerosol dynamics, gas and particle phase chemistry and a finer spatial and temporal resolution compared to that of available regional 3D-CTMs. These features make it among others ideally suited for urban plume studies. The aerosol dynamics model includes Brownian coagulation, dry deposition, wet deposition, in-cloud processing, condensation, evaporation, primary particle emissions and homogeneous nucleation. The gas phase chemistry model calculates the gas phase concentrations of 63 different species, using 119 different chemical reactions. Daily isoprene and monoterpene emissions from European forests were simulated separately with the vegetation model LPJ-GUESS, and included as input to ADCHEM. ADCHEM was used to simulate the ageing of the urban plumes from the city of Malmö in Southern Sweden (280 000 inhabitants). Several sensitivity tests were performed concerning the number of size bins, size structure method, coupled or uncoupled condensation, the volatility basis set (VBS) or traditional 2-product model for secondary organic aerosol formation, different aerosol dynamic processes and vertical and horizontal mixing. The simulations show that the full-stationary size structure gives accurate results with little numerical diffusion when more than 50 size bins are used between 1.5 and 2500 nm

  2. 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.

  3. 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

  4. Where does the electron go? Electron distribution and reactivity of peptide cation radicals formed by electron transfer in the gas phase.

    PubMed

    Turecek, Frantisek; Chen, Xiaohong; Hao, Changtong

    2008-07-01

    We report the first detailed analysis at correlated levels of ab initio theory of experimentally studied peptide cations undergoing charge reduction by collisional electron transfer and competitive dissociations by loss of H atoms, ammonia, and N-C alpha bond cleavage in the gas phase. Doubly protonated Gly-Lys, (GK + 2H) (2+), and Lys-Lys, (KK + 2H) (2+), are each calculated to exist as two major conformers in the gas phase. Electron transfer to conformers with an extended lysine chain triggers highly exothermic dissociation by loss of ammonia from the Gly residue, which occurs from the ground ( X ) electronic state of the cation radical. Loss of Lys ammonium H atoms is predicted to occur from the first excited ( A ) state of the charge-reduced ions. The X and A states are nearly degenerate and show extensive delocalization of unpaired electron density over spatially remote groups. This delocalization indicates that the captured electron cannot be assigned to reduce a particular charged group in the peptide cation and that superposition of remote local Rydberg-like orbitals plays a critical role in affecting the cation-radical reactivity. Electron attachment to ion conformers with carboxyl-solvated Lys ammonium groups results in spontaneous isomerization by proton-coupled electron transfer to the carboxyl group forming dihydroxymethyl radical intermediates. This directs the peptide dissociation toward NC alpha bond cleavage that can proceed by multiple mechanisms involving reversible proton migrations in the reactants or ion-molecule complexes. The experimentally observed formations of Lys z (+*) fragments from (GK + 2H) (2+) and Lys c (+) fragments from (KK + 2H) (2+) correlate with the product thermochemistry but are independent of charge distribution in the transition states for NC alpha bond cleavage. This emphasizes the role of ion-molecule complexes in affecting the charge distribution between backbone fragments produced upon electron transfer or capture

  5. 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.

  6. 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

    2016-10-01

    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.

  7. 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.

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

    PubMed

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

    2016-10-01

    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. Graphical Abstract ᅟ.

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

    PubMed

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

    2016-10-01

    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. Graphical Abstract ᅟ. PMID:27400696

  10. Model for the catalytic oxidation of CO, including gas-phase impurities and CO desorption

    NASA Astrophysics Data System (ADS)

    Buendía, G. M.; Rikvold, P. A.

    2013-07-01

    We present results of kinetic Monte Carlo simulations of a modified Ziff-Gulari-Barshad model for the reaction CO+O → CO2 on a catalytic surface. Our model includes impurities in the gas phase, CO desorption, and a modification known to eliminate the unphysical O poisoned phase. The impurities can adsorb and desorb on the surface, but otherwise remain inert. In a previous work that did not include CO desorption [Buendía and Rikvold, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.85.031143 85, 031143 (2012)], we found that the impurities have very distinctive effects on the phase diagram and greatly diminish the reactivity of the system. If the impurities do not desorb, once the system reaches a stationary state, the CO2 production disappears. When the impurities are allowed to desorb, there are regions where the CO2 reaction window reappears, although greatly reduced. Following experimental evidence that indicates that temperature effects are crucial in many catalytic processes, here we further analyze these effects by including a CO desorption rate. We find that the CO desorption has the effect to smooth the transition between the reactive and the CO rich phase, and most importantly it can counteract the negative effects of the presence of impurities by widening the reactive window such that now the system remains catalytically active in the whole range of CO pressures.

  11. 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.

  12. 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.

  13. Gas-phase doubly charged complexes of cyclic peptides with copper in +1, +2 and +3 formal oxidation states: formation, structures and electron capture dissociation.

    PubMed

    Afonso, Carlos; Tabet, Jean-Claude; Giorgi, Gianluca; Tureček, František

    2012-02-01

    Copper complexes with a cyclic D-His-β-Ala-L-His-L-Lys and all-L-His-β-Ala-His-Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D-His and L-His complexes. All complexes underwent peptide cross-ring cleavages upon electron capture. The modes of ring cleavage depended on the formal oxidation state of the Cu ion and peptide protonation. Density functional theory (DFT) calculations, using the B3LYP with an effective core potential at Cu and M06-2X functionals, identified several precursor ion structures in which the Cu ion was threecoordinated to pentacoordinated by the His and Lys side-chain groups and the peptide amide or enolimine groups. The electronic structure of the formally Cu(III) complexes pointed to an effective Cu(I) oxidation state with the other charge residing in the peptide ligand. The relative energies of isomeric complexes of the [Cu(c-HAHK + H)](2+) and [Cu(c-HAHK - H)](2+) type with closed electronic shells followed similar orders when treated by the B3LYP and M06-2X functionals. Large differences between relative energies calculated by these methods were obtained for open-shell complexes of the [Cu(c-HAHK)](2+) type. Charge reduction resulted in lowering the coordination numbers for some Cu complexes that depended on the singlet or triplet spin state being formed. For [Cu(c-HAHK - H)](2+) complexes, solution H/D exchange involved only the N-H protons, resulting in the exchange of up to seven protons, as established by ultra-high mass resolution measurements. Contrasting the experiments, DFT calculations found the lowest energy structures for the gas-phase ions that were deprotonated at the peptide C(α) positions.

  14. Reactive Transport Modeling of Vadose Zone Contamination: Feedback between Reactions and Gas-Phase Transport

    NASA Astrophysics Data System (ADS)

    Molins, S.; Mayer, K.

    2007-05-01

    The unsaturated zone acts as a buffer zone for contaminants on their way to the water table but can also attenuate the emission of contaminants leaving the subsurface environment through the gas phase. A reactive transport model that includes multicomponent gas transport has been developed to investigate the processes that contribute to the generation and attenuation of contaminants in the unsaturated zone. In particular, the model is suitable to study the feedback processes between advective-diffusive gas transport and geochemical reactions. The model is also able to estimate diffusive and advective contributions to gas transport in multicomponent systems. Two model applications are presented that investigate gas transport and reactions in mine tailings and at a site with organic contamination. In mine tailings, atmospheric oxygen transported into the sediment column is consumed in the oxidation of sulfide minerals. Gas volume loss caused by the consumption of atmospheric oxygen drives advective fluxes. In the absence of carbonate minerals, the advective component accounts for 16 % of the net oxygen flux into the column, while, in a carbonate-rich system, advection accounts for 10 % of the net oxygen flux. Dissolution of carbonate minerals has a moderating effect on advective gas transport since carbon dioxide can partially compensate for the depletion of oxygen. At an oil spill site, volatilization and degradation of organic contaminants cause advective and diffusive fluxes of organic vapors away from the source zone. At early stages, volatilization dominates and oxidation of these organic vapors attenuates the emission of contaminants to the atmosphere. The contribution of advection to organic vapor fluxes is significant initially but decreases with time. At later stages, the oil source becomes depleted of its most volatile fraction, and anaerobic degradation of aromatic compounds and heavier n-alkanes results in the production of methane. Up to 15 % of methane

  15. Comparison of gas-phase free-radical populations in tobacco smoke and model systems by HPLC.

    PubMed Central

    Flicker, T M; Green, S A

    2001-01-01

    We used an improved method for trapping carbon-centered radicals (.R) from the gas-phase to compare radical suites trapped from various tobacco smoke and model smoke systems. Using a nitroxide trap, 3-amino-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (3AP), on solid support, we trapped radicals directly from the gas phase, washed them off the support, and analyzed them with HPLC. Separation of the trapped radicals showed that each tobacco type produced a unique radical suite of 4-10 distinct peaks. Gas mixtures used to model tobacco smoke consisted of nitric oxide, air, isoprene, and methanol. The model systems produced radical suites of four major and several minor peaks, two of which matched peaks in tobacco smoke chromatograms. Quantities of radicals trapped from tobacco smoke were: 54 +/- 2 nmol .R per Marlboro cigarette, 66 +/- 9 nmol .R per Djarum clove cigarette, and 185 +/- 9 nmol .R per Swisher Sweet cigar. In these experiments oxygen competes with the nitroxide trap for gas-phase radicals. A kinetic analysis of the O2 competition shows that actual radical concentrations in the smoke were approximately 100-fold higher than measured. PMID:11564610

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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).

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

    PubMed

    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 utilised 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.

  3. 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.

  4. 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.

  5. 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.

  6. A model coupling the liquid and gas phases for a totally wetting evaporative meniscus

    NASA Astrophysics Data System (ADS)

    Doumenc, F.; Guerrier, B.

    2011-08-01

    An hydrodynamic model has been developed to get a complete description of an evaporative meniscus in complete wetting configuration. The coupling between the liquid and gas is explicitly taken into account. Scaling laws are derived for the different domains of the meniscus and validated by numerical simulations. Results are compared with previous models of the literature that use the electrostatic analogy proposed by Deegan and co-authors to describe the evaporative flux. We show that the different approaches differ for the description of the tip of the meniscus in the domain corresponding to the decrease of the evaporative flux but lead to the same scaling for the apparent macroscopic contact angle.

  7. Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides.

    PubMed

    Verstraelen, Toon; Pauwels, Ewald; De Proft, Frank; Van Speybroeck, Veronique; Geerlings, Paul; Waroquier, Michel

    2012-02-14

    The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q(0), that is suitable to describe biological systems bearing many locally charged functional groups.

  8. 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...

  9. MODELING AEROSOL FORMATION FROM ALPHA-PINENE + NOX IN THE PRESENCE OF NATURAL SUNLIGHT USING GAS PHASE KINETICS AND GAS-PARTICLE PARTITIONING THEORY. (R826771)

    EPA Science Inventory

    A kinetic mechanism was used to link and model the gas-phase reactions and
    aerosol accumulation resulting from src="/ncer/pubs/images/alpha.gif">-pinene reactions in the presence of sunlight,
    ozone (O3), and oxides of nitrogen
    (NO

  10. 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.

  11. Measurement and model results for gas phase OH and H2SO4 during PROPHET 2001.

    NASA Astrophysics Data System (ADS)

    Tanner, D.; Sjostedt, S.; Huey, G.; Slusher, D.; Chen, G.; Lefer, B.; Shetter, R.; Carroll, M.; Hengel, S.; Fortner, E.; Young, V.

    2002-12-01

    During the summer of 2001 a Chemical Ionization Mass Spectrometer (CIMS) was installed on top of the PROPHET tower to measure OH and H2SO4. Both OH and H2SO4 have a strong diurnal variation and correlate well with the measured ozone photolysis rate. Typical OH nighttime values are below the detection limit of 3e5 molecules cm-3. The maximum daytime value varied from 1-5 e6 molecules cm-3 with the highest OH levels corresponding to the lowest isoprene mixing ratios. The nighttime results are inconsistent with previous LIF measurements of high nighttime OH levels at this site and may indicate a systematic difference between the two techniques. However, the midday measured OH data is approximately 50% higher than the preliminary midday model values and is in accord with the previous LIF observations. A more detailed comparison of constrained photochemical models predictions to the observed OH levels will be presented. The daytime H2SO4 concentrations were highly variable and exceeded 5e7 molecules cm-3 on two days under "clean" northerly flow conditions. Evidence will be presented that suggest the source of the relatively high sulfuric acid concentrations is a large nickel smelting operation in Sudbury, Ontario. The nighttime levels of sulfuric acid were typically below the detection limit of the instrument of approximately 1e5 molecules cm-3. This data is consistent with the measured OH and suggests that large nighttime sources of radicals are not present in this environment.

  12. 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).

  13. 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.

  14. 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.

  15. Gas-phase synthesis and structure of monomeric ZnOH: a model species for metalloenzymes and catalytic surfaces.

    PubMed

    Zack, Lindsay N; Sun, Ming; Bucchino, Matthew P; Clouthier, Dennis J; Ziurys, Lucy M

    2012-02-16

    Monomeric ZnOH has been studied for the first time using millimeter and microwave gas-phase spectroscopy. ZnOH is important in surface processes and at the active site of the enzyme carbonic anhydrase. In the millimeter-wave direct-absorption experiments, ZnOH was synthesized by reacting zinc vapor, produced in a Broida-type oven, with water. In the Fourier-transform microwave measurements, ZnOH was produced in a supersonic jet expansion of CH(3)OH and zinc vapor, created by laser ablation. Multiple rotational transitions of six ZnOH isotopologues in their X(2)A' ground states were measured over the frequency range of 22-482 GHz, and splittings due to fine and hyperfine structure were resolved. An asymmetric top pattern was observed in the spectra, showing that ZnOH is bent, indicative of covalent bonding. From these data, spectroscopic constants and an accurate structure were determined. The Zn-O bond length was found to be similar to that in carbonic anhydrase and other model enzyme systems.

  16. 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

  17. 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

  18. A unified model for simulating liquid and gas phase, intermolecular energy transfer: N₂ + C₆F₆ collisions.

    PubMed

    Paul, Amit K; Kohale, Swapnil C; Pratihar, Subha; Sun, Rui; North, Simon W; Hase, William L

    2014-05-21

    Molecular dynamics simulations were used to study relaxation of a vibrationally excited C6F6* molecule in a N2 bath. Ab initio calculations were performed to develop N2-N2 and N2-C6F6 intermolecular potentials for the simulations. Energy transfer from "hot" C6F6 is studied versus the bath density (pressure) and number of bath molecules. For the large bath limit, there is no heating of the bath. As C6F6* is relaxed, the average energy of C6F6* is determined versus time, i.e., ⟨E(t)⟩, and for each bath density ⟨E(t)⟩ is energy dependent and cannot be fit by a single exponential. In the long-time limit C6F6 is fully equilibrated with the bath. For a large bath and low pressures, the simulations are in the fixed temperature, independent collision regime and the simulation results may be compared with gas phase experiments of collisional energy transfer. The derivative d[⟨E(t)⟩]/dt divided by the collision frequency ω of the N2 bath gives the average energy transferred from C6F6* per collision ⟨ΔE(c)⟩, which is in excellent agreement with experiment. For the ~100-300 ps simulations reported here, energy transfer from C6F6* is to N2 rotation and translation in accord with the equipartition model, with no energy transfer to N2 vibration. The energy transfer dynamics from C6F6* is not statistically sensitive to fine details of the N2-C6F6 intermolecular potential. Tests, with simulation ensembles of different sizes, show that a relatively modest ensemble of only 24 trajectories gives statistically meaningful results.

  19. 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

  20. 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.

  1. Structural investigation of naturally occurring peptides by electron capture dissociation and AMBER force field modelling

    NASA Astrophysics Data System (ADS)

    Polfer, Nick C.; Haselmann, Kim F.; Langridge-Smith, Pat R. R.; Barran, Perdita E.

    We present a detailed analysis of the relative yields in dissociation products of doubly protonated polypeptide cations obtained via electron capture dissociation (ECD). These experimental studies are complemented by molecular dynamics force field modelling, using the AMBER force field, to correlate with putative gas-phase conformations for these peptides. It is shown that the highest gas-phase basicity amino acid residue (i.e. arginine) is included in all the charged fragments. This is of particular use in determining the primary structure tryptic digest peptides, which will ordinarily posses a high basicity C-terminal residue (i.e. arginine or lysine). Further, these results suggest that the relative ECD dissociation pattern is related to the secondary structure of the peptide. In particular, the ECD fragmentation pattern in gonadatropin releasing hormone (GnRH) variants appears to depend on whether a β-turn or an extended α-helical structure is formed. In the peptide bradykinin, modelling suggests that the C-terminal arginine engages in much more extended solvation of the backbone than the N-terminal arginine. This strongly correlates with the observed dominance of c over z fragments. This work forms the first attempt at a systematic qualitative correlation of the low-energy structures of modelled gas-phase polypeptides, and their corresponding ECD dissociation pattern.

  2. Biogenic SOA formation through gas-phase oxidation and gas-to-particle partitioning - comparison between process models of varying complexity

    NASA Astrophysics Data System (ADS)

    Hermansson, E.; Roldin, P.; Rusanen, A.; Mogensen, D.; Kivekäs, N.; Boy, M.; Swietlicki, E.

    2014-05-01

    Biogenic volatile organic compounds (BVOCs) emitted by the vegetation play an important role for the aerosol mass loadings since the oxidation products of these compounds can take part in the formation and growth of secondary organic aerosols (SOA). The concentrations and properties of BVOCs and their oxidation products in the atmosphere are poorly characterized, which leads to high uncertainties in modeled SOA mass and properties. In this study the formation of SOA has been modeled along an air mass trajectory over the northern European boreal forest using two aerosol dynamics box models where the prediction of the condensable organics from the gas-phase oxidation of BVOC is handled with schemes of varying complexity. The use of box model simulations along an air mass trajectory allows us to, under atmospheric relevant conditions, compare different model parameterizations and their effect on SOA formation. The result of the study shows that the modeled mass concentration of SOA is highly dependent on the organic oxidation scheme used to predict the oxidation products. A near-explicit treatment of organic gas-phase oxidation (Master Chemical Mechanism version 3.2) was compared to oxidation schemes that use the volatility basis set (VBS) approach. The resulting SOA mass modeled with different VBS-schemes varies by a factor of about 7 depending on how the first generation oxidation products are parameterized and how they subsequently age (e.g. how fast the gas-phase oxidation products react with the OH-radical, how they respond to temperature changes and if they are allowed to fragment during the aging process). Since the VBS approach is frequently used in regional and global climate models due to its relatively simple treatment of the oxidation products compared to near-explicit oxidation schemes; better understanding of the abovementioned processes are needed. Compared to the most commonly used VBS-schemes, the near-explicit method produces less - but more oxidized

  3. Peptide models for membrane channels.

    PubMed Central

    Marsh, D

    1996-01-01

    Peptides may be synthesized with sequences corresponding to putative transmembrane domains and/or pore-lining regions that are deduced from the primary structures of ion channel proteins. These can then be incorporated into lipid bilayer membranes for structural and functional studies. In addition to the ability to invoke ion channel activity, critical issues are the secondary structures adopted and the mode of assembly of these short transmembrane peptides in the reconstituted systems. The present review concentrates on results obtained with peptides from ligand-gated and voltage-gated ion channels, as well as proton-conducting channels. These are considered within the context of current molecular models and the limited data available on the structure of native ion channels and natural channel-forming peptides. PMID:8615800

  4. Vibrational Spectroscopy and Gas-Phase Thermochemistry of the Model Dipeptide N-Acetyl Glycine Methyl Amide

    NASA Astrophysics Data System (ADS)

    Leavitt, Christopher; Raston, Paul; Moody, Grant; Shirley, Caitlyne; Douberly, Gary

    2014-06-01

    The structure-function relationship in proteins is widely recognized, motivating numerous investigations of isolated neutral and ionic polypeptides that generally employ conformation specific, multidimensional UV and IR spectroscopies. This data taken in conjunction with computed harmonic frequencies has provided a snapshot of the underlying molecular physics at play in many polypeptides, but few experiments have been able to probe the energetics of these systems. In this study, we use vibrational spectroscopy to measure the gas-phase enthalpy change for isomerization between two conformations of the dipeptide N-acetyl glycine methyl amide (NAGMA). A two-stage oven source is implemented producing a gas-phase equilibrium distribution of NAGMA molecules that is flash frozen upon pickup by He nanodroplets. Using polarization spectroscopy, the IR spectrum is assigned to a mixture of two conformers having intramolecular hydrogen bonds made up of either five- or seven-membered rings, C5 and C7, respectively. The interconversion enthalpy, obtained from the van't Hoff relation, is 4.52{±}0.12 kJ/mol for isomerization from the C7 to the C5-conformer. This experimental measurement is compared to computations employing a broad range of theoretical methods.

  5. 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.

  6. Strategy to improve the quantitative LC-MS analysis of molecular ions resistant to gas-phase collision induced dissociation: application to disulfide-rich cyclic peptides.

    PubMed

    Ciccimaro, Eugene; Ranasinghe, Asoka; D'Arienzo, Celia; Xu, Carrie; Onorato, Joelle; Drexler, Dieter M; Josephs, Jonathan L; Poss, Michael; Olah, Timothy

    2014-12-01

    Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here a methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte's surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte's unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma.

  7. 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

  8. 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.

  9. Biogenic SOA formation through gas-phase oxidation and gas-to-particle partitioning - a comparison between process models of varying complexity

    NASA Astrophysics Data System (ADS)

    Hermansson, E.; Roldin, P.; Rusanen, A.; Mogensen, D.; Kivekäs, N.; Väänänen, R.; Boy, M.; Swietlicki, E.

    2014-11-01

    Biogenic volatile organic compounds (BVOCs) emitted by vegetation play an important role for aerosol mass loadings since the oxidation products of these compounds can take part in the formation and growth of secondary organic aerosols (SOA). The concentrations and properties of BVOCs and their oxidation products in the atmosphere are poorly characterized, which leads to high uncertainties in modeled SOA mass and properties. In this study, the formation of SOA has been modeled along an air-mass trajectory over northern European boreal forest using two aerosol dynamics box models where the prediction of the condensable organics from the gas-phase oxidation of BVOC is handled with schemes of varying complexity. The use of box model simulations along an air-mass trajectory allows us to compare, under atmospheric relevant conditions, different model parameterizations and their effect on SOA formation. The result of the study shows that the modeled mass concentration of SOA is highly dependent on the organic oxidation scheme used to predict oxidation products. A near-explicit treatment of organic gas-phase oxidation (Master Chemical Mechanism version 3.2) was compared to oxidation schemes that use the volatility basis set (VBS) approach. The resulting SOA mass modeled with different VBS schemes varies by a factor of about 7 depending on how the first-generation oxidation products are parameterized and how they subsequently age (e.g., how fast the gas-phase oxidation products react with the OH radical, how they respond to temperature changes, and if they are allowed to fragment during the aging process). Since the VBS approach is frequently used in regional and global climate models due to its relatively simple treatment of the oxidation products compared to near-explicit oxidation schemes, a better understanding of the above-mentioned processes is needed. Based on the results of this study, fragmentation should be included in order to obtain a realistic SOA formation

  10. Examination of the coordination sphere of Al(III) in trifluoromethyl-heteroarylalkenolato complex ions by gas-phase IRMPD spectroscopy and computational modelling.

    PubMed

    Brückmann, Lisa; Tyrra, Wieland; Mathur, Sanjay; Berden, Giel; Oomens, Jos; Meijer, Anthony J H M; Schäfer, Mathias

    2012-06-01

    A series of aluminium complex ions with trifluoromethyl-heteroarylalkenolato (TMHA) ligands are studied by gas-phase infrared multiphoton-dissociation (IRMPD) spectroscopy and computational modelling. The selected series of aluminium TMHA complex ions are promising species for the initial study of intrinsic binding characteristics of Al(III) cations in the gas phase as corresponding molecular ions. They are readily available for examination by (+) and (-) electrospray ionization mass spectrometry (ESI-MS) by spraying of [Al(3+)⋅(L(-))(3)] solutions. The complex ions under investigation contain trivalent Al(3+) cations with two chelating anionic enolate ligands, [Al(3+)⋅(L(-))(2)](+), providing insights in the nature of the heteroatom-Al bonds. Additionally, the structure of a deprotonated benzimidazole ligand, L(-,) and an anionic complex ion of Al(III) with two doubly deprotonated benzimidazole ligands, [Al(3+)⋅(L(2-))(2)](-), are examined by (-)ESI-IRMPD spectroscopy. Experimental and computational results are highly consistent and allow a reliable identification of the ion structures. In all complex ions examined the planar TMHA ligands are oriented perpendicular to each other around the metal ion, leading to a tetrahedral coordination sphere in which aluminium interacts with the enolate oxygen and heteroaryl nitrogen atoms available in each of the bidentate ligands. PMID:22442004

  11. Examination of the coordination sphere of Al(III) in trifluoromethyl-heteroarylalkenolato complex ions by gas-phase IRMPD spectroscopy and computational modelling.

    PubMed

    Brückmann, Lisa; Tyrra, Wieland; Mathur, Sanjay; Berden, Giel; Oomens, Jos; Meijer, Anthony J H M; Schäfer, Mathias

    2012-06-01

    A series of aluminium complex ions with trifluoromethyl-heteroarylalkenolato (TMHA) ligands are studied by gas-phase infrared multiphoton-dissociation (IRMPD) spectroscopy and computational modelling. The selected series of aluminium TMHA complex ions are promising species for the initial study of intrinsic binding characteristics of Al(III) cations in the gas phase as corresponding molecular ions. They are readily available for examination by (+) and (-) electrospray ionization mass spectrometry (ESI-MS) by spraying of [Al(3+)⋅(L(-))(3)] solutions. The complex ions under investigation contain trivalent Al(3+) cations with two chelating anionic enolate ligands, [Al(3+)⋅(L(-))(2)](+), providing insights in the nature of the heteroatom-Al bonds. Additionally, the structure of a deprotonated benzimidazole ligand, L(-,) and an anionic complex ion of Al(III) with two doubly deprotonated benzimidazole ligands, [Al(3+)⋅(L(2-))(2)](-), are examined by (-)ESI-IRMPD spectroscopy. Experimental and computational results are highly consistent and allow a reliable identification of the ion structures. In all complex ions examined the planar TMHA ligands are oriented perpendicular to each other around the metal ion, leading to a tetrahedral coordination sphere in which aluminium interacts with the enolate oxygen and heteroaryl nitrogen atoms available in each of the bidentate ligands.

  12. 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.

  13. 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...

  14. Receptors useful for gas phase chemical sensing

    SciTech Connect

    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).

  15. 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...

  16. 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.

  17. 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.

  18. 2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence

    NASA Astrophysics Data System (ADS)

    Blomberg, Sara; Zhou, Jianfeng; Gustafson, Johan; Zetterberg, Johan; Lundgren, Edvin

    2016-11-01

    In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be

  19. 2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence.

    PubMed

    Blomberg, Sara; Zhou, Jianfeng; Gustafson, Johan; Zetterberg, Johan; Lundgren, Edvin

    2016-11-16

    In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be

  20. 2D and 3D imaging of the gas phase close to an operating model catalyst by planar laser induced fluorescence.

    PubMed

    Blomberg, Sara; Zhou, Jianfeng; Gustafson, Johan; Zetterberg, Johan; Lundgren, Edvin

    2016-11-16

    In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be

  1. 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.

  2. Relationship between gas-phase chemistries and surface processes in fluorocarbon etch plasmas: A process rate model

    SciTech Connect

    Sant, S. P.; Nelson, C. T.; Overzet, L. J.; Goeckner, M. J.

    2009-07-15

    In a typical plasma tool, both etch and deposition occur simultaneously. Extensive experimental measurements are used to help develop a general model of etch and deposition processes. This model employs reaction probabilities, or surface averaged cross sections, to link the measurable surface processes, etch and deposition, to the flux of various species to the surfaces. Because the cross sections are quantum mechanical in nature, this surface rate model should be applicable to many low temperature plasma processing systems. Further, the parameters that might be important in reaction cross sections are known from quantum mechanics, e.g., species, energy, temperature, and impact angle. Such parameters might vary from system to system, causing the wide processing variability observed in plasma tools. Finally the model is used to compare measurements of ion flux, ion energy, and fluorocarbon radical flux to the measured process rates. It is found that the model appears to be consistent with calculations of gain/loss rates for the various radicals present in the discharge as well as measured etch and deposition rates.

  3. 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

  4. 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.

  5. Back propagation neural network model for predicting the performance of immobilized cell biofilters handling gas-phase hydrogen sulphide and ammonia.

    PubMed

    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/m(3) ·h, while the NH3 biofilter showed REs ranging from 60 to 100% at ILRs varying between 0.5 and 5.5 g NH3/m(3) ·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 (R (2)) values. The results from this predictive modeling work showed that BPNNs were able to predict the RE of both the ICBs efficiently.

  6. 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

  7. Gas phase chemistry in comets

    NASA Technical Reports Server (NTRS)

    Oppenheimer, M.

    1976-01-01

    The significance of gas phase reactions in determining the nuclear structure of comets is discussed. The sublimation of parent molecules such as H2O, CH4, CO2, and NH3 from the surface of the nucleus and their subsequent photodissociation and ionization in forming observed cometary molecular species are elaborated.

  8. 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.

  9. A model for the formation of airborne particulate matter based on the gas-phase adsorption on amorphous carbon blacks.

    PubMed Central

    Risby, T H; Sehnert, S S

    1988-01-01

    This paper reports the physicochemical properties that describe the adsorption of a series of solutes onto the surfaces of amorphous carbon blacks. Adsorption was studied at concentrations that correspond to low surface coverages and in the presence of volatile solvent diluents. The adsorbates and adsorbents were selected for their relevance as models for environmental agent-particle complexes originating from incomplete combustion. The data clearly show that the major factors that determine the strength of adsorption are the surface properties of the adsorbent and the intermolecular forces between the surface and the adsorbing molecule. The heat of adsorption data have been used to predict the lifetime of the absorbate-adsorbent complexes. PMID:3383817

  10. 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

  11. 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.

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

    PubMed Central

    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, ε-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. PMID:25338221

  13. Spectroscopic and modeling investigations of the gas phase chemistry and composition in microwave plasma activated B2H6/CH4/Ar/H2 mixtures.

    PubMed

    Ma, Jie; Richley, James C; Davies, David R W; Ashfold, Michael N R

    2010-09-23

    A comprehensive study of microwave (MW) activated B2H6/CH4/Ar/H2 plasmas used for the chemical vapor deposition of B-doped diamond is reported. Absolute column densities of ground state B atoms, electronically excited H(n = 2) atoms, and BH, CH, and C2 radicals have been determined by cavity ring down spectroscopy, as functions of height (z) above a molybdenum substrate and of the plasma process conditions (B2H6, CH4, and Ar partial pressures; total pressure, p; and supplied MW power, P). Optical emission spectroscopy has also been used to explore variations in the relative densities of electronically excited H atoms, H2 molecules, and BH, CH, and C2 radicals, as functions of the same process conditions. These experimental data are complemented by extensive 2D(r, z) modeling of the plasma chemistry, which result in substantial refinements to the existing B/C/H/O thermochemistry and chemical kinetics. Comparison with the results of analogous experimental/modeling studies of B2H6/Ar/H2 and CH4/Ar/H2 plasmas in the same MW reactor show that: (i) trace B2H6 additions have negligible effect on a pre-established CH4/Ar/H2 plasma; (ii) the spatial extent of the B and BH concentration profiles in a B2H6/CH4/Ar/H2 plasma is smaller than in a hydrocarbon-free B2H6/Ar/H2 plasma operating at the same p, P, etc.; (iii) B/C coupling reactions (probably supplemented by reactions involving trace O2 present as air impurity in the process gas mixture) play an important role in determining the local BHx (x = 0-3) radical densities; and (iv) gas phase B atoms are the most likely source of the boron that incorporates into the growing B-doped diamond film. PMID:20735120

  14. Gas-phase models of γ turns: Effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Chin, Wutharath; Piuzzi, François; Dognon, Jean-Pierre; Dimicoli, Iliana; Mons, Michel

    2005-08-01

    The conformations of laser-desorbed jet-cooled short peptide chains Ac -Phe-Xxx-NH2 (Xxx =Gly, Ala, Val, and Pro) have been investigated by IR/UV double resonance spectroscopy and density-functional-theory (DFT) quantum chemistry calculations. Singly γ-folded backbone conformations (βL-γ) are systematically observed as the most stable conformers, showing that in these two-residue peptide chains, the local conformational preference of each residue is retained (βL for Phe and γ turn for Xxx). Besides, β turns are also spontaneously formed but appear as minor conformers. The theoretical analysis suggests negligible inter-residue interactions of the main conformers, which enables us to consider these species as good models of γ turns. In the case of valine, two similar types of γ turns, differing by the strength of their hydrogen bond, have been found both experimentally and theoretically. This observation provides evidence for a strong flexibility of the peptide chain, whose minimum-energy structures are controlled by side-chain/backbone interactions. The qualitative conformational difference between the present species and the reversed sequence Ac -Xxx-Phe-NH2 is also discussed.

  15. Gas Phase Reactions of Ions Derived from Anionic Uranyl Formate and Uranyl Acetate Complexes

    NASA Astrophysics Data System (ADS)

    Perez, Evan; Hanley, Cassandra; Koehler, Stephen; Pestok, Jordan; Polonsky, Nevo; Van Stipdonk, Michael

    2016-09-01

    The gas-phase oxidation of doubly protonated peptides containing neutral basic residues to various products, including [M + H + O]+, [M - H]+, and [M - H - NH3]+, is demonstrated here via ion/ion reactions with periodate. It was previously demonstrated that periodate anions are capable of oxidizing disulfide bonds and methionine, tryptophan, and S-alkyl cysteine residues. However, in the absence of these easily oxidized sites, we show here that systems containing neutral basic residues can undergo oxidation. Furthermore, we show that these neutral basic residues primarily undergo different types of oxidation (e.g., hydrogen abstraction) reactions than those observed previously (i.e., oxygen transfer to yield the [M + H + O]+ species) upon gas-phase ion/ion reactions with periodate anions. This chemistry is illustrated with a variety of systems, including a series of model peptides, a cell-penetrating peptide containing a large number of unprotonated basic sites, and ubiquitin, a roughly 8.6 kDa protein.

  16. Spectroscopic studies of cold, gas-phase biomolecular ions

    NASA Astrophysics Data System (ADS)

    Rizzo, Thomas R.; Stearns, Jaime A.; Boyarkin, Oleg V.

    While the marriage of mass spectrometry and laser spectroscopy is not new, developments over the last few years in this relationship have opened up new horizons for the spectroscopic study of biological molecules. The combination of electrospray ionisation for producing large biological molecules in the gas phase together with cooled ion traps and multiple-resonance laser schemes are allowing spectroscopic investigation of individual conformations of peptides with more than a dozen amino acids. Highly resolved infrared spectra of single conformations of such species provide important benchmarks for testing the accuracy of theoretical calculations. This review presents a number of techniques employed in our laboratory and in others for measuring the spectroscopy of cold, gas-phase protonated peptides. We show examples that demonstrate the power of these techniques and evaluate their extension to still larger biological molecules.

  17. Manual gas-phase isothiocyanate degradation.

    PubMed

    Brandt, W F; Frank, G

    1988-02-01

    We describe a manual gas-phase isothiocyanate degradation procedure for the primary structure determination of proteins and peptides. The proteins and peptides are applied to a polybrene-coated glass fiber filter wedged into a small glass column. The phenylisothiocyanate is directly pipetted onto the filter disk. The coupling and cleavage reactions are performed in small desiccators containing trimethylamine and trifluoroacetic acid vapors, respectively. The wash and extraction steps are performed by allowing the suitable solvents to percolate through the filter disk. The extracted anilinothiazolinone is then converted to the phenylthiohydantoin and identified by any one of a number of described methods. Our results show that this method is very sensitive and that the reactions proceed faster than those of the published automated procedure. No expensive equipment is required and the manual degradation can be performed by a laboratory assistant. A large number of samples can be simultaneously subjected to the degradation under identical conditions, making this an ideal method for physicochemical investigations into the isothiocyanate degradation. We also use this method to screen HPLC fractions after enzymatic protein fragmentation. Manually sequenced glass filters can be transferred to the automated instrument for more extended degradations.

  18. 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.

  19. An Effective Continuum Model for the Liquid-to-Gas Phase Change in a Porous Medium Driven by Solute Diffusion: I. Constant Pressure Decline Rates

    SciTech Connect

    Tsimpanogiannis, Ioannis N.; Yortsos, Yanis C.

    2001-08-15

    This report, focuses on the isothermal gas phase growth from a supersaturated, slightly compressible, binary liquid in a porous medium. This is driven by mass transfer, the extent of which is controlled by the application of either a constant-rate decline of the system pressure or the withdrawal of the liquid at a constant rate. This report deals with the first process. Pressure depletion due to constant-rate liquid withdrawal is analyzed in a companion report .

  20. Gas-Phase Reactivity of Carboxylic Acid Functional Groups with Carbodiimides

    PubMed Central

    Prentice, Boone M.; Gilbert, Joshua D.; Stutzman, John R.; Forrest, William P.; McLuckey, Scott A.

    2012-01-01

    Gas-phase modification of carboxylic acid functionalities is performed via ion/ion reactions with carbodiimide reagents [N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide (CMC) and [3-(3-Ethylcarbodiimide-1-yl)propyl]trimethylaminium (ECPT). Gas-phase ion/ion covalent chemistry requires the formation of a long-lived complex. In this instance, the complex is stabilized by an electrostatic interaction between the fixed charge quaternary ammonium group of the carbodiimide reagent cation and the analyte dianion. Subsequent activation results in characteristic loss of an isocyanate derivative from one side of the carbodiimide functionality, a signature for this covalent chemistry. The resulting amide bond is formed on the analyte at the site of the original carboxylic acid. Reactions involving analytes that do not contain available carboxylic acid groups (e.g., they have been converted to sodium salts) or reagents that do not have the carbodiimide functionality do not undergo a covalent reaction. This chemistry is demonstrated using PAMAM generation 0.5 dendrimer, ethylenediaminetetraacetic acid (EDTA), and the model peptide DGAILDGAILD. This work demonstrates the selective gas-phase covalent modification of carboxylic acid functionalities. PMID:23208744

  1. 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.

  2. Structure and chemistry of the heteronuclear oxo-cluster [VPO4]•+: a model system for the gas-phase oxidation of small hydrocarbons.

    PubMed

    Dietl, Nicolas; Wende, Torsten; Chen, Kai; Jiang, Ling; Schlangen, Maria; Zhang, Xinhao; Asmis, Knut R; Schwarz, Helmut

    2013-03-01

    The heteronuclear oxo-cluster [VPO4](•+) is generated via electrospray ionization and investigated with respect to both its electronic structure as well as its gas-phase reactivity toward small hydrocarbons, thus permitting a comparison to the well-known vanadium-oxide cation [V2O4](•+). As described in previous studies, the latter oxide exhibits no or just minor reactivity toward small hydrocarbons, such as CH4, C2H6, C3H8, n-C4H10, and C2H4, while substitution of one vanadium by a phosphorus atom yields the reactive [VPO4](•+) ion; the latter brings about oxidative dehydrogenation (ODH) of saturated hydrocarbons, e.g., propane and butane as well as oxygen-atom transfer (OAT) to unsaturated hydrocarbons, e.g. ethene, at thermal conditions. Further, the gas-phase structure of [VPO4](•+) is determined by IR photodissociation spectroscopy and compared to that of [V2O4](•+). DFT calculations help to elucidate the reaction mechanism. The results underline the crucial role of phosphorus in terms of C-H bond activation of hydrocarbons by mixed VPO clusters.

  3. Structure and chemistry of the heteronuclear oxo-cluster [VPO4]•+: a model system for the gas-phase oxidation of small hydrocarbons.

    PubMed

    Dietl, Nicolas; Wende, Torsten; Chen, Kai; Jiang, Ling; Schlangen, Maria; Zhang, Xinhao; Asmis, Knut R; Schwarz, Helmut

    2013-03-01

    The heteronuclear oxo-cluster [VPO4](•+) is generated via electrospray ionization and investigated with respect to both its electronic structure as well as its gas-phase reactivity toward small hydrocarbons, thus permitting a comparison to the well-known vanadium-oxide cation [V2O4](•+). As described in previous studies, the latter oxide exhibits no or just minor reactivity toward small hydrocarbons, such as CH4, C2H6, C3H8, n-C4H10, and C2H4, while substitution of one vanadium by a phosphorus atom yields the reactive [VPO4](•+) ion; the latter brings about oxidative dehydrogenation (ODH) of saturated hydrocarbons, e.g., propane and butane as well as oxygen-atom transfer (OAT) to unsaturated hydrocarbons, e.g. ethene, at thermal conditions. Further, the gas-phase structure of [VPO4](•+) is determined by IR photodissociation spectroscopy and compared to that of [V2O4](•+). DFT calculations help to elucidate the reaction mechanism. The results underline the crucial role of phosphorus in terms of C-H bond activation of hydrocarbons by mixed VPO clusters. PMID:23432112

  4. 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.

  5. Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water.

    PubMed

    Wang, Zhi-Xiang; Duan, Yong

    2004-11-15

    The effects of solvation on the conformations and energies of alanine dipeptide (AD) have been studied by ab initio calculations up to MP2/cc-pVTZ//MP2/6-31G**, utilizing the polarizable continuum model (PCM) to mimic solvation effects. The energy surfaces in the gas phase, ether, and water bear similar topological features carved by the steric hindrance, but the details differ significantly due to the solvent effects. The gas-phase energy map is qualitatively consistent with the Ramachandran plot showing seven energy minima. With respect to the gas-phase map, the significant changes of the aqueous map include (1) the expanded low-energy regions, (2) the emergence of an energy barrier between C5-beta and alpha(R)-beta(2) regions, (3) a clearly pronounced alpha(R) minimum, a new beta-conformer, and the disappearance of the gas-phase global minimum, and (4) the shift of the dominant region in LEII from the gas-phase C7(ax) region to the alpha(L) region. These changes bring the map in water to be much closer to the Ramachandran plot than the gas-phase map. The solvent effects on the geometries include the elongation of the exposed N-H and C=O bonds, the shortening of the buried HN--CO peptide bonds, and the enhanced planarity of the peptide bonds. The energy surface in ether has features similar to those both in the gas phase and in water. The free energy order computed in the gas phase and in ether is in good agreement with experimental studies that concluded that C5 and C7(eq) are the dominant species in both the gas phase and nonpolar solvents. The free energy order in water is consistent with the experimental observation that the dominant C7(eq) in the nonpolar solvent was largely replaced by P(II)-like (i.e., beta) and alpha(R) in the strong polar solvents. Based on calculations on AD + 4H(2)O and other AD-water clusters, we suggest that explicit water-AD interactions may distort C5 and beta (or alpha(R) and beta) to an intermediate conformation. Our analysis

  6. Correlation between computed gas-phase and experimentally determined solution-phase infrared spectra: models of the iron-iron hydrogenase enzyme active site.

    PubMed

    Tye, Jesse W; Darensbourg, Marcetta Y; Hall, Michael B

    2006-09-01

    Gas-phase density functional theory calculations (B3LYP, double zeta plus polarization basis sets) are used to predict the solution-phase infrared spectra for a series of CO- and CN-containing iron complexes. It is shown that simple linear scaling of the computed C--O and C--N stretching frequencies yields accurate predictions of the the experimentally determined nu(CO) and nu(CN) values for a variety of complexes of different charges and in solvents of varying polarity. As examples of the technique, the resulting correlation is used to assign structures to spectroscopically observed but structurally ambiguous species in two different systems. For the (mu-SCH2CH2CH2S)[Fe(CO)3]2 complex in tetrahydrofuran solution, our calculations show that the initial electrochemical reduction process leads to a simple one-electron reduced product with a structure very similar to the (mu-SCH2CH2CH2S)[Fe(CO)3]2 parent complex. For the iron-iron hydrogenase enzyme active site, our computations show that the absence or presence of a water molecule near the distal iron center (the iron center further from the [4Fe4S] cluster and protein backbone) has very little effect on the predicted infrared spectra.

  7. Hydrated metal ions in the gas phase.

    PubMed

    Beyer, Martin K

    2007-01-01

    Studying metal ion solvation, especially hydration, in the gas phase has developed into a field that is dominated by a tight interaction between experiment and theory. Since the studied species carry charge, mass spectrometry is an indispensable tool in all experiments. Whereas gas-phase coordination chemistry and reactions of bare metal ions are reasonably well understood, systems containing a larger number of solvent molecules are still difficult to understand. This review focuses on the rich chemistry of hydrated metal ions in the gas phase, covering coordination chemistry, charge separation in multiply charged systems, as well as intracluster and ion-molecule reactions. Key ideas of metal ion solvation in the gas phase are illustrated with rare-gas solvated metal ions.

  8. Computational modeling of peptide-aptamer binding.

    PubMed

    Rhinehardt, Kristen L; Mohan, Ram V; Srinivas, Goundla

    2015-01-01

    Evolution is the progressive process that holds each living creature in its grasp. From strands of DNA evolution shapes life with response to our ever-changing environment and time. It is the continued study of this most primitive process that has led to the advancement of modern biology. The success and failure in the reading, processing, replication, and expression of genetic code and its resulting biomolecules keep the delicate balance of life. Investigations into these fundamental processes continue to make headlines as science continues to explore smaller scale interactions with increasing complexity. New applications and advanced understanding of DNA, RNA, peptides, and proteins are pushing technology and science forward and together. Today the addition of computers and advances in science has led to the fields of computational biology and chemistry. Through these computational advances it is now possible not only to quantify the end results but also visualize, analyze, and fully understand mechanisms by gaining deeper insights. The biomolecular motion that exists governing the physical and chemical phenomena can now be analyzed with the advent of computational modeling. Ever-increasing computational power combined with efficient algorithms and components are further expanding the fidelity and scope of such modeling and simulations. This chapter discusses computational methods that apply biological processes, in particular computational modeling of peptide-aptamer binding.

  9. Gas-phase diffusivity and tortuosity of structured soils.

    PubMed

    Kristensen, Andreas H; Thorbjørn, Anne; Jensen, Maria P; Pedersen, Mette; Moldrup, Per

    2010-06-25

    Modeling gas-phase diffusion of volatile contaminants in the unsaturated zone relies on soil-gas diffusivity models often developed for repacked and structureless soil columns. These suffer from the flaw of not reflecting preferential diffusion through voids and fractures in the soil, thus possibly causing an underestimation of vapor migration towards building foundations and vapor intrusion to indoor environments. We measured the ratio of the gas diffusion coefficient in soil and in free air (D(p)/D(0)) for 42 variously structured, intact, and unsaturated soil cores taken from 6 Danish sites. Whilst the results from structureless fine sand were adequately described using previously proposed models, results that were obtained from glacial clay till and limestone exhibited a dual-porosity behavior. Instead, these data were successfully described using a dual-porosity model for gas-phase diffusivity, considering a presence of drained fractures surrounded by a lower diffusivity matrix. Based on individual model fits, the tortuosity of fractures in till and limestone was found to be highest in samples with a total porosity <40%, suggesting soil compaction to affect the geometry of the fractures. In summary, this study highlights a potential order of magnitude underestimation associated in the use of classical models for prediction of subsurface gas-phase diffusion coefficients in heterogeneous and fractured soils.

  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. 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.

  12. Analytical model of peptide mass cluster centres with applications

    PubMed Central

    Wolski, Witold E; Farrow, Malcolm; Emde, Anne-Katrin; Lehrach, Hans; Lalowski, Maciej; Reinert, Knut

    2006-01-01

    Background The elemental composition of peptides results in formation of distinct, equidistantly spaced clusters across the mass range. The property of peptide mass clustering is used to calibrate peptide mass lists, to identify and remove non-peptide peaks and for data reduction. Results We developed an analytical model of the peptide mass cluster centres. Inputs to the model included, the amino acid frequencies in the sequence database, the average length of the proteins in the database, the cleavage specificity of the proteolytic enzyme used and the cleavage probability. We examined the accuracy of our model by comparing it with the model based on an in silico sequence database digest. To identify the crucial parameters we analysed how the cluster centre location depends on the inputs. The distance to the nearest cluster was used to calibrate mass spectrometric peptide peak-lists and to identify non-peptide peaks. Conclusion The model introduced here enables us to predict the location of the peptide mass cluster centres. It explains how the location of the cluster centres depends on the input parameters. Fast and efficient calibration and filtering of non-peptide peaks is achieved by a distance measure suggested by Wool and Smilansky. PMID:16995952

  13. 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

  14. Importance of the gas phase role to the prediction of energetic material behavior: An experimental study

    SciTech Connect

    Ali, A.N.; Son, S.F.; Asay, B.W.; Sander, R.K.

    2005-03-15

    Various thermal (radiative, conductive, and convective) initiation experiments are performed to demonstrate the importance of the gas phase role in combustion modeling of energetic materials (EM). A previously published condensed phase model that includes a predicted critical irradiance above which ignition is not possible is compared to experimental laser ignition results for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 2,4,6-trinitrotoluene (TNT). Experimental results conflict with the predicted critical irradiance concept. The failure of the model is believed to result from a misconception about the role of the gas phase in the ignition process of energetic materials. The model assumes that ignition occurs at the surface and that evolution of gases inhibits ignition. High speed video of laser ignition, oven cook-off and hot wire ignition experiments captures the ignition of HMX and TNT in the gas phase. A laser ignition gap test is performed to further evaluate the effect of gas phase laser absorption and gas phase disruption on the ignition process. Results indicate that gas phase absorption of the laser energy is probably not the primary factor governing the gas phase ignition observations. It is discovered that a critical gap between an HMX pellet and a salt window of 6 mm{+-}0.4 mm exists below which ignition by CO{sub 2} laser is not possible at the tested irradiances of 29 W/cm{sup 2} and 38 W/cm{sup 2} for HMX ignition. These observations demonstrate that a significant disruption of the gas phase, in certain scenarios, will inhibit ignition, independent of any condensed phase processes. These results underscore the importance of gas phase processes and illustrate that conditions can exist where simple condensed phase models are inadequate to accurately predict the behavior of energetic materials.

  15. The physical chemistry of Criegee intermediates in the gas phase

    SciTech Connect

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular and bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.

  16. The physical chemistry of Criegee intermediates in the gas phase

    DOE PAGES

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular andmore » bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.« less

  17. 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.

  18. Numerical Computation of Flame Spread over a Thin Solid in Forced Concurrent Flow with Gas-phase Radiation

    NASA Technical Reports Server (NTRS)

    Jiang, Ching-Biau; T'ien, James S.

    1994-01-01

    Excerpts from a paper describing the numerical examination of concurrent-flow flame spread over a thin solid in purely forced flow with gas-phase radiation are presented. The computational model solves the two-dimensional, elliptic, steady, and laminar conservation equations for mass, momentum, energy, and chemical species. Gas-phase combustion is modeled via a one-step, second order finite rate Arrhenius reaction. Gas-phase radiation considering gray non-scattering medium is solved by a S-N discrete ordinates method. A simplified solid phase treatment assumes a zeroth order pyrolysis relation and includes radiative interaction between the surface and the gas phase.

  19. 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.

  20. 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

  1. Experimental Thermochemistry of Gas Phase Cytosine Tautomers

    NASA Astrophysics Data System (ADS)

    Morrison, A. M.; Douberly, G. E.

    2011-06-01

    Enthalpies of interconversion are measured for the three lowest energy tautomers of isolated cytosine. The equilibrium distribution of tautomers near 600 K is frozen upon the capture of the gas phase species by low temperature helium nanodroplets. The temperature dependence of the gas phase cytosine tautomer populations is determined with infrared laser spectroscopy of the helium solvated species. The interconverison enthalpies obtained from the van't Hoff relation are 1.14 ± 0.21 and 1.63 ± 0.12 for the C31 rightleftharpoons C32 and C31 rightleftharpoons C1 equilibria, respectively. C31 and C32 are rotamers of an enol tautomer, and C1 is a keto tautomer. The interconversion enthalpies are compared to recent CCSD(T) thermochemistry calculations of cytosine tautomers.

  2. 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.

  3. How to select gas-phase filters

    SciTech Connect

    Groeger, G.; Winters, P.

    1997-10-01

    Removing airborne molecular contamination (AMC) from indoor industrial air is a challenging problem. Under OSHA, companies must mitigate harmful effects from corrosive, acid and alkaline gases to protect employee health. Equally important, corrosive gases tremendously impact and compromise operation of sensitive plant instrumentation and process control devices. Gases such as SO{sub 2}, H{sub 2}S, VOCs, etc., are present in many manufacturing facilities. These contaminants can be controlled to tolerable levels with gas-phase filtration techniques. Because each manufacturing facility has its own unique problem, a one-size-fits-all-solution is not possible. The presented examples and laboratory data evaluate several gas-phase control technologies under varying contaminant concentrations and air stream velocities. Using this information, engineers can find the best solution for their AMC problem.

  4. Modeling peptide mass fingerprinting data using the atomic composition of peptides.

    PubMed

    Gay, S; Binz, P A; Hochstrasser, D F; Appel, R D

    1999-12-01

    The peptide mass fingerprinting technique is commonly used for identifying proteins analyzed by mass spectrometry (MS) after enzymatic digestion. Our goal is to build a theoretical model that predicts the mass spectra of such digestion products in order to improve the identification and characterization of proteins using this technique. We present here the first step towards a full MS model. We have modeled MS spectra using the atomic composition of peptides and evaluated the influence that this composition may have on the MS signals. Peptides deduced from the SWISS-PROT protein sequence database were used for the calculation. To validate the model, the variability of the peptide mass distribution in SWISS-PROT was compared to two theoretical, randomly generated databases. Functions have been built that describe the behavior of the isotopic distribution according to the mass of peptides. The variability of these functions was analyzed. In particular, the influence of sulfur was studied. This work, while representing only a first step in the construction of an MS model, yields immediate practical results, as the new isotopic distribution model significantly improves peak detection in MS spectra used by protein identification algorithms.

  5. Gas-Phase Analysis of the Complex of Fibroblast GrowthFactor 1 with Heparan Sulfate: A Traveling Wave Ion Mobility Spectrometry (TWIMS) and Molecular Modeling Study

    NASA Astrophysics Data System (ADS)

    Zhao, Yuejie; Singh, Arunima; Xu, Yongmei; Zong, Chengli; Zhang, Fuming; Boons, Geert-Jan; Liu, Jian; Linhardt, Robert J.; Woods, Robert J.; Amster, I. Jonathan

    2016-09-01

    Fibroblast growth factors (FGFs) regulate several cellular developmental processes by interacting with cell surface heparan proteoglycans and transmembrane cell surface receptors (FGFR). The interaction of FGF with heparan sulfate (HS) is known to induce protein oligomerization, increase the affinity of FGF towards its receptor FGFR, promoting the formation of the HS-FGF-FGFR signaling complex. Although the role of HS in the signaling pathways is well recognized, the details of FGF oligomerization and formation of the ternary signaling complex are still not clear, with several conflicting models proposed in literature. Here, we examine the effect of size and sulfation pattern of HS upon FGF1 oligomerization, binding stoichiometry and conformational stability, through a combination of ion mobility (IM) and theoretical modeling approaches. Ion mobility-mass spectrometry (IMMS) of FGF1 in the presence of several HS fragments ranging from tetrasaccharide (dp4) to dodecasaccharide (dp12) in length was performed. A comparison of the binding stoichiometry of variably sulfated dp4 HS to FGF1 confirmed the significance of the previously known high-affinity binding motif in FGF1 dimerization, and demonstrated that certain tetrasaccharide-length fragments are also capable of inducing dimerization of FGF1. The degree of oligomerization was found to increase in the presence of dp12 HS, and a general lack of specificity for longer HS was observed. Additionally, collision cross-sections (CCSs) of several FGF1-HS complexes were calculated, and were found to be in close agreement with experimental results. Based on the (CCSs) a number of plausible binding modes of 2:1 and 3:1 FGF1-HS are proposed.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Oxidation of methionine residues in polypeptide ions via gas-phase ion/ion chemistry.

    PubMed

    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.

  11. 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.

  12. Gas-phase metalloprotein complexes interrogated by ion mobility-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Faull, Peter A.; Korkeila, Karoliina E.; Kalapothakis, Jason M.; Gray, Andrew; McCullough, Bryan J.; Barran, Perdita E.

    2009-06-01

    Gas-phase biomolecular structure may be explored through a number of analytical techniques. Ion mobility-mass spectrometry (IM-MS) continues to prove itself as a sensitive and reliable bioanalytical tool for gas-phase structure determination due to intense study and development over the past 15 years. A vast amount of research interest, especially in protein and peptide conformational studies has generated a wealth of structural information for biological systems from small peptides to megadalton-sized biomolecules. In this work, linear low field IM-MS has been used to study gas-phase conformations and determine rotationally averaged collision cross-sections of three metalloproteins--cytochrome c, haemoglobin and calmodulin. Measurements have been performed on the MoQToF, a modified QToF 1 instrument (Micromass UK Ltd., Manchester, UK) modified in house. Gas-phase conformations and cross-sections of multimeric cytochrome c ions of the form [xM + nH+]n+ for x = 1-3 (monomer to trimer) have been successfully characterised and measured. We believe these to be the first reported collision cross-sections of higher order multimeric cytochrome c. Haemoglobin is investigated to obtain structural information on the associative mechanism of tetramer formation. Haemoglobin molecules, comprising apo- and holo-monomer chains, dimer and tetramer are transferred to the gas phase under a range of solution conditions. Structural information on the proposed critical intermediate, semi-haemoglobin, is reported. Cross-sections of the calcium binding protein calmodulin have been obtained under a range of calcium-bound conditions. Metalloprotein collision cross-sections from ion mobility measurements are compared with computationally derived values from published NMR and X-ray crystallography structural data. Finally we consider the change in the density of the experimentally measured rotationally averaged collision cross-section for compact geometries of the electrosprayed proteins.

  13. Biomimetic peptide-based models of [FeFe]-hydrogenases: utilization of phosphine-containing peptides.

    PubMed

    Roy, Souvik; Nguyen, Thuy-Ai D; Gan, Lu; Jones, Anne K

    2015-09-01

    Two synthetic strategies for incorporating diiron analogues of [FeFe]-hydrogenases into short peptides via phosphine functional groups are described. First, utilizing the amine side chain of lysine as an anchor, phosphine carboxylic acids can be coupled via amide formation to resin-bound peptides. Second, artificial, phosphine-containing amino acids can be directly incorporated into peptides via solution phase peptide synthesis. The second approach is demonstrated using three amino acids each with a different phosphine substituent (diphenyl, diisopropyl, and diethyl phosphine). In total, five distinct monophosphine-substituted, diiron model complexes were prepared by reaction of the phosphine-peptides with diiron hexacarbonyl precursors, either (μ-pdt)Fe2(CO)6 or (μ-bdt)Fe2(CO)6 (pdt = propane-1,3-dithiolate, bdt = benzene-1,2-dithiolate). Formation of the complexes was confirmed by UV/Vis, FTIR and (31)P NMR spectroscopy. Electrocatalysis by these complexes is reported in the presence of acetic acid in mixed aqueous-organic solutions. Addition of water results in enhancement of the catalytic rates.

  14. 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.

  15. Gas-phase thermochemistry of chloropyridines

    NASA Astrophysics Data System (ADS)

    Gomes, José R. B.; Amaral, Luísa M. P. F.; Ribeiro da Silva, Manuel A. V.

    2005-04-01

    The gas-phase standard molar enthalpy of formation of the 2,3,5-trichloropyridine compound was derived from the enthalpies of combustion of the crystalline solid measured by rotating-bomb calorimetry and its enthalpy of sublimation obtained by Calvet microcalorimetry at T = 298.15 K. The standard enthalpies of formation for this compound and for the other chlorosubstituted pyridines were determined by DFT calculations. The experimental enthalpy of formation of 2,3,5-trichloropyridine is (65.8 ± 2.3) kJ mol -1, in excellent agreement with the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G(d) value. The affinity of pyridine to some metal cations was also calculated at the same DFT level of theory and compared with experimental data.

  16. Gas phase acidity of substituted benzenes

    NASA Astrophysics Data System (ADS)

    Bouchoux, Guy

    2011-04-01

    Deprotonation thermochemistry of benzene derivatives C 6H 5X (X = H, F, Cl, OH, NH 2, CN, CHO, NO 2, CH 3, C 2H 5, CHCH 2, CCH) has been examined at the G3B3 level of theory. For X = F, Cl, CN, CHO and NO 2, the most favorable deprotonation site is the ortho position of the phenyl ring. This regio-specificity is directly related to the field/inductive effect of the substituent. G3B3 gas phase acidities, Δ acidH° and Δ acidG°, compare within less than 4 kJ mol -1 with experimental data. A noticeable exception is nitrobenzene for which tabulated acidity appear to be underestimated by ca. 120 kJ mol -1.

  17. Gas phase grown silicon germanium nanocrystals

    NASA Astrophysics Data System (ADS)

    Mohan, A.; Tichelaar, F. D.; Kaiser, M.; Verheijen, M. A.; Schropp, R. E. I.; Rath, J. K.

    2016-09-01

    We report on the gas phase synthesis of highly crystalline and homogeneously alloyed Si1-xGex nanocrystals in continuous and pulsed plasmas. Agglomerated nanocrystals have been produced with remarkable control over their composition by altering the precursor GeH4 gas flow in a continuous plasma. We specially highlight that in the pulsed plasma mode, we obtain quantum-sized free standing alloy nanocrystals with a mean size of 7.3 nm. The presence of Si1-xGex alloy particles is confirmed with multiple techniques, i.e. Raman spectroscopy, XRD (Xray diffraction) and HRTEM (high resolution transmission electron microscopy) studies, with each of these methods consistently yielding the same composition. The nanocrystals synthesized here have potential applications in band-gap engineering for multijunction solar cells.

  18. NMR-derived model for a peptide-antibody complex

    SciTech Connect

    Zilber, B.; Scherf, T.; Anglister, J. ); Levitt, M. )

    1990-10-01

    The TE34 monoclonal antibody against cholera toxin peptide 3 (CTP3; VEVPGSQHIDSQKKA) was sequenced and investigated by two-dimensional transferred NOE difference spectroscopy and molecular modeling. The V{sub H} sequence of TE34, which does not bind cholera toxin, shares remarkable homology to that of TE32 and TE33, which are both anti-CTP3 antibodies that bind the toxin. However, due to a shortened heavy chain CDR3, TE34 assumes a radically different combining site structure. The assignment of the combining site interactions to specific peptide residues was completed by use of AcIDSQRKA, a truncated peptide analogue in which lysine-13 was substituted by arginine, specific deuteration of individual polypeptide chains of the antibody, and a computer model for the Fv fragment of TE34. NMR-derived distance restraints were then applied to the calculated model of the Fv to generate a three-dimensional structure of the TE34/CTP3 complex. The combining site was found to be a very hydrophobic cavity composed of seven aromatic residues. Charged residues are found in the periphery of the combining site. The peptide residues HIDSQKKA form a {beta}-turn inside the combining site. The contact area between the peptide and the TE34 antibody is 388 {Angstrom}{sup 2}, about half of the contact area observed in protein-antibody complexes.

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

    PubMed

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

    2015-10-01

    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.

  20. 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.

  1. 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.

  2. Effect of additives on gas-phase catalysis with immobilised Thermoanaerobacter species alcohol dehydrogenase (ADH T).

    PubMed

    Trivedi, A H; Spiess, A C; Daussmann, T; Büchs, J

    2006-07-01

    This paper presents a strategy for preparing an efficient immobilised alcohol dehydrogenase preparation for a gas-phase reaction. The effects of additives such as buffers and sucrose on the immobilisation efficiency (residual activity and protein loading) and on the gas-phase reaction efficiency (initial reaction rate and half-life) of Thermoanaerobacter sp. alcohol dehydrogenase were studied. The reduction of acetophenone to 1-phenylethanol under in situ cofactor regeneration using isopropanol as co-substrate was used as a model reaction at fixed reaction conditions (temperature and thermodynamic activities). A strongly enhanced thermostability of the enzyme in the gas-phase reaction was achieved when the enzyme was immobilised with 50 mM phosphate buffer (pH 7) containing sucrose five times the protein amount (on weight/weight basis). This resulted in a remarkable productivity of 200 g L(-1) day(-1) even at non-optimised reaction conditions. The interaction of additives with the enzyme and water affects the immobilisation and gas-phase efficiencies of the enzyme. However, it was not possible to predict the effect of additives on the gas-phase reaction efficiency even after knowing their effect on the immobilisation efficiency.

  3. Infrared spectra of gas-phase polycyclic aromatic hydrocarbon molecules

    SciTech Connect

    Zhang, Keqing; Guo, B.; Bernath, P.F.

    1995-12-31

    Recording the spectra of gas-phase polycyclic aromatic hydrocarbon molecules is of great astronomical interest. Infrared spectra of gas-phase naphthalene, pyrene, and chrysene were obtained in absorption and emission. The band positions and relative intensities were measured and compared with theoretical calculations. These data will be compared to the astronomical observations of the unidentified infrared emission bands.

  4. 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.

  5. 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.

  6. Molecular modeling in the design of peptidomimetics and peptide surrogates.

    PubMed

    Perez, Juan J; Corcho, Francesc; Llorens, Oriol

    2002-12-01

    The most important natural sources of new leads are plant extracts, bacterial broths, animal venoms and peptides isolated from living organisms. However, only the three first have been used extensively in the development of new therapeutic agents. This is probably due to the low pharmacological profile exhibited by peptides, that requires a lengthy transformation to make them suitable as new leads. In contrast, bioactive compounds isolated from the other sources are regularly closer to be used as lead compounds. Nevertheless, the sources for compounds of this category are nowadays scarce. In contrast, there are new bioactive peptides discovered quite often and reported as ligands for different receptors. Under these circumstances peptides appear as an attractive source of prospective new leads. In order to reduce the time involved in the design of a potential lead from a peptide, molecular modeling tools have been developed in the last few years. The purpose of the present work is to review the different techniques available and to report various successful examples of design of new peptidomimetics published in the literature.

  7. Optical properties of anthocyanins in the gas phase

    NASA Astrophysics Data System (ADS)

    Ge, Xiaochuan; Calzolari, Arrigo; Baroni, Stefano

    2015-01-01

    The gas-phase optical properties of the six most common anthocyanins are studied using time-dependent density-functional theory. Different anthocyanins are classified into three groups, according to the number of low-frequency peaks displayed in the UV-vis spectrum. This behavior is analyzed in terms of one-electron transitions and interaction effects, the latter being rationalized using a suitable double-pole model. Moving from PBE to hybrid exchange-correlation functionals results in a hypsochromic shift of the optical gap. While the colors thus predicted do not quite match those observed in solution, thus highlighting the importance of solvation effects, adoption of hybrid functionals remarkably determines a greater chromatic uniformity of different molecules, in qualitative agreement with experimental evidence in acidic solutions.

  8. 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.

  9. 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

  10. Gas-phase purification enables accurate, large-scale, multiplexed proteome quantification with isobaric tagging

    PubMed Central

    Wenger, Craig D; Lee, M Violet; Hebert, Alexander S; McAlister, Graeme C; Phanstiel, Douglas H; Westphall, Michael S; Coon, Joshua J

    2011-01-01

    We describe a mass spectrometry method, QuantMode, which improves the accuracy of isobaric tag–based quantification by alleviating the pervasive problem of precursor interference—co-isolation of impurities—through gas-phase purification. QuantMode analysis of a yeast sample ‘contaminated’ with interfering human peptides showed substantially improved quantitative accuracy compared to a standard scan, with a small loss of spectral identifications. This technique will allow large-scale, multiplexed quantitative proteomics analyses using isobaric tagging. PMID:21963608

  11. 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.

  12. 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.

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

    DOE PAGES

    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

  14. Peptide neuromodulation in invertebrate model systems

    PubMed Central

    Taghert, Paul H.; Nitabach, Michael N.

    2012-01-01

    Neuropeptides modulate neural circuits controlling adaptive animal behaviors and physiological processes, such as feeding/metabolism, reproductive behaviors, circadian rhythms, central pattern generation, and sensorimotor integration. Invertebrate model systems have enabled detailed experimental analysis using combined genetic, behavioral, and physiological approaches. Here we review selected examples of neuropeptide modulation in crustaceans, mollusks, insects, and nematodes, with a particular emphasis on the genetic model organisms Drosophila melanogaster and Caenorhabditis elegans, where remarkable progress has been made. On the basis of this survey, we provide several integrating conceptual principles for understanding how neuropeptides modulate circuit function, and also propose that continued progress in this area requires increased emphasis on the development of richer, more sophisticated behavioral paradigms. PMID:23040808

  15. Automated gas-phase purification for accurate, multiplexed quantification on a stand-alone ion trap mass spectrometer

    PubMed Central

    Vincent, Catherine E.; Rensvold, Jarred W.; Westphall, Michael S.; Pagliarini, David J.; Coon, Joshua J.

    2012-01-01

    Isobaric tagging enables the acquisition of highly-multiplexed proteome quantification but is hindered by the pervasive problem of precursor interference. The elimination of co-isolated contaminants prior to reporter tag generation can be achieved through the use of gas-phase purification via proton transfer ion/ion reactions (QuantMode); however, the original QuantMode technique was implemented on the high resolution linear ion trap-Orbitrap hybrid mass spectrometer enabled with electron transfer dissociation (ETD). Here we extend this technology to stand-alone linear ion trap systems (trapQuantMode). Facilitated by the use of inlet beam-type activation (i.e., trapHCD) for production and observation of the low mass-to-charge reporter region, this scan sequence comprises three separate events to maximize peptide identifications, minimize duty cycle requirements, and increase quantitative accuracy, precision, and dynamic range. Significant improvements in quantitative accuracy were attained over standard methods when using trapQuantMode (trapQM) to analyze an interference model system comprising tryptic peptides of yeast that we contaminated with human peptides. Finally, we demonstrate practical benefits of this method by analysis of the proteomic changes that occur during mouse skeletal muscle myoblast differentiation. While trapQM’s reduced duty cycle led to the identification of fewer proteins than conventional operation (4,050 vs. 2,964), trapQM identified more significant differences (>1.5 fold, 1,362 vs 1,132, respectively; P<0.05) between the proteomes of undifferentiated myoblasts and differentiated myotubes and nearly ten-fold more differences with changes greater than 5-fold (96 vs. 12). We further show that our trapQM dataset is superior for identifying changes in protein abundance that are consistent with the metabolic and structural changes known to accompany myotube formation. PMID:23046161

  16. Modeling of mixed-mode chromatography of peptides.

    PubMed

    Bernardi, Susanna; Gétaz, David; Forrer, Nicola; Morbidelli, Massimo

    2013-03-29

    Mixed-mode chromatographic materials are more and more often used for the purification of biomolecules, such as peptides and proteins. In many instances they in fact exhibit better selectivity values and therefore improve the purification efficiency compared to classical materials. In this work, a model to describe biomolecules retention in cation-exchange/reversed-phase (CIEX-RP) mixed-mode columns under diluted conditions has been developed. The model accounts for the effect of the salt and organic modifier concentration on the biomolecule Henry coefficient through three parameters: α, β and γ. The α parameter is related to the adsorption strength and ligand density, β represents the number of organic modifier molecules necessary to displace one adsorbed biomolecule and γ represents the number of salt molecules necessary to desorb one biomolecule. The latter parameter is strictly related to the number of charges on the biomolecule surface interacting with the ion-exchange ligands and it is shown experimentally that its value is close to the biomolecule net charge. The model reliability has been validated by a large set of experimental data including retention times of two different peptides (goserelin and insulin) on five columns: a reversed-phase C8 column and four CIEX-RP columns with different percentages of sulfonic groups and various concentration values of the salt and organic modifier. It has been found that the percentage of sulfonic groups on the surface strongly affects the peptides adsorption strength, and in particular, in the cases investigated, a CIEX ligand density around 0.04μmol/m(2) leads to optimal retention values. PMID:23433883

  17. 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.

  18. Estimation of gas phase mixing in packed beds

    SciTech Connect

    Frigerio, S.; Thunman, H.; Leckner, B.; Hermansson, S.

    2008-04-15

    An improved model is presented for estimation of the mixing of gaseous species in a packed bed for fuel conversion. In particular, this work clarifies the main characteristics of mixing of volatiles and oxidizers in a burning bed of high-volatile solid fuel. Expressions are introduced to represent the active role of degradation of the solid particles in the mixing within the gas phase. During drying and devolatilization the solids modify the behavior of the gas flow: the volatiles released from the surface of the particles increase the turbulence in the system, and hence the rates of the homogeneous reactions under mixing-limited conditions. Numerical experiments are carried out to test the validity of this conclusion regarding mixing in different geometries. The flow of volatiles leaving the fuel particles is shown to contribute significantly to mixing, especially at low air flows through a bed. However, the fraction of the particle surface where volatiles are released and its orientation in the bed should be better determined in order to increase the accuracy of the estimates of turbulent mixing. (author)

  19. Insights into the molecular interactions between aminopeptidase and amyloid beta peptide using molecular modeling techniques.

    PubMed

    Dhanavade, Maruti J; Sonawane, Kailas D

    2014-08-01

    Amyloid beta (Aβ) peptides play a central role in the pathogenesis of Alzheimer's disease. The accumulation of Aβ peptides in AD brain was caused due to overproduction or insufficient clearance and defects in the proteolytic degradation of Aβ peptides. Hence, Aβ peptide degradation could be a promising therapeutic approach in AD treatment. Recent experimental report suggests that aminopeptidase from Streptomyces griseus KK565 (SGAK) can degrade Aβ peptides but the interactive residues are yet to be known in detail at the atomic level. Hence, we developed the three-dimensional model of aminopeptidase (SGAK) using SWISS-MODEL, Geno3D and MODELLER. Model built by MODELLER was used for further studies. Molecular docking was performed between aminopeptidase (SGAK) with wild-type and mutated Aβ peptides. The docked complex of aminopeptidase (SGAK) and wild-type Aβ peptide (1IYT.pdb) shows more stability than the other complexes. Molecular docking and MD simulation results revealed that the residues His93, Asp105, Glu139, Glu140, Asp168 and His255 are involved in the hydrogen bonding with Aβ peptide and zinc ions. The interactions between carboxyl oxygen atoms of Glu139 of aminopeptidase (SGAK) with water molecule suggest that the Glu139 may be involved in the nucleophilic attack on Ala2-Glu3 peptide bond of Aβ peptide. Hence, amino acid Glu139 of aminopeptidase (SGAK) might play an important role to degrade Aβ peptides, a causative agent of Alzheimer's disease.

  20. 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

  1. 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

  2. Kinetic analysis of photocatalytic oxidation of gas-phase formaldehyde over titanium dioxide.

    PubMed

    Liu, Hongmin; Lian, Zhiwei; Ye, Xiaojiang; Shangguan, Wenfeng

    2005-07-01

    Degradation of formaldehyde with different initial concentration over titanium dioxide was carried out in a photocatalytic reactor. Photocatalytic rates were well described by the simplified Langmuir-Hinshelwood model. The kinetic analysis shows that the apparent first-order reaction coefficient is lower and half-life of photocatalysis is longer for low concentration than for high concentration formaldehyde. A network formation model of the photocatalytic products was established. Experimental results and analysis demonstrate that carbon dioxide concentration and carbon monoxide concentration in gas phase vary exponentially with the illumination time and may be even higher than gas-phase formaldehyde concentration if there is much pre-adsorbed formaldehyde in adsorption equilibrium on catalysts before illumination. Carbon monoxide is found to be one of the by-products during formaldehyde photooxidation.

  3. Prediction of peptide retention at different HPLC conditions from multiple linear regression models.

    PubMed

    Baczek, Tomasz; Wiczling, Paweł; Marszałł, Michał; Heyden, Yvan Vander; Kaliszan, Roman

    2005-01-01

    To quantitatively characterize the structure of a peptide and to predict its gradient retention time at given HPLC conditions three structural descriptors are used: (i) logarithm of the sum of retention times of the amino acids composing the peptide, log SumAA, (ii) logarithm of the van der Waals volume of the peptide, log VDW(Vol), (iii) and the logarithm of the peptide's calculated n-octanol-water partition coefficient, clog P. The log SumAA descriptor is obtained from empirical data for 20 natural amino acids, determined in a given HPLC system. The two other descriptors are calculated from the peptides' structural formulas using molecular modeling methods. The quantitative structure-retention relationships (QSRR), build by multiple linear regression, describe HPLC retention of peptide on a given chromatographic system on which the retention of the 20 amino acids was predetermined. A structurally diversified series of 98 peptides was employed. The predicted gradient retention times on several chromatographic systems were in good agreement with the experimental data. The QSRR equations, derived for a given system operated at variable gradient times and temperatures allowed for the prediction of peptide retention in that system. Matching the experimental HPLC retention to the theoretically predicted for a presumed peptide could facilitate original protein identification in proteomics. In conjunction with MS data, prediction of the retention time for a given peptide might be used to improve the confidence of peptide identifications and to increase the number of correctly identified peptides.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. CHAOS III: Gas-phase Abundances in NGC 5457

    NASA Astrophysics Data System (ADS)

    Croxall, Kevin V.; Pogge, Richard W.; Berg, Danielle A.; Skillman, Evan D.; Moustakas, John

    2016-10-01

    We present Large Binocular Telescope observations of 109 H ii regions in NGC 5457 (M101) obtained with the Multi-Object Double Spectrograph. We have robust measurements of one or more temperature-sensitive auroral emission lines for 74 H ii regions, permitting the measurement of “direct” gas-phase abundances. Comparing the temperatures derived from the different ionic species, we find: (1) strong correlations of T[N ii] with T[S iii] and T[O iii], consistent with little or no intrinsic scatter; (2) a correlation of T[S iii] with T[O iii], but with significant intrinsic dispersion; (3) overall agreement between T[N ii], T[S ii], and T[O ii], as expected, but with significant outliers; (4) the correlations of T[N ii] with T[S iii] and T[O iii] match the predictions of photoionization modeling while the correlation of T[S iii] with T[O iii] is offset from the prediction of photoionization modeling. Based on these observations, which include significantly more observations of lower excitation H ii regions, missing in many analyses, we inspect the commonly used ionization correction factors (ICFs) for unobserved ionic species and propose new empirical ICFs for S and Ar. We have discovered an unexpected population of H ii regions with a significant offset to low values in Ne/O, which defies explanation. We derive radial gradients in O/H and N/O which agree with previous studies. Our large observational database allows us to examine the dispersion in abundances, and we find intrinsic dispersions of 0.074 ± 0.009 in O/H and 0.095 ± 0.009 in N/O (at a given radius). We stress that this measurement of the intrinsic dispersion comes exclusively from direct abundance measurements of H ii regions in NGC 5457.

  9. 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).

  10. 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).

  11. Compelling Evidence for Lucky Survivor and Gas Phase Protonation: The Unified MALDI Analyte Protonation Mechanism

    NASA Astrophysics Data System (ADS)

    Jaskolla, Thorsten W.; Karas, Michael

    2011-06-01

    This work experimentally verifies and proves the two long since postulated matrix-assisted laser desorption/ionization (MALDI) analyte protonation pathways known as the Lucky Survivor and the gas phase protonation model. Experimental differentiation between the predicted mechanisms becomes possible by the use of deuterated matrix esters as MALDI matrices, which are stable under typical sample preparation conditions and generate deuteronated reagent ions, including the deuterated and deuteronated free matrix acid, only upon laser irradiation in the MALDI process. While the generation of deuteronated analyte ions proves the gas phase protonation model, the detection of protonated analytes by application of deuterated matrix compounds without acidic hydrogens proves the survival of analytes precharged from solution in accordance with the predictions from the Lucky Survivor model. The observed ratio of the two analyte ionization processes depends on the applied experimental parameters as well as the nature of analyte and matrix. Increasing laser fluences and lower matrix proton affinities favor gas phase protonation, whereas more quantitative analyte protonation in solution and intramolecular ion stabilization leads to more Lucky Survivors. The presented results allow for a deeper understanding of the fundamental processes causing analyte ionization in MALDI and may alleviate future efforts for increasing the analyte ion yield.

  12. Gas-phase NMR studies of alcohols. Intrinsic acidities

    NASA Astrophysics Data System (ADS)

    Chauvel, J. Paul; True, Nancy S.

    1985-05-01

    Gas-phase (≈100 Torr) 1H NMR spectra of eighteen simple aliphatic and unsaturated alcohols, four fluorinated alcohols, and two thiols were obtained at 148.6°C where hydrogen bonding has little effect on chemical shifts. For the methanol, ethanol, n-propanol, i-propanol, t-butanol, i- butanol, neopentanol, 2,2,2-trifluoroethanol and benzyl alcohol, the observed hydroxylic proton chemical shifts correlate with previously obtained relative gas-phase acidities from thermochemical analysis which employed equilibrium constants of proton transfer reactions measured via mass spectroscopic and ion cyclotron resonance techniques. The correlational dependence is 10.3(0.5) kcal/mol ppm with a correlation coefficient of 0.99. These results demonstrate that the trend of increasing acidity with increasing size of the alkyl substituent is also reflected in the neutral forms of the alcohols, indicating that the polarizability of the ionic forms is not the only determining factor in relative gas-phase acidities of alcohols. Although factors affecting the hydroxylic proton chemical shifts of the larger substituted and unsaturated alcohols are more complex, their observed 1H NMR spectra also reflect this trend. For methanol and ethanol observed gas-phase 1H chemical shifts are also compared with recent theoritical calculations. 3JHH coupling constants across CO bonds are ≈ 5.5 Hz, significantly smaller than typical 3JHH coupling across sp 3 hybrid C C bonds.

  13. NMR study of stable radicals in the gas phase

    NASA Astrophysics Data System (ADS)

    Obynochny, A. A.; Maryasov, A. G.; Shakirov, M. M.; Grigoriev, I. A.

    1993-05-01

    The temperature dependence of the NMR spectrum of methyl-substituted nitroxyl radical of the imidazoline series has been studied. The NMR signal induced by radicals in the gas phase has been observed. A shift of the lines of the NMR spectrum in the gas phase according to the Curie law is observed which allows one to determine the value of the hfi constant of the protons of different racial groups. The hfi constant for methyl-substituted radical within experimental accuracy coincides with those measured by other methods in the liquid phase. In the absorbed phase of the samples under study, a substantial contribution is made by the volumetric susceptibility of the liquid film. The diamagnetic contribution to the magnetic susceptibility of the radical in the liquid state has been measured (in the film of 2 × 10 -6). When the thickness of the adsorbed film is small, the molecular exchange between the liquid and gas phases becomes noticeable, causing a corresponding additional shift of the lines. The gas-kinetic cross section for the radical (120 Å 2) has been estimated from the temperature dependence of the line width in the gas phase.

  14. 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...

  15. 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)

  16. 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)

  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. 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.

  19. Development of a gas-phase stereochemical protocol. Intrinsic diastereoselectivity in hydride reductions of cyclohexanones

    SciTech Connect

    Yeunghaw Ho; Squires, R.R. )

    1992-12-30

    A common feature of classical, intuitive models and modern molecular orbital-based theories for diastereoselectivity in ketone reduction reactions is an emphasis on the structural and electronic properties of the substrate, despite the fact that the stereochemical outcome of these reactions often displays marked sensitivity to the solvent and the type of counter-ion employed with ionic and polar reducing agents. One way to separate intrinsic and extrinsic effects on the stereochemistry of ketone reduction reactions is to examine them in the gas phase, where solvent and counterion effects are absent. The authors describe here an experimental method for distinguishing the diastereomeric products of gas-phase hydride reduction reactions, and its application in determining the intrinsic diastereoselectivity involved in reductions of alkyl-substituted cyclohexanones. 1 tab.

  20. Determination of gas phase adsorption isotherms--a simple constant volume method.

    PubMed

    Kim, Daekeun; Cai, Zhangli; Sorial, George A

    2006-08-01

    Single and ternary solute gas phase adsorption isotherms were conducted in this study to evaluate the effectiveness of a simple constant volume method, which was utilized by using Tedlar gas sampling bags as a constant volume batch reactor. For this purpose, gas phase adsorption of toluene, methyl ethyl ketone (MEK), and methyl isobutyl ketone (MIBK) on two types of activated carbons, BPL-bituminous base and OVC--coconut base, were investigated. For the single solute adsorption, the experimental adsorption data were found to be well correlated with Freundlich and Myers adsorption equations. The pore size distribution of adsorbents was found to affect their adsorption capacities; its effect was dependant on the solute concentration. The ternary adsorption experimental isotherms were accurately predicted by using the well-known model, i.e., ideal adsorbed solution theory (IAST).

  1. Uridine Nucleoside Thiation: Gas-Phase Structures and Energetics

    NASA Astrophysics Data System (ADS)

    Hamlow, Lucas; Lee, Justin; Rodgers, M. T.; Berden, Giel; Oomens, Jos

    2016-06-01

    The naturally occurring thiated uridine nucleosides, 4-thiouridine (s4Urd) and 2-thiouridine (s2Urd), play important roles in the function and analysis of a variety of RNAs. 2-Thiouridine and its C5 modified analogues are commonly found in tRNAs and are believed to play an important role in codon recognition possibly due to their different structure, which has been shown by NMR to be predominantly C3'-endo. 2-Thiouridine may also play an important role in facilitating nonenzymatic RNA replication and transcription. 4-Thiouridine is a commonly used photoactivatable crosslinker that is often used to study RNA-RNA and RNA-protein cross-linking behavior. Differences in the base pairing between uracil and 4-thiouracil with adenine and guanine are an important factor in their role as a cross linker. The photoactivity of s4Urd may also aid in preventing near-UV lethality in cells. An understanding of their intrinsic structure in the gas-phase may help further elucidate the roles these modified nucleosides play in the regulation of RNAs. In this work, infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of s2Urd and s4Urd were collected in the IR fingerprint region. Structural information is determined by comparison with theoretical linear IR spectra generated from density functional theory calculations using molecular modeling to generate low-energy candidate structures. Present results are compared with analogous results for the protonated forms of uridine and 2'-deoxyuridine as well as solution phase NMR data and crystal structures.

  2. 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.

  3. Gas-phase basicities of polyfunctional molecules. Part 4: Carbonyl groups as basic sites.

    PubMed

    Bouchoux, Guy

    2015-01-01

    This article constitutes the fourth part of a general review of the gas-phase protonation thermochemistry of polyfunctional molecules (Part 1: Theory and methods, Mass Spectrom Rev 2007, 26:775-835, Part 2: Saturated basic sites, Mass Spectrom Rev 2012, 31:353-390, Part 3: Amino acids, Mass Spectrom Rev 2012, 31:391-435). This fourth part is devoted to carbonyl containing polyfunctional molecules. After a short reminder of the methods of determination of gas-phase basicity and the underlying physicochemical concepts, specific examples are examined under two major chapters. In the first one, aliphatic and unsaturated (conjugated and cyclic) ketones, diketones, ketoalcohols, and ketoethers are considered. A second chapter describes the protonation energetic of gaseous acids and derivatives including diacids, diesters, diamides, anhydrides, imides, ureas, carbamates, amino acid derivatives, and peptides. Experimental data were re-evaluated according to the presently adopted basicity scale. Structural and energetic information given by G3 and G4 quantum chemistry computations on typical systems are presented.

  4. 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.

  5. 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.

  6. Ion yields for some salts in MALDI: mechanism for the gas-phase ion formation from preformed ions.

    PubMed

    Moon, Jeong Hee; Shin, Young Sik; Bae, Yong Jin; Kim, Myung Soo

    2012-01-01

    Preformed ion emission is the main assumption in one of the prevailing theories for peptide and protein ion formation in matrix-assisted laser desorption ionization (MALDI). Since salts are in preformed ion forms in the matrix-analyte mixture, they are ideal systems to study the characteristics of preformed ion emission. In this work, a reliable method to measure the ion yield (IY) in MALDI was developed and used for a solid salt benzyltriphenylphosphonium chloride and two room-temperature ionic liquids 1-butyl-3-methylimidazolium hexafluorophosphate and trihexyltetradecylphosphonium bis(2,4,4-trimethylpentyl)phosphinate. IY for the matrix (α-cyano-4-hydroxycinnamic acid, CHCA) was also measured. Taking 1 pmol salts in 25 nmol CHCA as examples, IYs for three salts were similar, (4-8) × 10(-4), and those for CHCA were (0.8-1.2) × 10(-7). Even though IYs for the salts and CHCA remained virtually constant at low analyte concentration, they decreased as the salt concentrations increased. Two models, Model 1 and Model 2, were proposed to explain low IYs for the salts and the concentration dependences. Both models are based on the fact that the ion-pair formation equilibrium is highly shifted toward the neutral ion pair. In Model 1, the gas-phase analyte cations were proposed to originate from the same cations in the solid that were dielectrically screened from counter anions by matrix neutrals. In Model 2, preformed ions were assumed to be released from the solid sample in the form of neutral ion pairs and the anions in the ion pairs were assumed to be eliminated via reactions with matrix-derived cations.

  7. Radical Formation in the Gas-Phase Ozonolysis of Deprotonated Cysteine.

    PubMed

    Khairallah, George N; Maccarone, Alan T; Pham, Huong T; Benton, Timothy M; Ly, Tony; da Silva, Gabriel; Blanksby, Stephen J; O'Hair, Richard A J

    2015-10-26

    Although the deleterious effects of ozone on the human respiratory system are well-known, many of the precise chemical mechanisms that both cause damage and afford protection in the pulmonary epithelial lining fluid are poorly understood. As a key first step to elucidating the intrinsic reactivity of ozone with proteins, its reactions with deprotonated cysteine [Cys-H](-) are examined in the gas phase. Reaction proceeds at near the collision limit to give a rich set of products including 1) sequential oxygen atom abstraction reactions to yield cysteine sulfenate, sulfinate and sulfonate anions, and significantly 2) sulfenate radical anions formed by ejection of a hydroperoxy radical. The free-radical pathway occurs only when both thiol and carboxylate moieties are available, implicating electron-transfer as a key step in this reaction. This novel and facile reaction is also observed in small cys-containing peptides indicating a possible role for this chemistry in protein ozonolysis. PMID:26480331

  8. Binding Energies of Protonated Betaine Complexes: A Probe of Zwitterion Structure in the Gas Phase

    PubMed Central

    Price, William D.; Jockusch, Rebecca A.

    2005-01-01

    The dissociation kinetics of proton-bound dimers of betaine with molecules of comparable gas-phase basicity were investigated using blackbody infrared radiative dissociation (BIRD). Threshold dissociation energies were obtained from these data using master equation modeling. For bases that have comparable or higher gas-phase basicity, the binding energy of the protonated base·betaine complex is ~1.4 eV. For molecules that are ~2 kcal/mol or more less basic, the dissociation energy of the complexes is ~1.2 eV. The higher binding energy of the former is attributed to an ion–zwitterion structure which has a much larger ion–dipole interaction. The lower binding energy for molecules that are ~2 kcal/mol or more less basic indicates that an ion–molecule structure is more favored. Semiempirical calculations at both the AM1 and PM3 levels indicate the most stable ion–molecule structure is one in which the base interacts with the charged quaternary ammonium end of betaine. These results indicate that the measurement of binding energies of neutral molecules to biological ions could provide a useful probe for the presence of zwitterions and salt bridges in the gas phase. From the BIRD data, the gas-phase basicity of betaine obtained from the kinetic method is found to be 239.2 ± 1.0 kcal/mol. This value is in excellent agreement with the value of 239.3 kcal/mol (298 K) from ab initio calculations at the MP2/6-31+g** level. The measured value is slightly higher than those reported previously. This difference is attributed to entropy effects. The lower ion internal energy and longer time frame of BIRD experiments should provide values closer to those at standard temperature. PMID:16543945

  9. 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.

  10. 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.

  11. Insights into gas-phase reaction mechanisms of small carbon radicals using isomer-resolved product detection.

    PubMed

    Trevitt, Adam J; Goulay, Fabien

    2016-02-17

    For reactive gas-phase environments, including combustion, extraterrestrials atmospheres and our Earth's atmosphere, the availability of quality chemical data is essential for predictive chemical models. These data include reaction rate coefficients and product branching fractions. This perspective overviews recent isomer-resolved production detection experiments for reactions of two of the most reactive gas phase radicals, the CN and CH radicals, with a suite of small hydrocarbons. A particular focus is given to flow-tube experiments using synchrotron photoionization mass spectrometry. Coupled with computational studies and other experiment techniques, flow tube isomer-resolved product detection have provided significant mechanistic details of these radical + neutral reactions with some general patterns emerging.

  12. 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.

  13. 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

  14. Gas-Phase Studies of Formamidopyrimidine Glycosylase (Fpg) Substrates.

    PubMed

    Kiruba, G S M; Xu, Jiahui; Zelikson, Victoria; Lee, Jeehiun K

    2016-03-01

    Gas-phase thermochemical properties (tautomerism, acidity, and proton affinity) have been measured and calculated for a series of nucleobase derivatives that have not heretofore been examined under vacuum. The studied species are substrates for the enzyme formamidopyrimidine glycosylase (Fpg), which cleaves damaged nucleobases from DNA. The gas-phase results are compared and contrasted to solution-phase data, to afford insight into the Fpg mechanism. Calculations are also used to probe the energetics of various possible mechanisms and to predict isotope effects that could potentially allow for discrimination between different mechanisms. Specifically, (18) O substitution at the ribose O4' is predicted to result in a normal kinetic isotope effect (KIE) for a ring-opening "endocyclic" mechanism and an inverse KIE for a direct base excision "exocyclic" pathway.

  15. Gas-Phase Studies of Formamidopyrimidine Glycosylase (Fpg) Substrates.

    PubMed

    Kiruba, G S M; Xu, Jiahui; Zelikson, Victoria; Lee, Jeehiun K

    2016-03-01

    Gas-phase thermochemical properties (tautomerism, acidity, and proton affinity) have been measured and calculated for a series of nucleobase derivatives that have not heretofore been examined under vacuum. The studied species are substrates for the enzyme formamidopyrimidine glycosylase (Fpg), which cleaves damaged nucleobases from DNA. The gas-phase results are compared and contrasted to solution-phase data, to afford insight into the Fpg mechanism. Calculations are also used to probe the energetics of various possible mechanisms and to predict isotope effects that could potentially allow for discrimination between different mechanisms. Specifically, (18) O substitution at the ribose O4' is predicted to result in a normal kinetic isotope effect (KIE) for a ring-opening "endocyclic" mechanism and an inverse KIE for a direct base excision "exocyclic" pathway. PMID:26894440

  16. 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.

  17. The Nucleoside Uridine Isolated in the Gas Phase**

    PubMed Central

    Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2016-01-01

    Herein we present the first experimental observation of the isolated nucleoside uridine, placed in the gas phase by laser ablation and characterized by Fourier transform microwave techniques. Free from the bulk effects of their native environments, anti/C2’-endo-g+ conformation has been revealed as the most stable form of uridine. Intramolecular hydrogen bonds involving uracil and ribose moieties have been found to play an important role in the stabilization of the nucleoside. PMID:25683559

  18. The nucleoside uridine isolated in the gas phase.

    PubMed

    Peña, Isabel; Cabezas, Carlos; Alonso, José L

    2015-03-01

    Herein we present the first experimental observation of the isolated nucleoside uridine, placed in the gas phase by laser ablation and characterized by Fourier transform (FT) microwave techniques. Free from the bulk effects of their native environments, anti/C2'-endo-g+ conformation has been revealed as the most stable form of uridine. Intramolecular hydrogen bonds involving uracil and ribose moieties have been found to play an important role in the stabilization of the nucleoside.

  19. Gas phase chemical detection with an integrated chemical analysis system

    SciTech Connect

    CASALNUOVO,STEPHEN A.; FRYE-MASON,GREGORY CHARLES; KOTTENSTETTE,RICHARD; HELLER,EDWIN J.; MATZKE,CAROLYN M.; LEWIS,PATRICK R.; MANGINELL,RONALD P.; BACA,ALBERT G.; HIETALA,VINCENT M.

    2000-04-12

    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 preconcentrator 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.

  20. 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...

  1. C-peptide promotes lesion development in a mouse model of arteriosclerosis.

    PubMed

    Vasic, Dusica; Marx, Nikolaus; Sukhova, Galina; Bach, Helga; Durst, Renate; Grüb, Miriam; Hausauer, Angelina; Hombach, Vinzenz; Rottbauer, Wolfgang; Walcher, Daniel

    2012-04-01

    Patients with insulin resistance and early type 2 diabetes exhibit an increased propensity to develop a diffuse and extensive pattern of arteriosclerosis. Typically, these patients show elevated serum levels of the proinsulin cleavage product C-peptide and immunohistochemical data from our group revealed C-peptide deposition in early lesions of these individuals. Moreover, in vitro studies suggest that C-peptide could promote atherogenesis. This study examined whether C-peptide promotes vascular inflammation and lesion development in a mouse model of arteriosclerosis. ApoE-deficient mice on a high fat diet were treated with C-peptide or control injections for 12 weeks and the effect on lesion size and plaque composition was analysed. C-peptide treatment significantly increased C-peptide blood levels by 4.8-fold without having an effect on glucose or insulin levels, nor on the lipid profile. In these mice, C-peptide deposition in atherosclerotic plaques was significantly increased compared with controls. Moreover, lesions of C-peptide-treated mice contained significantly more macrophages (1.6 ± 0.3% versus 0.7 ± 0.2% positive area; P < 0.01) and more vascular smooth muscle cells (4.8 ± 0.6% versus 2.4 ± 0.3% positive area; P < 0.01). Finally, lipid deposition measured by Oil-red-O staining in the aortic arch was significantly higher in the C-peptide group compared with controls. Our results demonstrate that elevated C-peptide levels promote inflammatory cell infiltration and lesion development in ApoE-deficient mice without having metabolic effects. These data obtained in a mouse model of arteriosclerosis support the hypothesis that C-peptide may have an active role in atherogenesis in patients with diabetes and insulin resistance.

  2. A hypothetical model for the peptide binding domain of hsp70 based on the peptide binding domain of HLA.

    PubMed Central

    Rippmann, F; Taylor, W R; Rothbard, J B; Green, N M

    1991-01-01

    The sequences of the peptide binding domains of 33 70 kd heat shock proteins (hsp70) have been aligned and a consensus secondary structure has been deduced. Individual members showed no significant deviation from the consensus, which showed a beta 4 alpha motif repeated twice, followed by two further helices and a terminus rich in Pro and Gly. The repeated motif could be aligned with the secondary structure of the functionally equivalent peptide binding domain of human leucocyte antigen (HLA) class I maintaining equivalent residues in structurally important positions in the two families and a model was built based on this alignment. The interaction of this domain with the ATP domain is considered. The overall model is shown to be consistent with the properties of products of chymotryptic cleavage. PMID:2022182

  3. 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

  4. Fundamental thermochemical properties of amino acids: gas-phase and aqueous acidities and gas-phase heats of formation.

    PubMed

    Stover, Michele L; Jackson, Virgil E; Matus, Myrna H; Adams, Margaret A; Cassady, Carolyn J; Dixon, David A

    2012-03-01

    The gas-phase acidities of the 20 L-amino acids have been predicted at the composite G3(MP2) level. A broad range of structures of the neutral and anion were studied to determine the lowest energy conformer. Excellent agreement is found with the available experimental gas-phase deprotonation enthalpies, and the calculated values are within experimental error. We predict that tyrosine is deprotonated at the CO(2)H site. Cysteine is predicted to be deprotonated at the SH but the proton on the CO(2)H is shared with the S(-) site. Self-consistent reaction field (SCRF) calculations with the COSMO parametrization were used to predict the pK(a)'s of the non-zwitterion form in aqueous solution. The differences in the non-zwitterion pK(a) values were used to estimate the free energy difference between the zwitterion and nonzwitterion forms in solution. The heats of formation of the neutral compounds were calculated from atomization energies and isodesmic reactions to provide the first reliable set of these values in the gas phase. Further calculations were performed on five rare amino acids to predict their heats of formation, acidities, and pK(a) values.

  5. Development of an in vitro digestive model for studying the peptide profile of breast milk.

    PubMed

    Dall'Asta, Chiara; Florio, Paola; Lammardo, Anna Maria; Prandi, Barbara; Mazzeo, Teresa; Budelli, Andrea; Pellegrini, Nicoletta

    2015-01-01

    Human milk is a highly valuable food for newborns and infants. Its protein fraction plays an important role for the development of the newborn. In the present study, an in vitro digestive model, developed for resembling closely the digestive system of an infant, was applied to human milk in order to identify and characterize the peptide profile. The peptide profile obtained after digestion was analyzed by μLC-LTQ-Orbitrap-MS. A total of 149 peptides from β-casein, 30 peptides from α-lactalbumin, 26 peptides from αs1-casein, 24 peptides from κ-casein, 28 peptides from osteopontin, and 29 from lactoferrin was recovered. The identified peptide profile of partially hydrolyzed proteins, such as caseins, α-lactalbumin, and osteopontin, was different from that previously reported demonstrating a different performance of the developed neonatal digestive system with respect to other previously applied. These results would be useful as a starting point to investigate the physiological function of breast milk peptides.

  6. 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

  7. C-peptide promotes lesion development in a mouse model of arteriosclerosis

    PubMed Central

    Vasic, Dusica; Marx, Nikolaus; Sukhova, Galina; Bach, Helga; Durst, Renate; Grüb, Miriam; Hausauer, Angelina; Hombach, Vinzenz; Rottbauer, Wolfgang; Walcher, Daniel

    2012-01-01

    Abstract Patients with insulin resistance and early type 2 diabetes exhibit an increased propensity to develop a diffuse and extensive pattern of arteriosclerosis. Typically, these patients show elevated serum levels of the proinsulin cleavage product C-peptide and immunohistochemical data from our group revealed C-peptide deposition in early lesions of these individuals. Moreover, in vitro studies suggest that C-peptide could promote atherogenesis. This study examined whether C-peptide promotes vascular inflammation and lesion development in a mouse model of arteriosclerosis. ApoE-deficient mice on a high fat diet were treated with C-peptide or control injections for 12 weeks and the effect on lesion size and plaque composition was analysed. C-peptide treatment significantly increased C-peptide blood levels by 4.8-fold without having an effect on glucose or insulin levels, nor on the lipid profile. In these mice, C-peptide deposition in atherosclerotic plaques was significantly increased compared with controls. Moreover, lesions of C-peptide–treated mice contained significantly more macrophages (1.6 ± 0.3% versus 0.7 ± 0.2% positive area; P < 0.01) and more vascular smooth muscle cells (4.8 ± 0.6% versus 2.4 ± 0.3% positive area; P < 0.01). Finally, lipid deposition measured by Oil-red-O staining in the aortic arch was significantly higher in the C-peptide group compared with controls. Our results demonstrate that elevated C-peptide levels promote inflammatory cell infiltration and lesion development in ApoE-deficient mice without having metabolic effects. These data obtained in a mouse model of arteriosclerosis support the hypothesis that C-peptide may have an active role in atherogenesis in patients with diabetes and insulin resistance. PMID:21707916

  8. 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

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

    PubMed

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

    2015-12-04

    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.

  10. Gas-phase chemistry of ruthenium and rhodium carbonyl complexes.

    PubMed

    Cao, Shiwei; Wang, Yang; Qin, Zhi; Fan, Fangli; Haba, Hiromitsu; Komori, Yukiko; Wu, Xiaolei; Tan, Cunmin; Zhang, Xin

    2016-01-01

    Short-lived ruthenium and rhodium isotopes were produced from a (252)Cf spontaneous fission (SF) source. Their volatile carbonyl complexes were formed in gas-phase reactions in situ with the carbon-monoxide containing gas. A gas-jet system was employed to transport the volatile carbonyls from the recoil chamber to the chemical separation apparatus. The gas-phase chemical behaviors of these carbonyl complexes were studied using an online low temperature isothermal chromatography (IC) technique. Long IC columns made up of FEP Teflon were used to obtain the chemical information of the high-volatile Ru and Rh carbonyls. By excluding the influence of precursor effects, short-lived isotopes of (109-110)Ru and (111-112)Rh were used to represent the chemical behaviours of Ru and Rh carbonyls. Relative chemical yields of about 75% and 20% were measured for Ru(CO)5 and Rh(CO)4, respectively, relative to the yields of KCl aerosols transported in Ar gas. The adsorption enthalpies of ruthenium and rhodium carbonyl complexes on a Teflon surface were determined to be around ΔHads = -33(+1)(-2) kJ mol(-1) and -36(+2)(-1) kJ mol(-1), respectively, by fitting the breakthrough curves of the corresponding carbonyl complexes with a Monte Carlo simulation program. Different from Mo and Tc carbonyls, a small amount of oxygen gas was found to be not effective for the chemical yields of ruthenium and rhodium carbonyl complexes. The general chemical behaviors of short-lived carbonyl complexes of group VI-IX elements were discussed, which can be used in the future study on the gas-phase chemistry of superheavy elements - Bh, Hs, and Mt carbonyls. PMID:26573993

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Discriminating Properties of Alkali Metal Ions Towards the Constituents of Proteins and Nucleic Acids. Conclusions from Gas-Phase and Theoretical Studies.

    PubMed

    Rodgers, Mary T; Armentrout, Peter B

    2016-01-01

    Quantitative insight into the structures and thermodynamics of alkali metal cations interacting with biological molecules can be obtained from studies in the gas phase combined with theoretical work. In this chapter, the fundamentals of the experimental and theoretical techniques are first summarized and results for such work on complexes of alkali metal cations with amino acids, small peptides, and nucleobases are reviewed. Periodic trends in how these interactions vary as the alkali metal cations get heavier are highlighted.

  17. Design of amphiphilic oligopeptides as models for fine tuning peptide assembly with plasmid DNA.

    PubMed

    Goparaju, Geetha N; Gupta, Pardeep K

    2014-08-01

    We discuss the design of novel amphiphilic oligopeptides with hydrophobic and cationic amino acids to serve as models to understand peptide-DNA assembly. Biophysical and thermodynamic characterization of interaction of these amphiphilic peptides with plasmid DNA is presented. Peptides with at least +4 charges favor stable complex formation. Surface potential is dependent on the type of hydrophobic amino acid for a certain charge. Thermodynamically it is a spontaneous interaction between most of the peptides and plasmid DNA. Lys(7) and Tyr peptides with +4/+5 charges indicate cooperative binding with pDNA without saturation of interaction while Val(2)-Gly-Lys(4), Val-Gly-Lys(5), and Phe-Gly-Lys(5) lead to saturation of interaction indicating condensed pDNA within the range of N/Ps studied. We show that the biophysical properties of DNA-peptide complexes could be modulated by design and the peptides presented here could be used as building blocks for creating DNA-peptide complexes for various biomedical applications, mainly nucleic acid delivery.

  18. 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

  19. 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

  20. 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.

  1. Collision cross sections of proteins and their complexes: a calibration framework and database for gas-phase structural biology.

    PubMed

    Bush, Matthew F; Hall, Zoe; Giles, Kevin; Hoyes, John; Robinson, Carol V; Ruotolo, Brandon T

    2010-11-15

    Collision cross sections in both helium and nitrogen gases were measured directly using a drift cell with RF ion confinement inserted within a quadrupole/ion mobility/time-of-flight hybrid mass spectrometer (Waters Synapt HDMS, Manchester, U.K.). Collision cross sections for a large set of denatured peptide, denatured protein, native-like protein, and native-like protein complex ions are reported here, forming a database of collision cross sections that spans over 2 orders of magnitude. The average effective density of the native-like ions is 0.6 g cm(-3), which is significantly lower than that for the solvent-excluded regions of proteins and suggests that these ions can retain significant memory of their solution-phase structures rather than collapse to globular structures. Because the measurements are acquired using an instrument that mimics the geometry of the commercial Synapt HDMS instrument, this database enables the determination of highly accurate collision cross sections from traveling-wave ion mobility data through the use of calibration standards with similar masses and mobilities. Errors in traveling-wave collision cross sections determined for native-like protein complexes calibrated using other native-like protein complexes are significantly less than those calibrated using denatured proteins. This database indicates that collision cross sections in both helium and nitrogen gases can be well-correlated for larger biomolecular ions, but non-correlated differences for smaller ions can be more significant. These results enable the generation of more accurate three-dimensional models of protein and other biomolecular complexes using gas-phase structural biology techniques.

  2. DSMC Convergence for Microscale Gas-Phase Heat Conduction

    NASA Astrophysics Data System (ADS)

    Rader, D. J.; Gallis, M. A.; Torczynski, J. R.

    2004-11-01

    The convergence of Bird's Direct Simulation Monte Carlo (DSMC) method is investigated for gas-phase heat conduction at typical microscale conditions. A hard-sphere gas is confined between two fully accommodating walls of unequal temperature. Simulations are performed for small system and local Knudsen numbers, so continuum flow exists outside the Knudsen layers. The ratio of the DSMC thermal conductivity to the Chapman-Enskog value in the central region is determined for over 200 combinations of time step, cell size, and number of computational molecules per cell. In the limit of vanishing error, this ratio approaches 1.000 to within the correlation uncertainty. In the limit of infinite computational molecules per cell, the difference from unity depends quadratically on time step and cell size as these quantities become small. The coefficients of these quadratic terms are in good agreement with Green-Kubo values found by Hadjiconstantinou, Garcia, and co-workers. These results demonstrate that DSMC can accurately simulate microscale gas-phase heat conduction. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  3. Gas-phase molecular structure and energetics of anionic silicates

    NASA Astrophysics Data System (ADS)

    Gomes, José R. B.; Cordeiro, M. Natália D. S.; Jorge, Miguel

    2008-09-01

    The gas-phase stabilities of linear, branched and cyclic silicates made of up to five silicon atoms were studied with density functional theory (DFT). The starting geometries for the DFT calculations at the B3LYP/6-311+G(2d,2p) level of theory were obtained from classical molecular dynamics simulations. We have observed that geometric parameters and charges are mainly affected by the degree of deprotonation. Charges on Si atoms are also influenced by their degree of substitution. The enthalpy of deprotonation of the neutral species was found to decrease with the size of the molecule, while the average deprotonation enthalpy of highly charged compounds increased with molecular size. Furthermore, the formation of rings in highly charged silicates is enthalpically preferred to chain growth. These observations result from two competing effects: the easier distribution of negative charge in silicates with low charge density and the strong intramolecular repulsions present in silicates with high charge density. As a consequence, highly charged silicates in the gas phase tend to be as small and as highly condensed as possible, which is in line with experimental observations from solution NMR.

  4. High resolution dissociative electron attachment to gas phase adenine

    SciTech Connect

    Huber, D.; Beikircher, M.; Denifl, S.; Zappa, F.; Matejcik, S.; Bacher, A.; Grill, V.; Maerk, T. D.; Scheier, P.

    2006-08-28

    The dissociative electron attachment to the gas phase nucleobase adenine is studied using two different experiments. A double focusing sector field mass spectrometer is utilized for measurements requiring high mass resolution, high sensitivity, and relative ion yields for all the fragment anions and a hemispherical electron monochromator instrument for high electron energy resolution. The negative ion mass spectra are discussed at two different electron energies of 2 and 6 eV. In contrast to previous gas phase studies a number of new negative ions are discovered in the mass spectra. The ion efficiency curves for the negative ions of adenine are measured for the electron energy range from about 0 to 15 eV with an electron energy resolution of about 100 meV. The total anion yield derived via the summation of all measured fragment anions is compared with the total cross section for negative ion formation measured recently without mass spectrometry. For adenine the shape of the two cross section curves agrees well, taking into account the different electron energy resolutions; however, for thymine some peculiar differences are observed.

  5. 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.

  6. Star formation and gas phase history of the cosmic web

    NASA Astrophysics Data System (ADS)

    Snedden, Ali; Coughlin, Jared; Phillips, Lara Arielle; Mathews, Grant; Suh, In-Saeng

    2016-01-01

    We present a new method of tracking and characterizing the environment in which galaxies and their associated circumgalactic medium evolve. We have developed a structure finding algorithm that uses the rate of change of the density gradient to self-consistently parse and follow the evolution of groups/clusters, filaments and voids in large-scale structure simulations. We use this to trace the complete evolution of the baryons in the gas phase and the star formation history within each structure in our simulated volume. We vary the structure measure threshold to probe the complex inner structure of star-forming regions in poor clusters, filaments and voids. We find that the majority of star formation occurs in cold, condensed gas in filaments at intermediate redshifts (z ˜ 3). We also show that much of the star formation above a redshift z = 3 occurs in low-contrast regions of filaments, but as the density contrast increases at lower redshift, star formation switches to the high-contrast regions, or inner parts, of filaments. Since filaments bridge the void and cluster regions, it suggests that the majority of star formation occurs in galaxies in intermediate density regions prior to the accretion on to groups/clusters. We find that both filaments and poor clusters are multiphase environments distinguishing themselves by different distributions of gas phases.

  7. Determination of gas phase and surface reactions in plasma polymerization

    NASA Astrophysics Data System (ADS)

    Hegemann, Dirk

    2009-10-01

    Using macroscopic kinetics, the reactions within the gas phase are governed by the reaction parameter power input per gas flow W/F, which corresponds to a specific energy, while reactions by energetic particle bombardment at the growing film surface are rather related to power input W alone. Assuming activation reactions, the mass deposition rate per gas flow can be described by an Arrhenius-like approach: [ RmF=G( -EaW / W F . - F ) ] Mixtures of hydrocarbons (C2H4) and reactive gases (CO2, N2+H2) were examined within low pressure RF plasmas. Thus, functional a-C:H:O or a-C:H:N plasma coatings result. At increasing energy input it is found that the deposited mass shows a deviation from the above equation, commonly related to energetic particle interactions. However, using the same range of W/F with varying power input W, it was found that the observed drop in deposition rate scales solely with energy input W/F for a-C:H:O, i.e. depending on plasma chemistry. a-C:H:N films, on the other hand, show both chemical and physical influences on the film growth. Hence, gas phase reactions such as a change of film-forming species play a major role in plasma polymerization.

  8. 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.

  9. Thermochemical aspects of proton transfer in the gas phase.

    PubMed

    Gal, J F; Maria, P C; Raczyńska, E D

    2001-07-01

    The beginning of the twentieth century saw the development of new theories of acidity and basicity, which are currently well accepted. The thermochemistry of proton transfer in the absence of solvent attracted much interest during this period, because of the fundamental importance of the process. Nevertheless, before the 1950s, few data were available, either from lattice energy evaluations or from calculations using the emerging molecular orbital theory. Advances in mass spectrometry during the last 40 years allowed studies of numerous systems with better accuracy. Thousands of accurate gas-phase acidities or basicities are now available, for simple atomic and molecular systems and for large biomolecules. The intrinsic effect of structure on the Brønsted basic or acidic properties of molecules and the influence of solvents have been unravelled. In this tutorial, the basics of the thermodynamic principles involved are given, and the mass spectrometric techniques are briefly reviewed. Advances in the design and measurements of gas-phase superacids and superbases are described. Recent studies concerning biomolecules are also evoked.

  10. Gas-phase Dissociation of homo-DNA Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Stucki, Silvan R.; Désiron, Camille; Nyakas, Adrien; Marti, Simon; Leumann, Christian J.; Schürch, Stefan

    2013-12-01

    Synthetic modified oligonucleotides are of interest for diagnostic and therapeutic applications, as their biological stability, pairing selectivity, and binding strength can be considerably increased by the incorporation of unnatural structural elements. Homo-DNA is an oligonucleotide homologue based on dideoxy-hexopyranosyl sugar moieties, which follows the Watson-Crick A-T and G-C base pairing system, but does not hybridize with complementary natural DNA and RNA. Homo-DNA has found application as a bioorthogonal element in templated chemistry applications. The gas-phase dissociation of homo-DNA has been investigated by ESI-MS/MS and MALDI-MS/MS, and mechanistic aspects of its gas-phase dissociation are discussed. Experiments revealed a charge state dependent preference for the loss of nucleobases, which are released either as neutrals or as anions. In contrast to DNA, nucleobase loss from homo-DNA was found to be decoupled from backbone cleavage, thus resulting in stable products. This renders an additional stage of ion activation necessary in order to generate sequence-defining fragment ions. Upon MS3 of the primary base-loss ion, homo-DNA was found to exhibit unspecific backbone dissociation resulting in a balanced distribution of all fragment ion series.

  11. 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.

  12. Characterization of a DAPI-RIT-DAPI system for gas-phase ion/molecule and ion/ion reactions.

    PubMed

    Lin, Ziqing; Tan, Lei; Garimella, Sandilya; Li, Linfan; Chen, Tsung-Chi; Xu, Wei; Xia, Yu; Ouyang, Zheng

    2014-01-01

    The discontinuous atmospheric pressure interface (DAPI) has been developed as a facile means for efficiently introducing ions generated at atmospheric pressure to an ion trap in vacuum [e.g., a rectilinear ion trap (RIT)] for mass analysis. Introduction of multiple beams of ions or neutral species through two DAPIs into a single RIT has been previously demonstrated. In this study, a home-built instrument with a DAPI-RIT-DAPI configuration has been characterized for the study of gas-phase ion/molecule and ion/ion reactions. The reaction species, including ions or neutrals, can be introduced from both ends of the RIT through the two DAPIs without complicated ion optics or differential pumping stages. The primary reactant ions were isolated prior to reaction and the product ions were mass analyzed after controlled reaction time period. Ion/molecule reactions involving peptide radical ions and proton-transfer ion/ion reactions have been carried out using this instrument. The gas dynamic effect due to the DAPI operation on internal energy deposition and the reactivity of peptide radical ions has been characterized. The DAPI-RIT-DAPI system also has a unique feature for allowing the ion reactions to be carried out at significantly elevated pressures (in 10(-1) Torr range), which has been found to be helpful to speed up the reactions. The viability and flexibility of the DAPI-RIT-DAPI system for the study of gas-phase ion reactions have been demonstrated.

  13. Characterization of a DAPI-RIT-DAPI System for Gas-Phase Ion/Molecule and Ion/Ion Reactions

    NASA Astrophysics Data System (ADS)

    Lin, Ziqing; Tan, Lei; Garimella, Sandilya; Li, Linfan; Chen, Tsung-Chi; Xu, Wei; Xia, Yu; Ouyang, Zheng

    2014-01-01

    The discontinuous atmospheric pressure interface (DAPI) has been developed as a facile means for efficiently introducing ions generated at atmospheric pressure to an ion trap in vacuum [e.g., a rectilinear ion trap (RIT)] for mass analysis. Introduction of multiple beams of ions or neutral species through two DAPIs into a single RIT has been previously demonstrated. In this study, a home-built instrument with a DAPI-RIT-DAPI configuration has been characterized for the study of gas-phase ion/molecule and ion/ion reactions. The reaction species, including ions or neutrals, can be introduced from both ends of the RIT through the two DAPIs without complicated ion optics or differential pumping stages. The primary reactant ions were isolated prior to reaction and the product ions were mass analyzed after controlled reaction time period. Ion/molecule reactions involving peptide radical ions and proton-transfer ion/ion reactions have been carried out using this instrument. The gas dynamic effect due to the DAPI operation on internal energy deposition and the reactivity of peptide radical ions has been characterized. The DAPI-RIT-DAPI system also has a unique feature for allowing the ion reactions to be carried out at significantly elevated pressures (in 10-1 Torr range), which has been found to be helpful to speed up the reactions. The viability and flexibility of the DAPI-RIT-DAPI system for the study of gas-phase ion reactions have been demonstrated.

  14. Toluene gas phase biofiltration by Paecilomyces lilacinus and isolation and identification of a hydrophobin protein produced thereof.

    PubMed

    Vigueras, Gabriel; Shirai, Keiko; Martins de Souza, Daniel; Martins, Daniel; Franco, Telma Teixeira; Fleuri, Luciana Francisco; Revah, Sergio

    2008-08-01

    Paecilomyces lilacinus consumed toluene as the sole carbon source in a gas-phase biofilter packed with perlite obtaining an average elimination capacity of 50 g m(-3) h(-1), a removal efficiency of 53%, and a final biomass of 31.6 mg biomass g dry support(-1). Hydrophobin proteins from the mycelium produced in the biofilter were purified by formic acid extraction and precipitated by electrobubbling, and the molecular weight was found to be 10.6 +/- 0.3 kDa. The peptide mass fingerprinting analysis of the purified hydrophobin by matrix-assisted laser desorption/ionization time-of-flight resulted in the identification of two peptides that presented high homology with sequences of class I hydrophobin proteins from other ascomycetous fungi when compared against the National Center for Biotechnology Information database. The yield of hydrophobin (PLHYD) from P. lilacinus was 1.1 mg PLHYD g biomass(-1). These proteins modified the hydrophobicity of Teflon by lowering the contact angle from 130.1 (+/-2) degrees to 57.0 (+/-5) degrees supporting hot sodium dodecyl sulfate washing. This work is the first report about biodegradation of toluene by the nematophagous fungus P. lilacinus in a gas-phase biofilter and the identification of its hydrophobin protein.

  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. Synthetic peptide models for the redox-active disulfide loop of glutaredoxin. Conformational studies

    SciTech Connect

    Kishore, R.; Raghothama, S.; Balaram, P.

    1988-04-05

    Two cyclic peptide disulfides have been synthesized as models for the 14-membered redox-active disulfide loop glutaredoxin. /sup 1/H NMR studies at 270 MHz in chloroform solutions establish a type I ..beta..-turn conformation for the Pro-X segment in both peptides, stabilized by a 4 ..-->.. 1 hydrogen bond between the Cys(1) CO and Cys(4) NH groups. Nuclear Overhauser effects establish that the aromatic ring in the X = Phe peptide is oriented over the central peptide unit. In dimethyl sulfoxide solutions two conformational species are observed in slow exchange on the NMR time scale, for both peptides. These are assigned to type I and type II ..beta..-turn structures with -Pro-Tyr(Phe)-as the corner resides. The structural assignments are based on correlation of NMR parameters with model 14-membered cyclic cystine peptides with Pro-X spacers. Circular dichroism studies based on the -S-S-n-sigma* transition suggest a structural change in the disulfide bridge with changing solvent polarity, establishing conformational coupling between the peptide backbone and the disulfide linkage in these systems.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. Shape resonances, overtones, and electron energy loss spectroscopy of gas phase and physisorbed diatomic molecules

    NASA Astrophysics Data System (ADS)

    Gadzuk, J. W.

    1983-10-01

    Electron energy loss spectra of O2 and N2 physisorbed on metallic substrates showing a series of high overtone losses have recently been reported. In the case of N2, the intense overtone excitation is credited to the formation of a well-known temporary negative ion state with a resonance lifetime ˜10-15 s for gas phase N2-. The principal distinction between the gaseous and physisorbed molecule EELS spectrum is a significant depletion of the overtone intensity which has been attributed to a surface-induced decrease in the resonance lifetime. In the present work, a time dependent quantum mechanical model applicable to vibrational excitation in resonance scattering is outlined which quantitatively accounts for the observed spectra and, in particular, the surface modifications to the gas phase results. The essential feature of the model is one in which the intramolecular dynamics of the intermediate state is characterized by nuclear propagation over a harmonic potential curve spatially displaced from the ground state curve for a time duration equal to the resonance lifetime. The resulting calculated overtone spectra agree well with the experimentally observed ones. The results suggest that the physisorbed N-2 lifetime is about 40% of that of the free molecule.

  5. 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.

  6. Gas-phase synthesis of magnetic metal/polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Starsich, Fabian H. L.; Hirt, Ann M.; Stark, Wendelin J.; Grass, Robert N.

    2014-12-01

    Highly magnetic metal Co nanoparticles were produced via reducing flame spray pyrolysis, and directly coated with an epoxy polymer in flight. The polymer content in the samples varied between 14 and 56 wt% of nominal content. A homogenous dispersion of Co nanoparticles in the resulting nanocomposites was visualized by electron microscopy. The size and crystallinity of the metallic fillers was not affected by the polymer, as shown by XRD and magnetic hysteresis measurements. The good control of the polymer content in the product nanocomposite was shown by elemental analysis. Further, the successful polymerization in the gas phase was demonstrated by electron microscopy and size measurements. The presented effective, dry and scalable one-step synthesis method for highly magnetic metal nanoparticle/polymer composites presented here may drastically decrease production costs and increase industrial yields.

  7. Gas-phase synthesis of magnetic metal/polymer nanocomposites.

    PubMed

    Starsich, Fabian H L; Hirt, Ann M; Stark, Wendelin J; Grass, Robert N

    2014-12-19

    Highly magnetic metal Co nanoparticles were produced via reducing flame spray pyrolysis, and directly coated with an epoxy polymer in flight. The polymer content in the samples varied between 14 and 56 wt% of nominal content. A homogenous dispersion of Co nanoparticles in the resulting nanocomposites was visualized by electron microscopy. The size and crystallinity of the metallic fillers was not affected by the polymer, as shown by XRD and magnetic hysteresis measurements. The good control of the polymer content in the product nanocomposite was shown by elemental analysis. Further, the successful polymerization in the gas phase was demonstrated by electron microscopy and size measurements. The presented effective, dry and scalable one-step synthesis method for highly magnetic metal nanoparticle/polymer composites presented here may drastically decrease production costs and increase industrial yields. PMID:25422410

  8. Synthesis and Gas Phase Thermochemistry of Germanium-Containing Compounds

    SciTech Connect

    Nathan Robert Classen

    2002-12-31

    The driving force behind much of the work in this dissertation was to gain further understanding of the unique olefin to carbene isomerization observed in the thermolysis of 1,1-dimethyl-2-methylenesilacyclobutane by finding new examples of it in other silicon and germanium compounds. This lead to the examination of a novel phenylmethylenesilacyclobut-2-ene, which did not undergo olefin to carbene rearrangement. A synthetic route to methylenegermacyclobutanes was developed, but the methylenegermacyclobutane system exhibited kinetic instability, making the study of the system difficult. In any case the germanium system decomposed through a complex mechanism which may not include olefin to carbene isomerization. However, this work lead to the study of the gas phase thermochemistry of a series of dialkylgermylene precursors in order to better understand the mechanism of the thermal decomposition of dialkylgermylenes. The resulting dialkylgermylenes were found to undergo a reversible intramolecular {beta} C-H insertion mechanism.

  9. Conformational Study of Taurine in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Cortijo, Vanessa; Sanz, M. Eugenia; López, Juan C.; Alonso, José L.

    2009-08-01

    The conformational preferences of the amino sulfonic acid taurine (NH2-CH2-CH2-SO3H) have been investigated in the gas phase by laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) in the 6-14 GHz frequency range. One conformer has been observed, and its rotational, centrifugal distortion, and hyperfine quadrupole coupling constants have been determined from the analysis of its rotational spectrum. Comparison of the experimental constants with those calculated theoretically identifies the detected conformer unambiguously. The observed conformer of taurine is stabilized by an intramolecular hydrogen bond O-H···N between the hydrogen of the sulfonic acid group and the nitrogen atom of the amino group.

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

    NASA Technical Reports Server (NTRS)

    Constantinescu, Ileana C.; Finn, John E.; LeVan, M. Douglas; Lung, Bernadette (Technical Monitor)

    2000-01-01

    Tests of a pre-prototype regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an adsorbent column have been performed at 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. During the normal operation mode, contaminants are removed from the air on the column. Regeneration of the column is performed on-line. During regeneration, contaminants are displaced and destroyed inside the closed oxidation loop. In this presentation we discuss initial experimental results for the performance of RAPS in the removal and treatment of several important spacecraft contaminant species from air.

  11. Silicon Nanowire-Based Devices for Gas-Phase Sensing

    PubMed Central

    Cao, Anping; Sudhölter, Ernst J.R.; de Smet, Louis C.P.M.

    2014-01-01

    Since their introduction in 2001, SiNW-based sensor devices have attracted considerable interest as a general platform for ultra-sensitive, electrical detection of biological and chemical species. Most studies focus on detecting, sensing and monitoring analytes in aqueous solution, but the number of studies on sensing gases and vapors using SiNW-based devices is increasing. This review gives an overview of selected research papers related to the application of electrical SiNW-based devices in the gas phase that have been reported over the past 10 years. Special attention is given to surface modification strategies and the sensing principles involved. In addition, future steps and technological challenges in this field are addressed. PMID:24368699

  12. Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase

    NASA Astrophysics Data System (ADS)

    MacLeod, N. A.; Simons, J. P.

    2007-03-01

    Protonated neurotransmitters have been produced in the gas phase via a novel photochemical scheme: complexes of the species of interest, 1-phenylethylamine, 2-amino-1-phenylethanol and the diastereo-isomers, ephedrine and pseudoephedrine, with a suitable proton donor, phenol (or indole), are produced in a supersonic expansion and ionized by resonant two photon ionization of the donor. Efficient proton transfer generates the protonated neurotransmitters, complexed to a phenoxy radical. Absorption of infrared radiation, and subsequent evaporation of the phenoxy tag, coupled with time of flight mass spectrometry, provides vibrational spectra of the protonated (and also hydrated) complexes for comparison with the results of quantum chemical computation. Comparison with the conformational structures of the neutral neurotransmitters (established previously) reveals the effect of protonation on their structure. The photochemical proton transfer strategy allows spectra to be recorded from individual laser shots and their quality compares favourably with that obtained using electro-spray or matrix assisted laser desorption ion sources.

  13. Ion/Ion Reactions with "Onium" Reagents: An Approach for the Gas-phase Transfer of Organic Cations to Multiply-Charged Anions

    NASA Astrophysics Data System (ADS)

    Gilbert, Joshua D.; Prentice, Boone M.; McLuckey, Scott A.

    2015-05-01

    The use of ion/ion reactions to effect gas-phase alkylation is demonstrated. Commonly used fixed-charge "onium" cations are well-suited for ion/ion reactions with multiply deprotonated analytes because of their tendency to form long-lived electrostatic complexes. Activation of these complexes results in an SN2 reaction that yields an alkylated anion with the loss of a neutral remnant of the reagent. This alkylation process forms the basis of a general method for alkylation of deprotonated analytes generated via electrospray, and is demonstrated on a variety of anionic sites. SN2 reactions of this nature are demonstrated empirically and characterized using density functional theory (DFT). This method for modification in the gas phase is extended to the transfer of larger and more complex R groups that can be used in later gas-phase synthesis steps. For example, N-cyclohexyl- N'-(2-morpholinoethyl)carbodiimide (CMC) is used to transfer a carbodiimide functionality to a peptide anion containing a carboxylic acid. Subsequent activation yields a selective reaction between the transferred carbodiimide group and a carboxylic acid, suggesting the carbodiimide functionality is retained through the transfer process. Many different R groups are transferable using this method, allowing for new possibilities for charge manipulation and derivatization in the gas phase.

  14. Ion/Ion Reactions with “Onium” Reagents: An Approach for the Gas-phase Transfer of Organic Cations to Multiply-Charged Anions

    PubMed Central

    Gilbert, Joshua D.; Prentice, Boone M.; McLuckey, Scott A.

    2015-01-01

    The use of ion/ion reactions to effect gas-phase alkylation is demonstrated. Commonly used fixed-charge “onium” cations are well-suited for ion/ion reactions with multiply deprotonated analytes because of their tendency to form long-lived electrostatic complexes. Activation of these complexes results in an SN2 reaction that yields an alkylated anion with the loss of a neutral remnant of the reagent. This alkylation process forms the basis of a general method for alkylation of deprotonated analytes generated via electrospray, and is demonstrated on a variety of anionic sites. SN2 reactions of this nature are demonstrated empirically and characterized using density functional theory (DFT). This method for modification in the gas phase is extended to the transfer of larger and more complex R groups that can be used in later gas-phase synthesis steps. For example, N-cyclohexyl-N′-(2-morpholinoethyl)carbodiimide (CMC) is used to transfer a carbodiimide functionality to a peptide anion containing a carboxylic acid. Subsequent activation yields a selective reaction between the transferred carbodiimide group and a carboxylic acid, suggesting the carbodiimide functionality is retained through the transfer process. Many different R groups are transferable using this method, allowing for new possibilities for charge manipulation and derivatization in the gas phase. PMID:25652935

  15. Ion/ion reactions with "onium" reagents: an approach for the gas-phase transfer of organic cations to multiply-charged anions.

    PubMed

    Gilbert, Joshua D; Prentice, Boone M; McLuckey, Scott A

    2015-05-01

    The use of ion/ion reactions to effect gas-phase alkylation is demonstrated. Commonly used fixed-charge "onium" cations are well-suited for ion/ion reactions with multiply deprotonated analytes because of their tendency to form long-lived electrostatic complexes. Activation of these complexes results in an SN2 reaction that yields an alkylated anion with the loss of a neutral remnant of the reagent. This alkylation process forms the basis of a general method for alkylation of deprotonated analytes generated via electrospray, and is demonstrated on a variety of anionic sites. SN2 reactions of this nature are demonstrated empirically and characterized using density functional theory (DFT). This method for modification in the gas phase is extended to the transfer of larger and more complex R groups that can be used in later gas-phase synthesis steps. For example, N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide (CMC) is used to transfer a carbodiimide functionality to a peptide anion containing a carboxylic acid. Subsequent activation yields a selective reaction between the transferred carbodiimide group and a carboxylic acid, suggesting the carbodiimide functionality is retained through the transfer process. Many different R groups are transferable using this method, allowing for new possibilities for charge manipulation and derivatization in the gas phase. PMID:25652935

  16. Surfactants from the gas phase may promote cloud droplet formation.

    PubMed

    Sareen, Neha; Schwier, Allison N; Lathem, Terry L; Nenes, Athanasios; McNeill, V Faye

    2013-02-19

    Clouds, a key component of the climate system, form when water vapor condenses upon atmospheric particulates termed cloud condensation nuclei (CCN). Variations in CCN concentrations can profoundly impact cloud properties, with important effects on local and global climate. Organic matter constitutes a significant fraction of tropospheric aerosol mass, and can influence CCN activity by depressing surface tension, contributing solute, and influencing droplet activation kinetics by forming a barrier to water uptake. We present direct evidence that two ubiquitous atmospheric trace gases, methylglyoxal (MG) and acetaldehyde, known to be surface-active, can enhance aerosol CCN activity upon uptake. This effect is demonstrated by exposing acidified ammonium sulfate particles to 250 parts per billion (ppb) or 8 ppb gas-phase MG and/or acetaldehyde in an aerosol reaction chamber for up to 5 h. For the more atmospherically relevant experiments, i.e., the 8-ppb organic precursor concentrations, significant enhancements in CCN activity, up to 7.5% reduction in critical dry diameter for activation, are observed over a timescale of hours, without any detectable limitation in activation kinetics. This reduction in critical diameter enhances the apparent particle hygroscopicity up to 26%, which for ambient aerosol would lead to cloud droplet number concentration increases of 8-10% on average. The observed enhancements exceed what would be expected based on Köhler theory and bulk properties. Therefore, the effect may be attributed to the adsorption of MG and acetaldehyde to the gas-aerosol interface, leading to surface tension depression of the aerosol. We conclude that gas-phase surfactants may enhance CCN activity in the atmosphere.

  17. Surfactants from the gas phase may promote cloud droplet formation.

    PubMed

    Sareen, Neha; Schwier, Allison N; Lathem, Terry L; Nenes, Athanasios; McNeill, V Faye

    2013-02-19

    Clouds, a key component of the climate system, form when water vapor condenses upon atmospheric particulates termed cloud condensation nuclei (CCN). Variations in CCN concentrations can profoundly impact cloud properties, with important effects on local and global climate. Organic matter constitutes a significant fraction of tropospheric aerosol mass, and can influence CCN activity by depressing surface tension, contributing solute, and influencing droplet activation kinetics by forming a barrier to water uptake. We present direct evidence that two ubiquitous atmospheric trace gases, methylglyoxal (MG) and acetaldehyde, known to be surface-active, can enhance aerosol CCN activity upon uptake. This effect is demonstrated by exposing acidified ammonium sulfate particles to 250 parts per billion (ppb) or 8 ppb gas-phase MG and/or acetaldehyde in an aerosol reaction chamber for up to 5 h. For the more atmospherically relevant experiments, i.e., the 8-ppb organic precursor concentrations, significant enhancements in CCN activity, up to 7.5% reduction in critical dry diameter for activation, are observed over a timescale of hours, without any detectable limitation in activation kinetics. This reduction in critical diameter enhances the apparent particle hygroscopicity up to 26%, which for ambient aerosol would lead to cloud droplet number concentration increases of 8-10% on average. The observed enhancements exceed what would be expected based on Köhler theory and bulk properties. Therefore, the effect may be attributed to the adsorption of MG and acetaldehyde to the gas-aerosol interface, leading to surface tension depression of the aerosol. We conclude that gas-phase surfactants may enhance CCN activity in the atmosphere. PMID:23382211

  18. Ab initio kinetics of gas phase decomposition reactions.

    PubMed

    Sharia, Onise; Kuklja, Maija M

    2010-12-01

    The thermal and kinetic aspects of gas phase decomposition reactions can be extremely complex due to a large number of parameters, a variety of possible intermediates, and an overlap in thermal decomposition traces. The experimental determination of the activation energies is particularly difficult when several possible reaction pathways coexist in the thermal decomposition. Ab initio calculations intended to provide an interpretation of the experiment are often of little help if they produce only the activation barriers and ignore the kinetics of the decomposition process. To overcome this ambiguity, a theoretical study of a complete picture of gas phase thermo-decomposition, including reaction energies, activation barriers, and reaction rates, is illustrated with the example of the β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) molecule by means of quantum-chemical calculations. We study three types of major decomposition reactions characteristic of nitramines: the HONO elimination, the NONO rearrangement, and the N-NO(2) homolysis. The reaction rates were determined using the conventional transition state theory for the HONO and NONO decompositions and the variational transition state theory for the N-NO(2) homolysis. Our calculations show that the HMX decomposition process is more complex than it was previously believed to be and is defined by a combination of reactions at any given temperature. At all temperatures, the direct N-NO(2) homolysis prevails with the activation barrier at 38.1 kcal/mol. The nitro-nitrite isomerization and the HONO elimination, with the activation barriers at 46.3 and 39.4 kcal/mol, respectively, are slow reactions at all temperatures. The obtained conclusions provide a consistent interpretation for the reported experimental data. PMID:21077597

  19. Can an ab initio three-body virial equation describe the mercury gas phase?

    PubMed

    Wiebke, J; Wormit, M; Hellmann, R; Pahl, E; Schwerdtfeger, P

    2014-03-27

    We report a sixth-order ab initio virial equation of state (EOS) for mercury. The virial coefficients were determined in the temperature range from 500 to 7750 K using a three-body approximation to the N-body interaction potential. The underlying two-body and three-body potentials were fitted to highly accurate Coupled-Cluster interaction energies of Hg2 (Pahl, E.; Figgen, D.; Thierfelder, C.; Peterson, K. A.; Calvo, F.; Schwerdtfeger, P. J. Chem. Phys. 2010, 132, 114301-1) and equilateral-triangular configurations of Hg3. We find the virial coefficients of order four and higher to be negative and to have large absolute values over the entire temperature range considered. The validity of our three-body, sixth-order EOS seems to be limited to small densities of about 1.5 g cm(-3) and somewhat higher densities at higher temperatures. Termwise analysis and comparison to experimental gas-phase data suggest a small convergence radius of the virial EOS itself as well as a failure of the three-body interaction model (i.e., poor convergence of the many-body expansion for mercury). We conjecture that the nth-order term of the virial EOS is to be evaluated from the full n-body interaction potential for a quantitative picture. Consequently, an ab initio three-body virial equation cannot describe the mercury gas phase. PMID:24547987

  20. Gas-phase structure and reactivity of the keto tautomer of the deoxyguanosine radical cation.

    PubMed

    Feketeová, Linda; Chan, Bun; Khairallah, George N; Steinmetz, Vincent; Maître, Philippe; Radom, Leo; O'Hair, Richard A J

    2015-10-21

    Guanine radical cations are formed upon oxidation of DNA. Deoxyguanosine (dG) is used as a model, and the gas-phase infrared (IR) spectroscopic signature and gas-phase unimolecular and bimolecular chemistry of its radical cation, dG˙(+), A, which is formed via direct electrospray ionisation (ESI/MS) of a methanolic solution of Cu(NO3)2 and dG, are examined. Quantum chemistry calculations have been carried out on 28 isomers and comparisons between their calculated IR spectra and the experimentally-measured spectra suggest that A exists as the ground-state keto tautomer. Collision-induced dissociation (CID) of A proceeds via cleavage of the glycosidic bond, while its ion–molecule reactions with amine bases occur via a number of pathways including hydrogen-atom abstraction, proton transfer and adduct formation. A hidden channel, involving isomerisation of the radical cation via adduct formation, is revealed through the use of two stages of CID, with the final stage of CID showing the loss of CH2O as a major fragmentation pathway from the reformed radical cation, dG˙(+). Quantum chemistry calculations on the unimolecular and bimolecular reactivity are also consistent with A being present as a ground-state keto tautomer. PMID:25942055

  1. Gas-Phase Lasers - a Historical Perspective in Relation to the GEC

    NASA Astrophysics Data System (ADS)

    Hays, Gerry

    1997-10-01

    Understanding of gas-phase lasers inevitably involves an expertise in many of the specialties of the GEC community - especially homogenous and heterogeneous kinetics, collision cross-sections, gas breakdown physics and fundamental swarm parameters. The GEC community decided early in the evolution of gas-phase lasers to include papers on this topic and the result was many years of contributions to the evolution of and improvement in our understanding of this important class of lasers. Many of the ground-breaking results in gas laser technology were presented at the GEC over the last 3 decades as the traditional rare-gas atomic physics and low-temperature plasma groups turned their attention to parameters of interest to the laser modelers and experimenters. This paper will trace the development of this field, especially as it pertained to the GEC. Some of the key results will be highlighted, together with some of the unpublished trivia and anecdotal incidents in order to capture the flavor of the rapid developments in the early days. The talk will include speculation as to the direction this field is taking, and some suggestions as to opportunities. This work supported by the United States Department of Energy under Contract DE-AC04-94AL85000. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the United States Department of Energy.

  2. The gas-phase iron abundance in Herbig-Haro objects

    NASA Technical Reports Server (NTRS)

    Beck-Winchatz, B.; Bohm, K. H.; Noriega-Crespo, A.

    1994-01-01

    The gas-phase abundance ratios Fe/S and Fe/O have been determined for the Herbig-Haro objects HH 1, HH 7, HH 11, HH 43A, and 'Burnham's Nebula' (HH 255). It is the purpose of this study to decide whether a sizeable fraction of the Fe in these HH objects is still bound in dust grains or whether the observed matter has gone through sufficiently fast shock waves so that the dust grains have been essentially destroyed and most of the iron has gone back into the gas phase. We have determined the abundance ratios using statistical equilibrium calculations for the ions Fe(+), S(+), and O(+). (These are the most abundant ions of the elements in question.) Abundance determinations have been made using homogeneous models of the HH objects for which electron temperatures and densities have been determined observationally from forbidden line ratios. The results show that the Fe/S ratio in the objects HH 1, HH 7, HH 11, and HH 43A agrees very well with the Population I abundance ratio. Only Burnham's Nebula (HH255) shows an Fe/S ratio which is about three times lower indicating a shock-wave history which is quite different from that of the other HH objects.

  3. Aqueous and Gas Phase Sorption Properties of Mercury in Burned Soils

    NASA Astrophysics Data System (ADS)

    Jay, J.; Ferreira, M.; Burke, M.; Hogue, T.

    2008-12-01

    Wildfires are a common occurrence in the Mediterranean climate of Southern California. Many studies have focused on the post-fire physical impacts however; there is a lack of studies on the potential for post-fire metal transport, in particular mercury (Hg). Inorganic Hg contamination is present even in pristine areas due to atmospheric deposition, which can be microbially transformed to methylmercury (a bioaccumulative neurotoxin) in aquatic systems. In order to model the transport of mercury in burned soils, we need to understand the sorption properties of mercury in soils exposed to fire. To test the hypothesis that burned soils have different sorption properties than unburned ones, we have collected samples of unburned soils, and burned them in a controlled setting at different temperatures to simulate several fire intensities. Then, we applied traditional aqueous sorption techniques to determine the binding properties of mercury to each burned soil. Experimental data were fitted with FITEQL to derive constants for sorption reactions, which were in agreement with values observed in literature. Since Southern California does not receive much rain, most of the atmospheric mercury deposition is in form of dry deposition. Thus, we have designed and applied a novel sorption technique to determine the binding of mercury in the gas phase to the burned soils. Trends in sorption affinity and capacity with burning temperature are discussed, as well as a comparison between aqueous and gas phase sorption properties is made.

  4. A comparison of the gas phase acidities of phospholipid headgroups: experimental and computational studies.

    PubMed

    Thomas, Michael C; Mitchell, Todd W; Blanksby, Stephen J

    2005-06-01

    Proton-bound dimers consisting of two glycerophospholipids with different headgroups were prepared using negative ion electrospray ionization and dissociated in a triple quadrupole mass spectrometer. Analysis of the tandem mass spectra of the dimers using the kinetic method provides, for the first time, an order of acidity for the phospholipid classes in the gas phase of PE < PA < PG < PS < PI. Hybrid density functional calculations on model phospholipids were used to predict the absolute deprotonation enthalpies of the phospholipid classes from isodesmic proton transfer reactions with phosphoric acid. The computational data largely support the experimental acidity trend, with the exception of the relative acidity ranking of the two most acidic phospholipid species. Possible causes of the discrepancy between experiment and theory are discussed and the experimental trend is recommended. The sequence of gas phase acidities for the phospholipid headgroups is found to (1) have little correlation with the relative ionization efficiencies of the phospholipid classes observed in the negative ion electrospray process, and (2) correlate well with fragmentation trends observed upon collisional activation of phospholipid [M - H](-) anions. PMID:15907707

  5. Cellular uptake of antisense oligonucleotides after complexing or conjugation with cell-penetrating model peptides.

    PubMed

    Oehlke, J; Birth, P; Klauschenz, E; Wiesner, B; Beyermann, M; Oksche, A; Bienert, M

    2002-08-01

    The uptake by mammalian cells of phosphorothioate oligonucleotides was compared with that of their respective complexes or conjugates with cationic, cell-penetrating model peptides of varying helix-forming propensity and amphipathicity. An HPLC-based protocol for the synthesis and purification of disulfide bridged conjugates in the 10-100 nmol range was developed. Confocal laser scanning microscopy (CLSM) in combination with gel-capillary electrophoresis and laser induced fluorescence detection (GCE-LIF) revealed cytoplasmic and nuclear accumulationin all cases. The uptake differences between naked oligonucleotides and their respective peptide complexes or conjugates were generally confined to one order of magnitude. No significant influence of the structural properties of the peptide components upon cellular uptake was found. Our results question the common belief that the increased biological activity of oligonucleotides after derivatization with membrane permeable peptides may be primarily due to improved membrane translocation.

  6. Ab initio quantum mechanical models of peptide helices and their vibrational spectra.

    PubMed

    Bour, Petr; Kubelka, Jan; Keiderling, Timothy A

    2002-10-01

    Structural parameters for standard peptide helices (alpha, 3(10), 3(1) left-handed) were fully ab initio optimized for Ac-(L-Ala)(9)-NHMe and for Ac-(L-Pro)(9)-NHMe (poly-L-proline-PLP I and PLP II-forms), in order to better understand the relative stability and minimum energy geometries of these conformers and the dependence of the ir absorption and vibrational CD (VCD) spectra on detailed variation in these conformations. Only the 3(10)-helical Ala-based conformation was stable in vacuum for this decaamide structure, but both Pro-based conformers minimized successfully. Inclusion of solvent effects, by use of the conductor-like screening solvent model (COSMO), enabled ab initio optimizations [at the DFT/B3LYP/SV(P) level] without any constraints for the alpha- and 3(10)-helical Ala-based peptides as well as the two Pro-based peptides. The geometries obtained compare well with peptide chain torsion angles and hydrogen-bond distances found for these secondary structure types in x-ray structures of peptides and proteins. For the simulation of VCD spectra, force field and intensity response tensors were obtained ab initio for the complete Ala-based peptides in vacuum, but constrained to the COSMO optimized torsional angles, due to limitations of the solvent model. Resultant spectral patterns reproduce well many aspects of the experimental spectra and capture the differences observed for these various helical types.

  7. High resolution ion mobility measurements for gas phase proteins: correlation between solution phase and gas phase conformations

    NASA Astrophysics Data System (ADS)

    Hudgins, Robert R.; Woenckhaus, Jürgen; Jarrold, Martin F.

    1997-11-01

    Our high resolution ion mobility apparatus has been modified by attaching an electrospray source to perform measurements for biological molecules. While the greater resolving power permits the resolution of more conformations for BPTI and cytochrome c, the resolved features are generally much broader than expected for a single rigid conformation. A major advantage of the new experimental configuration is the much gentler introduction of ions into the drift tube, so that the observed gas phase conformations appear to more closely reflect those present in solution. For example, it is possible to distinguish between the native state of cytochrome c and the methanol-denatured form on the basis of the ion mobility measurements; the mass spectra alone are not sensitive enough to detect this change. Thus this approach may provide a quick and sensitive tool for probing the solution phase conformations of biological molecules.

  8. Second order rate constants for intramolecular conversions: Application to gas-phase NMR relaxation times

    NASA Astrophysics Data System (ADS)

    Bauer, S. H.; Lazaar, K. I.

    1983-09-01

    The usually quoted expression for the second order rate constant, for a unimolecular reaction at the low pressure limit, is valid only for strictly irreversible processes. Its application to isomerization reactions (which are to some extent reversible) is demonstrably in error; corrected expressions have been published. Attention is directed to intramolecular conversions over low barriers, for which the inappropriateness of the unidirectional expression becomes obvious. For such isomerizations we propose a model which incorporates only operationally observable states, so that an essential conceptual ambiguity is avoided. Use of this model is illustrated for the syn⇄anti conversions of methyl nitrite, derived from a gas phase NMR coalescence curve (Mc:Tc). The present data suggest that during isomerization the alkyl nitrites may not be completely ergodic on a time scale of 10-9 s. A regional phase-space model is proposed which has the appropriate formalism to account for this behavior.

  9. Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues

    PubMed Central

    2010-01-01

    Background We aim to propose interactions between the parathyroid hormone-2 receptor (PTH2R) and its ligand the tuberoinfundibular peptide of 39 residues (TIP39) by constructing a homology model of their complex. The two related peptides parathyroid hormone (PTH) and parathyroid hormone related protein (PTHrP) are compared with the complex to examine their interactions. Findings In the model, the hydrophobic N-terminus of TIP39 is buried in a hydrophobic part of the central cavity between helices 3 and 7. Comparison of the peptide sequences indicates that the main discriminator between the agonistic peptides TIP39 and PTH and the inactive PTHrP is a tryptophan-phenylalanine replacement. The model indicates that the smaller phenylalanine in PTHrP does not completely occupy the binding site of the larger tryptophan residue in the other peptides. As only TIP39 causes internalisation of the receptor and the primary difference being an aspartic acid in position 7 of TIP39 that interacts with histidine 396 in the receptor, versus isoleucine/histidine residues in the related hormones, this might be a trigger interaction for the events that cause internalisation. Conclusions A model is constructed for the complex and a trigger interaction for full agonistic activation between aspartic acid 7 of TIP39 and histidine 396 in the receptor is proposed. PMID:20979597

  10. Identification of Guest-Host Inclusion Complexes in the Gas Phase by Electrospray Ionization-Mass Spectrometry

    ERIC Educational Resources Information Center

    Mendes, De´bora C.; Ramamurthy, Vaidhyanathan; Da Silva, Jose´ P.

    2015-01-01

    In this laboratory experiment, students follow a step-by-step procedure to prepare and study guest-host complexes in the gas phase using electrospray ionization-mass spectrometry (ESI-MS). Model systems are the complexes of hosts cucurbit[7]uril (CB7) and cucurbit[8]uril (CB8) with the guest 4-styrylpyridine (SP). Aqueous solutions of CB7 or CB8…

  11. Proteomic investigation of natural killer cell microsomes using gas-phase fractionation by mass spectrometry.

    PubMed

    Blonder, Josip; Rodriguez-Galan, Maria Cecilia; Lucas, David A; Young, Howard A; Issaq, Haleem J; Veenstra, Timothy D; Conrads, Thomas P

    2004-04-01

    We have explored the utility of gas-phase fractionation by mass spectrometry (MS) in the mass-to-charge (m/z) dimension (GPF(m/z)) for increasing the effective number of protein identifications in cases where sample quantity limits the use of multi-dimensional chromatographic fractionation. A peptide digestate from proteins isolated from the membrane fraction of natural killer (NK) cells was analyzed by microcapillary reversed-phase liquid chromatography coupled online to an ion-trap (IT) mass spectrometer. Performing GPF(m/z) using eight narrow precursor ion scan m/z ranges enabled the identification of 340 NK cell proteins from 12 microg of digestate, representing more than a fivefold increase in the number of proteins identified as compared to the same experiment employing a standard precursor ion survey scan m/z range (i.e., m/z 400-2000). The results show that GPF(m/z) represents an effective technique for increasing protein identifications in global proteomic investigations especially when sample quantity is limited.

  12. Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST.

    PubMed

    López-Ferrer, Daniel; Martínez-Bartolomé, Salvador; Villar, Margarita; Campillos, Mónica; Martín-Maroto, Fernando; Vázquez, Jesús

    2004-12-01

    Recent technological advances have made multidimensional peptide separation techniques coupled with tandem mass spectrometry the method of choice for high-throughput identification of proteins. Due to these advances, the development of software tools for large-scale, fully automated, unambiguous peptide identification is highly necessary. In this work, we have used as a model the nuclear proteome from Jurkat cells and present a processing algorithm that allows accurate predictions of random matching distributions, based on the two SEQUEST scores Xcorr and DeltaCn. Our method permits a very simple and precise calculation of the probabilities associated with individual peptide assignments, as well as of the false discovery rate among the peptides identified in any experiment. A further mathematical analysis demonstrates that the score distributions are highly dependent on database size and precursor mass window and suggests that the probability associated with SEQUEST scores depends on the number of candidate peptide sequences available for the search. Our results highlight the importance of adjusting the filtering criteria to discriminate between correct and incorrect peptide sequences according to the circumstances of each particular experiment.

  13. Strategies for generating peptide radical cations via ion/ion reactions.

    PubMed

    Gilbert, Joshua D; Fisher, Christine M; Bu, Jiexun; Prentice, Boone M; Redwine, James G; McLuckey, Scott A

    2015-02-01

    Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon-iodine (C-I) bond are subjected to UVPD with 266-nm photons, which selectively cleaves the C-I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even-electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non-covalent complexes in the electrospray process.

  14. Influence of the choice of gas-phase mechanism on predictions of key gaseous pollutants during the AQMEII phase-2 intercomparison

    EPA Science Inventory

    The formulations of tropospheric gas-phase chemistry (“mechanisms”)used in the regional-scale chemistry-transport models participating in theAir Quality Modelling Evaluation International Initiative (AQMEII) Phase2 are intercompared by the means of box model studies. Simulations ...

  15. Gas-Phase Structures of Ketene and Acetic Acid from Acetic Anhydride Using Very-High-Temperature Gas Electron Diffraction.

    PubMed

    Atkinson, Sandra J; Noble-Eddy, Robert; Masters, Sarah L

    2016-03-31

    The gas-phase molecular structure of ketene has been determined using samples generated by the pyrolysis of acetic anhydride (giving acetic acid and ketene), using one permutation of the very-high-temperature (VHT) inlet nozzle system designed and constructed for the gas electron diffraction (GED) apparatus based at the University of Canterbury. The gas-phase structures of acetic anhydride, acetic acid, and ketene are presented and compared to previous electron diffraction and microwave spectroscopy data to show improvements in data extraction and manipulation with current methods. Acetic anhydride was modeled with two conformers, rather than a complex dynamic model as in the previous study, to allow for inclusion of multiple pyrolysis products. The redetermined gas-phase structure of acetic anhydride (obtained using the structure analysis restrained by ab initio calculations for electron diffraction method) was compared to that from the original study, providing an improvement on the description of the low vibrational torsions compared to the dynamic model. Parameters for ketene and acetic acid (both generated by the pyrolysis of acetic anhydride) were also refined with higher accuracy than previously reported in GED studies, with structural parameter comparisons being made to prior experimental and theoretical studies. PMID:26916368

  16. Gas-Phase Structures of Ketene and Acetic Acid from Acetic Anhydride Using Very-High-Temperature Gas Electron Diffraction.

    PubMed

    Atkinson, Sandra J; Noble-Eddy, Robert; Masters, Sarah L

    2016-03-31

    The gas-phase molecular structure of ketene has been determined using samples generated by the pyrolysis of acetic anhydride (giving acetic acid and ketene), using one permutation of the very-high-temperature (VHT) inlet nozzle system designed and constructed for the gas electron diffraction (GED) apparatus based at the University of Canterbury. The gas-phase structures of acetic anhydride, acetic acid, and ketene are presented and compared to previous electron diffraction and microwave spectroscopy data to show improvements in data extraction and manipulation with current methods. Acetic anhydride was modeled with two conformers, rather than a complex dynamic model as in the previous study, to allow for inclusion of multiple pyrolysis products. The redetermined gas-phase structure of acetic anhydride (obtained using the structure analysis restrained by ab initio calculations for electron diffraction method) was compared to that from the original study, providing an improvement on the description of the low vibrational torsions compared to the dynamic model. Parameters for ketene and acetic acid (both generated by the pyrolysis of acetic anhydride) were also refined with higher accuracy than previously reported in GED studies, with structural parameter comparisons being made to prior experimental and theoretical studies.

  17. Gas-phase H2O and CO2 towards massive protostars

    NASA Astrophysics Data System (ADS)

    Boonman, A. M. S.; van Dishoeck, E. F.; Lahuis, F.; Wright, C. M.; Doty, S. D.

    2000-11-01

    We present a study of gas-phase H2O and CO2 towards a sample of 14 massive protostars with the ISO-SWS. Modeling of the H2O spectra using a homogeneous model with a constant excitation temperature Tex shows that the H2O abundances increase with temperature, up to a few times 10-5 with respect to H2 for the hottest sources (Tex~ 500 K). This is still a factor of 10 lower than the H2O ice abundances observed towards cold sources in which evaporation is not significant (Keane et al. 2000). Gas-phase CO2 is not abundant in our sources. The abundances are nearly constant for Tex >~ 100 K at a value of a few times 10-7, much lower than the solid-state abundances of ~1-3× 10-6 (Gerakines et al. 1999). Gas/solid ratios have been determined, using the solid-state features of H2O (Keane et al. 2000) and CO2 (Gerakines et al. 1999) as observed with ISO-SWS towards the same objects. For both H2O and CO2 the gas/solid ratio increases with temperature, but the increase is much stronger for H2O than for CO2, suggesting a different type of chemistry. In addition to the homogeneous models, a power law model has been developed for one of our sources, based on the physical structure of this region as determined from submillimeter data by van der Tak et al. (1999). The resulting H2O model spectrum gives a good fit to the data.

  18. LSENS, a general chemical kinetics and sensitivity analysis code for gas-phase reactions: User's guide

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan; Bittker, David A.

    1993-01-01

    A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS, are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include static system, steady, one-dimensional, inviscid flow, shock initiated reaction, and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method, which works efficiently for the extremes of very fast and very slow reaction, is used for solving the 'stiff' differential equation systems that arise in chemical kinetics. For static reactions, sensitivity coefficients of all dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters can be computed. This paper presents descriptions of the code and its usage, and includes several illustrative example problems.

  19. Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale.

    PubMed

    Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D

    2014-12-01

    Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.

  20. Enhancement of gas-phase diffusion in the presence of liquid

    NASA Astrophysics Data System (ADS)

    Webb, S.; Angert, A.

    2003-04-01

    Gas diffusion in porous media occurs in both the gas and liquid phases. In many instances, gas diffusion in the liquid phase is ignored. However, under many conditions, gas diffusion in the liquid phase may be more important than gas diffusion in the gas phase. Two different cases will be examined in this work. The first case is a continuous liquid path between the gas concentrations of interest modeled after Jury et al. (1984). The second case is the situation at low liquid saturation where liquid islands exist. For the first case, Jury's model can be rewritten as a ratio of the total gas diffusion in the gas and liquid phases to that just in the gas phase. The liquid diffusion coefficient is approximately 10-4 times the gas diffusion coefficient consistent with Jury et al. (1984). The ratio of total diffusion to gas-phase diffusion is then only a function of Henry's constant and the liquid saturation. For higher values of Henry's constant, such as for CO2 and O2, the effect of diffusion in the liquid phase is small except at high liquid saturations. For small values of Henry's constant, such as for some VOCs and explosive compounds, diffusion in the liquid phase dominates for low and moderate liquid saturation values. The second case is the enhancement of diffusion caused by liquid islands at low liquid saturation. Enhanced vapor diffusion across liquid islands has been observed and modeled by Webb and Ho (1999), where condensation and evaporation occur on opposite ends of the liquid island. Vapor diffusion enhancement of up to a factor of 10 has been observed. Similarly, gas can diffuse through the liquid island. For high values of Henry's constant, gas diffusion through liquid islands is negligible and can be ignored. For small values of Henry's constant, diffusion through liquid islands may be much greater than diffusion through gas, so the rate is enhanced. The work was sponsored by the Geneva International Center for Humanitarian Demining (GICHD) under the

  1. The estimation of affinity constants for the binding of model peptides to DNA by equilibrium dialysis.

    PubMed Central

    Standke, K C; Brunnert, H

    1975-01-01

    The binding of lysine model peptides of the type Lys-X-Lys, Lys-X-X-Lys and Lys-X-X-X-Lys (X = different aliphatic and aromatic amino acids) has been studied by equilibrium dialysis. It was shown that the strong electrostatic binding forces generated by protonated amino groups of lysine can be distinguished from the weak forces stemming from neutral and aromatic spacer amino acids. The overall binding strength of the lysine model peptides is modified by these weak binding forces and the apparent binding constants are influenced more by the hydrophobic character of the spacer amino acid side chains than by the chainlength of the spacers. PMID:1187347

  2. 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).

  3. 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

  4. Full field gas phase velocity measurements in microgravity

    NASA Technical Reports Server (NTRS)

    Griffin, Devon W.; Yanis, William

    1995-01-01

    Measurement of full-field velocities via Particle Imaging Velocimetry (PIV) is common in research efforts involving fluid motion. While such measurements have been successfully performed in the liquid phase in a microgravity environment, gas-phase measurements have been beset by difficulties with seeding and laser strength. A synthesis of techniques developed at NASA LeRC exhibits promise in overcoming these difficulties. Typical implementation of PIV involves forming the light from a pulsed laser into a sheet that is some fraction of a millimeter thick and 50 or more millimeters wide. When a particle enters this sheet during a pulse, light scattered from the particle is recorded by a detector, which may be a film plane or a CCD array. Assuming that the particle remains within the boundaries of the sheet for the second pulse and can be distinguished from neighboring particles, comparison of the two images produces an average velocity vector for the time between the pulses. If the concentration of particles in the sampling volume is sufficiently large but the particles remain discrete, a full field map may be generated.

  5. Gas-phase chemistry of alkylcarbonate anions and radicals

    NASA Astrophysics Data System (ADS)

    Soldi-Lose, Héloïse; Schröder, Detlef; Schwarz, Helmut

    2008-02-01

    Alkylcarbonate anions and radicals ROCOO-/ (R = H, CH3, C2H5, i-C3H7, and t-C4H9) are investigated in the gas phase by means of mass spectrometry and ab initio calculations. Structural parameters and energies are obtained at the MP2/6-311++G(3df,3pd)//MP2/6-311++G(d,p) level of theoryE Standard enthalpies of formation for the anions and radicals are determined via atomization energies and isodesmic reactions using the CBS-Q method. Further, alkylcarbonate anions are probed by metastable ion and collisional activation experiments, and the chemistry of the neutral radicals is investigated by charge-reversal and neutralization-reionization mass spectrometry. Although decarboxylation dominates the unimolecular reactivity of the species for both charge states, some other interesting features are observed, particularly for the anions, such as the formation of the CO3- radical anion or the presence of ionic fragments formed via hydrogen atom transfer.

  6. Gas phase plasma impact on phenolic compounds in pomegranate juice.

    PubMed

    Herceg, Zoran; Kovačević, Danijela Bursać; Kljusurić, Jasenka Gajdoš; Jambrak, Anet Režek; Zorić, Zoran; Dragović-Uzelac, Verica

    2016-01-01

    The aim of the study was to evaluate the effect of gas phase plasma on phenolic compounds in pomegranate juice. The potential of near infrared reflectance spectroscopy combined with partial least squares for monitoring the stability of phenolic compounds during plasma treatment was explored, too. Experiments are designed to investigate the effect of plasma operating conditions (treatment time 3, 5, 7 min; sample volume 3, 4, 5 cm(3); gas flow 0.75, 1, 1.25 dm(3) min(-1)) on phenolic compounds and compared to pasteurized and untreated pomegranate juice. Pasteurization and plasma treatment resulted in total phenolic content increasing by 29.55% and 33.03%, respectively. Principal component analysis and sensitivity analysis outputted the optimal treatment design with plasma that could match the pasteurized sample concerning the phenolic stability (5 min/4 cm(3)/0.75 dm(3) min(-1)). Obtained results demonstrate the potential of near infrared reflectance spectroscopy that can be successfully used to evaluate the quality of pomegranate juice upon plasma treatment considering the phenolic compounds.

  7. Gas-phase study of Fe sup + -benzyne with alkanes

    SciTech Connect

    Yongqing Huang; Freiser, B.S. )

    1989-03-29

    The unimolecular chemistry of Fe{sup +}-benzyne and its reactivity with small alkanes in the gas phase are studied by Fourier transform mass spectrometry (FTMS). Collision-induced dissociation of Fe{sup +}-benzyne yields benzyne loss exclusively. In contrast, photodissociation of Fe{sup +}-benzyne yields not only cleavage of benzyne from Fe{sup +}, but competitive loss of C{sub 2}H{sub 2} and C{sub 4}H{sub 2} as well. The Fe{sup +}-benzyne is formed from chlorobenzene by loss of HCl. This dehydrochlorination of chlorobenzene also occurs in secondary reactions up to six times forming products of the type Fe{sup +}-polyphenylene. Fe{sup +}-benzyne reacts with alkanes larger than methane to form a wide variety of product ions by mechanisms including hydrogenation and methanation of the benzyne ligand. All of the product ions can be explained by mechanisms based on Fe{sup +} insertion into either C-C or C-H bonds as the reaction-initiating step, followed by either alkyl or H migration from Fe{sup +} onto the benzyne ligand or, alternatively, by the migratory insertion of benzyne into a metal-carbon or metal-hydrogen bond. Photodissociation and ion-molecule reaction studies yield a value for the metal-ligand bond energy of D{degree} (Fe{sup +}-benzyne) = 76 {plus minus} 10 kcal/mol.

  8. Gas-phase electronic spectrum of the indole radical cation

    NASA Astrophysics Data System (ADS)

    Chalyavi, N.; Catani, K. J.; Sanelli, J. A.; Dryza, V.; Bieske, E. J.

    2015-08-01

    The visible and near-UV electronic spectrum of the indole radical cation is measured in the gas phase by photodissociation of indole+-Ar and indole+-He complexes in a tandem mass spectrometer. A series of resolved vibronic transitions extending from 610 to 460 nm are assigned to the D2 ← D0 band system, while weak transitions between 390 and 360 nm are assigned to the D3 ← D0 system, and a stronger, broad, unresolved absorption between 350 and 300 nm is attributed to the D4 ← D0 system. Time-dependent density functional theory calculations are used to assign vibronic structure of the D2 ← D0 band system, and show that the main active vibrational modes correspond to in-plane ring deformations. The strongest D2 ← D0 vibronic transitions of indole+-He do not correspond with any catalogued diffuse interstellar bands, even considering band displacements of up to 50 cm-1possibly caused by the attached He atom.

  9. Project ARGO: Gas phase formation in simulated microgravity

    NASA Technical Reports Server (NTRS)

    Powell, Michael R.; Waligora, James M.; Norfleet, William T.; Kumar, K. Vasantha

    1993-01-01

    The ARGO study investigated the reduced incidence of joint pain decompression sickness (DCS) encountered in microgravity as compared with an expected incidence of joint pain DCS experienced by test subjects in Earth-based laboratories (unit gravity) with similar protocols. Individuals who are decompressed from saturated conditions usually acquire joint pain DCS in the lower extremities. Our hypothesis is that the incidence of joint pain DCS can be limited by a significant reduction in the tissue gas micronuclei formed by stress-assisted nucleation. Reductions in dynamic and kinetic stresses in vivo are linked to hypokinetic and adynamic conditions of individuals in zero g. We employed the Doppler ultrasound bubble detection technique in simulated microgravity studies to determine quantitatively the degree of gas phase formation in the upper and lower extremities of test subjects during decompression. We found no evidence of right-to-left shunting through pulmonary vasculature. The volume of gas bubble following decompression was examined and compared with the number following saline contrast injection. From this, we predict a reduced incidence of DCS on orbit, although the incidence of predicted mild DCS still remains larger than that encountered on orbit.

  10. Microwave spectrum and gas phase structure of maleimide

    NASA Astrophysics Data System (ADS)

    Pejlovas, Aaron M.; Oncer, Onur; Kang, Lu; Kukolich, Stephen G.

    2016-01-01

    The rotational spectrum of maleimide was measured in the 5-12 GHz range using a Flygare-Balle type, pulsed-beam Fourier transform microwave spectrometer. Rotational transitions were measured for the parent, all unique singly substituted 13C isotopologues, and an sbnd ND, deuterium substituted isotopologue. The parent (or normal isotopologue) rotational constants, centrifugal distortion constants, and quadrupole coupling constants are A = 6815.3251(12) MHz, B = 2361.85011(64) MHz, C = 1754.32750(64) MHz, DJ = 0.232(24) kHz, DJK = 0.546(54) kHz, 1.5χaa = 2.4227(53) MHz, and 0.25(χbb-χcc) = 1.3679(15) MHz. A best fit gas phase structure was determined using the experimental rotational constants of the isotopologues and some parameters from calculations. The inertial defect is Δ = -0.054 amu Å2, indicating a planar structure for maleimide, with no large amplitude motions observed on the sbnd NH hydrogen atom. Calculations using B3LYP/aug-cc-pVTZ provided rotational constants which are much closer (within 1-2%) to the experimental values compared to the MP2/aug-cc-pVTZ calculated values.

  11. Experimental Determination of Gas Phase Thermodynamic Properties of Bimolecular Complexes

    NASA Astrophysics Data System (ADS)

    Hansen, Anne S.; Maroun, Zeina; Mackeprang, Kasper; Kjaergaard, Henrik G.

    2016-06-01

    Accurate determination of the atmospheric abundance of hydrogen bound bimolecular complexes is necessary, as hydrogen bonds are partly responsible for the formation and growth of aerosol particles. The abundance of a complex is related to the Gibbs free energy of complex formation (Δ G), which is often obtained from quantum chemical calculations that rely on calculated values of the enthalpy (Δ H) and entropy (Δ S) of complex formation. However, calculations of Δ H and in particular Δ S are associated with large uncertainties, and accurate experimental values are therefore crucial for theoretical benchmarking studies. Infrared measurements of gas phase hydrogen bound complexes were performed in the 300 to 373 K range, and lead to a purely experimental determination of Δ H using the van't Hoff equation. Equilibrium constants were determined by combining an experimental and calculated OH-stretching intensity, from which values of Δ G and hence Δ S could be determined. Thus we can determine Δ G, Δ H and Δ S for a bimolecular complex. We find that in the 300 to 373 K temperature range the determined Δ H and Δ S values are independent of temperature.

  12. Relating gas phase to solution conformations: Lessons from disordered proteins

    PubMed Central

    Beveridge, Rebecca; Phillips, Ashley S.; Denbigh, Laetitia; Saleem, Hassan M.; MacPhee, Cait E.

    2015-01-01

    In recent years both mass spectrometry (MS) and ion mobility mass spectrometry (IM‐MS) have been developed as techniques with which to study proteins that lack a fixed tertiary structure but may contain regions that form secondary structure elements transiently, namely intrinsically disordered proteins (IDPs). IM‐MS is a suitable method for the study of IDPs which provides an insight to conformations that are present in solution, potentially enabling the analysis of lowly populated structural forms. Here, we describe the IM‐MS data of two IDPs; α‐Synuclein (α‐Syn) which is implicated in Parkinson's disease, and Apolipoprotein C‐II (ApoC‐II) which is involved in cardiovascular diseases. We report an apparent discrepancy in the way that ApoC‐II behaves in the gas phase. While most IDPs, including α‐Syn, present in many charge states and a wide range of rotationally averaged collision cross sections (CCSs), ApoC‐II presents in just four charge states and a very narrow range of CCSs, independent of solution conditions. Here, we compare MS and IM‐MS data of both proteins, and rationalise the differences between the proteins in terms of different ionisation processes which they may adhere to. PMID:25920945

  13. Relating gas phase to solution conformations: Lessons from disordered proteins.

    PubMed

    Beveridge, Rebecca; Phillips, Ashley S; Denbigh, Laetitia; Saleem, Hassan M; MacPhee, Cait E; Barran, Perdita E

    2015-08-01

    In recent years both mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS) have been developed as techniques with which to study proteins that lack a fixed tertiary structure but may contain regions that form secondary structure elements transiently, namely intrinsically disordered proteins (IDPs). IM-MS is a suitable method for the study of IDPs which provides an insight to conformations that are present in solution, potentially enabling the analysis of lowly populated structural forms. Here, we describe the IM-MS data of two IDPs; α-Synuclein (α-Syn) which is implicated in Parkinson's disease, and Apolipoprotein C-II (ApoC-II) which is involved in cardiovascular diseases. We report an apparent discrepancy in the way that ApoC-II behaves in the gas phase. While most IDPs, including α-Syn, present in many charge states and a wide range of rotationally averaged collision cross sections (CCSs), ApoC-II presents in just four charge states and a very narrow range of CCSs, independent of solution conditions. Here, we compare MS and IM-MS data of both proteins, and rationalise the differences between the proteins in terms of different ionisation processes which they may adhere to. PMID:25920945

  14. Phosphorylation-mediated RNA/peptide complex coacervation as a model for intracellular liquid organelles

    NASA Astrophysics Data System (ADS)

    Aumiller, William M.; Keating, Christine D.

    2016-02-01

    Biological cells are highly organized, with numerous subcellular compartments. Phosphorylation has been hypothesized as a means to control the assembly/disassembly of liquid-like RNA- and protein-rich intracellular bodies, or liquid organelles, that lack delimiting membranes. Here, we demonstrate that charge-mediated phase separation, or complex coacervation, of RNAs with cationic peptides can generate simple model liquid organelles capable of reversibly compartmentalizing biomolecules. Formation and dissolution of these liquid bodies was controlled by changes in peptide phosphorylation state using a kinase/phosphatase enzyme pair. The droplet-generating phase transition responded to modification of even a single serine residue. Electrostatic interactions between the short cationic peptides and the much longer polyanionic RNAs drove phase separation. Coacervates were also formed on silica beads, a primitive model for localization at specific intracellular sites. This work supports phosphoregulation of complex coacervation as a viable mechanism for dynamic intracellular compartmentalization in membraneless organelles.

  15. Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization.

    PubMed

    Schafroth, Heather D; Floudas, Christodoulos A

    2004-02-15

    Development of a computational prediction method based on molecular modeling, global optimization, and implicit solvation has produced accurate structure and relative binding affinity predictions for peptide amino acids binding to five pockets of the MHC molecule HLA-DRB1*0101. Because peptide binding to MHC molecules is essential to many immune responses, development of such a method for understanding and predicting the forces that drive binding is crucial for pharmaceutical design and disease treatment. Underlying the development of this prediction method are two hypotheses. The first is that pockets formed by the peptide binding groove of MHC molecules are independent, separating the prediction of peptide amino acids that bind within individual pockets from those that bind between pockets. The second hypothesis is that the native state of a system composed of an amino acid bound to a protein pocket corresponds to the system's lowest free energy. The prediction method developed from these hypotheses uses atomistic-level modeling, deterministic global optimization, and three methods of implicit solvation: solvent-accessible area, solvent-accessible volume, and Poisson-Boltzmann electrostatics. The method predicts relative binding affinities of peptide amino acids for pockets of HLA-DRB1*0101 by determining computationally an amino acid's global minimum energy conformation. Prediction results from the method are in agreement with X-ray crystallography data and experimental binding assays.

  16. GAS PHASE SELECTIVE PHOTOXIDATION OF ALCOHOLS USING LIGHT-ACTIVATED TITANIUM DIOXIDE AND MOLECULAR OXYGEN

    EPA Science Inventory

    Gas Phase Selective Oxidation of Alcohols Using Light-Activated Titanium Dioxide and Molecular Oxygen

    Gas phase selective oxidations of various primary and secondary alcohols are studied in an indigenously built stainless steel up-flow photochemical reactor using ultravi...

  17. Gas-phase reactions and energy transfer at very low temperatures.

    PubMed

    Sims, I R; Smith, I W

    1995-01-01

    Experimental studies of gas-phase chemical reactions and molecular energy transfer at very low temperatures and between electrically neutral species are reviewed. Although work of collisionally induced vibrational and rotational transfer is described, emphasis is placed on very recent results on the rates of free radical reactions obtained by applying the pulsed laser photolysis (PLP)-laser-induced fluorescence (LIF) technique in a CRESU (Cinétique de Réactions en Ecoulement Supersonique Uniforme) apparatus at temperatures as low as 13 K. These measurements demonstrate that quite a wide variety of reactions-including those between two radicals, those between radicals and unsaturated molecules, and even some of those between radicals and saturated molecules-remain rapid at very low temperatures. Theoretical efforts to explain some of these results are described, as is their impact on attempts to model the synthesis of molecules in interstellar clouds.

  18. Prophylactic uses of integrin CD18-βA peptide in a murine polymicrobial peritonitis model

    PubMed Central

    Wong, Kwong-Fai; Wo, Jana; Ho, David; Poon, Ronnie T; Casasnovas, José M; Luk, John M

    2010-01-01

    AIM: To evaluate the prophylactic properties of integrin CD18-βA peptide in a murine model of abdominal polymicrobial peritonitis and sepsis. METHODS: Bacterial sepsis was induced in Institute of Cancer Research (ICR) mice by cecal ligation and puncture (CLP) surgery. Inflicted mice were then injected with either sterile saline or CD18-βA peptide intraperitoneally at 2 h after surgery, and were sacrificed at 12 and 24 h after surgery. Blood samples were immediately collected, and analyzed for endotoxin activity and tumor necrosis factor (TNF)-α and interleukin (IL)-6. Lungs and liver were studied for CD45+ leukocyte and CD3 mRNA content. Pulmonary expression of intercellular adhesion molecule (ICAM)-1, vascular cell adhesion molecule (VCAM) and E-selectin was also determined. RESULTS: Intraperitoneal injection of CD18-βA peptide significantly suppressed circulating endotoxin activity (P < 0.01) at 24 h, as well as serum levels of TNF-α (P < 0.05 at 12 and 24 h) and IL-6 (P < 0.01 at 12 h, P < 0.05 at 24 h) in CLP-inflicted mice. CD18-βA peptide also abrogated leukocyte infiltration into liver and lungs as unveiled by reduced CD45+ leukocyte and CD3 mRNA contents. Furthermore, the peptide significantly reduced pulmonary expression of VCAM (P < 0.01 at 12 h, P < 0.001 at 24 h), E-selectin (P < 0.01 at 12 and 24 h), and ICAM-1 (P < 0.01 at 12 h, P < 0.001 at 24 h). These actions of CD18-βA peptide collectively protected septic mice against lethality (P < 0.01). CONCLUSION: CD18-βA peptide is a potent endotoxin antagonist that can protect surgical patients against sepsis-associated lethality. PMID:20518087

  19. Support Vector Machine Classification of Probability Models and Peptide Features for Improved Peptide Identification from Shotgun Proteomics

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Oehmen, Chris S.; Cannon, William R.

    2007-12-01

    Proteomics is a rapidly advancing field offering a new perspective to biological systems. Mass spectrometry (MS) is a popular experimental approach because it allows global protein characterization of a sample in a high-throughput manner. The identification of a protein is based on the spectral signature of fragments of the constituent proteins, i.e., peptides. This peptide identification is typically performed with a computational database search algorithm; however, these database search algorithms return a large number of false positive identifications. We present a new scoring algorithm that uses a SVM to integrate database scoring metrics with peptide physiochemical properties, resulting in an improved ability to separate true from false peptide identification from MS. The Peptide Identification Classifier SVM (PICS) score using only five variables is significantly more accurate than the single best database metric, quantified as the area under a Receive Operating Characteristic curve of ~0.94 versus ~0.90.

  20. Effect of multilayer ice chemistry on gas-phase deuteration in starless cores

    NASA Astrophysics Data System (ADS)

    Sipilä, O.; Caselli, P.; Taquet, V.

    2016-06-01

    Context. Astrochemical models commonly used to study the deuterium chemistry in starless cores consider a two-phase approach in which the ice on the dust grains is assumed to be entirely reactive. Recent experimental studies suggest that cold interstellar ices are mostly inert, and a multilayer model distinguishing the chemical processes at the surface and in the ice bulk would be more appropriate. Aims: We investigate whether the multilayer model can be as successful as the bulk model in reproducing the observed abundances of various deuterated gas-phase species toward starless cores. Methods: We calculated abundances for various deuterated species as functions of time using a pseudo-time-dependent chemical model adopting fixed physical conditions. We also estimated abundance gradients in starless cores by adopting a modified Bonnor-Ebert sphere as a core model. In the multilayer ice scenario, we consider desorption from one or several monolayers on the surface. Results: We find that the multilayer model predicts abundances of DCO+ and N2D+ that are about an order of magnitude lower than observed; the difference is caused by the trapping of CO and N2 within the grain mantle. As a result of the mantle trapping, deuteration efficiency in the gas phase increases and we find stronger deuterium fractionation in ammonia than has been observed. Another distinguishing feature of the multilayer model is that becomes the main deuterated ion at high density. The bulk ice model is generally easily reconciled with observations. Conclusions: Our results underline that more theoretical and experimental work is needed to understand the composition and morphology of interstellar ices, and the desorption processes that can act on them. With the current constraints, the bulk ice model appears to reproduce the observations more accurately than the multilayer ice model. According to our results, the abundance ratio of H2D+ to N2D+ is higher than 100 in the multilayer model, while only

  1. THEORETICAL STUDY ON THE INTERACTION BETWEEN XENON AND POSITIVE SILVER CLUSTERS IN GAS PHASE AND ON THE (001) CHABAZITE SURFACE

    SciTech Connect

    Hunter, D.

    2009-03-16

    A systematic study on the adsorption of xenon on silver clusters in the gas phase and on the (001) surface of silver-exchanged chabazite is reported. Density functional theory at the B3LYP level with the cluster model was employed. The results indicate that the dominant part of the binding is the {sigma} donation, which is the charge transfer from the 5p orbital of Xe to the 5s orbital of Ag and is not the previously suggested d{sub {pi}}-d{sub {pi}} back-donation. A correlation between the binding energy and the degree of {sigma} donation is found. Xenon was found to bind strongly to silver cluster cations and not to neutral ones. The binding strength decreases as the cluster size increases for both cases, clusters in the gas-phase and on the chabazite surface. The Ag{sup +} cation is the strongest binding site for xenon both in gas phase and on the chabazite surface with the binding energies of 73.9 and 14.5 kJ/mol, respectively. The results also suggest that the smaller silver clusters contribute to the negative chemical shifts observed in the {sup 129}Xe NMR spectra in experiments.

  2. Description and control of dissociation channels in gas-phase protein complexes

    NASA Astrophysics Data System (ADS)

    Thachuk, Mark; Fegan, Sarah K.; Raheem, Nigare

    2016-08-01

    Using molecular dynamics simulations of a coarse-grained model of the charged apo-hemoglobin protein complex, this work expands upon our initial report [S. K. Fegan and M. Thachuk, J. Am. Soc. Mass Spectrom. 25, 722-728 (2014)] about control of dissociation channels in the gas phase using specially designed charge tags. Employing a charge hopping algorithm and a range of temperatures, a variety of dissociation channels are found for activated gas-phase protein complexes. At low temperatures, a single monomer unfolds and becomes charge enriched. At higher temperatures, two additional channels open: (i) two monomers unfold and charge enrich and (ii) two monomers compete for unfolding with one eventually dominating and the other reattaching to the complex. At even higher temperatures, other more complex dissociation channels open with three or more monomers competing for unfolding. A model charge tag with five sites is specially designed to either attract or exclude charges. By attaching this tag to the N-terminus of specific monomers, the unfolding of those monomers can be decidedly enhanced or suppressed. In other words, using charge tags to direct the motion of charges in a protein complex provides a mechanism for controlling dissociation. This technique could be used in mass spectrometry experiments to direct forces at specific attachment points in a protein complex, and hence increase the diversity of product channels available for quantitative analysis. In turn, this could provide insight into the function of the protein complex in its native biological environment. From a dynamics perspective, this system provides an interesting example of cooperative behaviour involving motions with differing time scales.

  3. LSPRAY: Lagrangian Spray Solver for Applications With Parallel Computing and Unstructured Gas-Phase Flow Solvers

    NASA Technical Reports Server (NTRS)

    Raju, Manthena S.

    1998-01-01

    Sprays occur in a wide variety of industrial and power applications and in the processing of materials. A liquid spray is a phase flow with a gas as the continuous phase and a liquid as the dispersed phase (in the form of droplets or ligaments). Interactions between the two phases, which are coupled through exchanges of mass, momentum, and energy, can occur in different ways at different times and locations involving various thermal, mass, and fluid dynamic factors. An understanding of the flow, combustion, and thermal properties of a rapidly vaporizing spray requires careful modeling of the rate-controlling processes associated with the spray's turbulent transport, mixing, chemical kinetics, evaporation, and spreading rates, as well as other phenomena. In an attempt to advance the state-of-the-art in multidimensional numerical methods, we at the NASA Lewis Research Center extended our previous work on sprays to unstructured grids and parallel computing. LSPRAY, which was developed by M.S. Raju of Nyma, Inc., is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and/or Monte Carlo probability density function (PDF) solver. The LSPRAY solver accommodates the use of an unstructured mesh with mixed triangular, quadrilateral, and/or tetrahedral elements in the gas-phase solvers. It is used specifically for fuel sprays within gas turbine combustors, but it has many other uses. The spray model used in LSPRAY provided favorable results when applied to stratified-charge rotary combustion (Wankel) engines and several other confined and unconfined spray flames. The source code will be available with the National Combustion Code (NCC) as a complete package.

  4. Selective Gas-Phase Oxidation and Localization of Alkylated Cysteine Residues in Polypeptide Ions via Ion/Ion Chemistry.

    PubMed

    Pilo, Alice L; Zhao, Feifei; McLuckey, Scott A

    2016-09-01

    The thiol group in cysteine residues is susceptible to several post-translational modifications (PTMs), including prenylation, nitrosylation, palmitoylation, and the formation of disulfide bonds. Additionally, cysteine residues involved in disulfide bonds are commonly reduced and alkylated prior to mass spectrometric analysis. Several of these cysteine modifications, specifically S-alkyl modifications, are susceptible to gas-phase oxidation via selective ion/ion reactions with periodate anions. Multiply protonated peptides containing modified cysteine residues undergo complex formation upon ion/ion reaction with periodate anions. Activation of the ion/ion complexes results in oxygen transfer from the reagent to the modified sulfur residue to create a sulfoxide functionality. Further activation of the sulfoxide derivative yields abundant losses of the modification with the oxidized sulfur as a sulfenic acid (namely, XSOH) to generate a dehydroalanine residue. This loss immediately indicates the presence of an S-alkyl cysteine residue, and the mass of the loss can be used to easily deduce the type of modification. An additional step of activation can be used to localize the modification to a specific residue within the peptide. Selective cleavage to create c- and z-ions N-terminal to the dehydroalanine residue is often noted. As these types of ions are not typically observed upon collision-induced dissociation (CID), they can be used to immediately indicate where in the peptide the PTM was originally located. PMID:27476698

  5. Selective Gas-Phase Oxidation and Localization of Alkylated Cysteine Residues in Polypeptide Ions via Ion/Ion Chemistry.

    PubMed

    Pilo, Alice L; Zhao, Feifei; McLuckey, Scott A

    2016-09-01

    The thiol group in cysteine residues is susceptible to several post-translational modifications (PTMs), including prenylation, nitrosylation, palmitoylation, and the formation of disulfide bonds. Additionally, cysteine residues involved in disulfide bonds are commonly reduced and alkylated prior to mass spectrometric analysis. Several of these cysteine modifications, specifically S-alkyl modifications, are susceptible to gas-phase oxidation via selective ion/ion reactions with periodate anions. Multiply protonated peptides containing modified cysteine residues undergo complex formation upon ion/ion reaction with periodate anions. Activation of the ion/ion complexes results in oxygen transfer from the reagent to the modified sulfur residue to create a sulfoxide functionality. Further activation of the sulfoxide derivative yields abundant losses of the modification with the oxidized sulfur as a sulfenic acid (namely, XSOH) to generate a dehydroalanine residue. This loss immediately indicates the presence of an S-alkyl cysteine residue, and the mass of the loss can be used to easily deduce the type of modification. An additional step of activation can be used to localize the modification to a specific residue within the peptide. Selective cleavage to create c- and z-ions N-terminal to the dehydroalanine residue is often noted. As these types of ions are not typically observed upon collision-induced dissociation (CID), they can be used to immediately indicate where in the peptide the PTM was originally located.

  6. Modeling of conformational transitions of fibrillogenic peptide, homologous to beta-domain of human alpha-lactalbumin

    NASA Astrophysics Data System (ADS)

    Kadochnikov, V. V.; Egorov, V. V.; Shvetsov, A. V.; Kuklin, A. I.; Isaev-Ivanov, V. V.; Lebedev, D. V.

    2016-01-01

    The behavior of the peptide corresponding to beta domain of human alpha-lactalbumin (GYDTQAIVENNESTEYG, WT) has been simulated by the molecular dynamics method. It is shown that, within the model considered, the monomer of this peptide does not tend to form a stable secondary structure; however, simulation of the behavior of several peptide molecules revealed the occurrence of beta structures due to the formation of intermolecular hydrogen bonds. Since the aforementioned interactions involve the terminal portions of peptides, the influence of the tetrapeptide corresponding to the N-terminal portion of WT, TDYG (R), on the secondary structure has been analyzed. The model calculations show that the interaction of this peptide with WT monomer facilitates formation of beta-structures. It is suggested that peptide R may affect the quaternary structure of WT.

  7. Gas-phase NMR. Part I. Conformational energies of 1,2-disubstituted propanes and a comparison with MM2 and MNDO calculations

    NASA Astrophysics Data System (ADS)

    Miyajima, Takashi; Hirano, Tsuneo; Sato, Hisaya

    1984-11-01

    Gas-phase 1H NMR spectra of 1,2-dichloropropane (1,2-DCP) and 1,2-di(methoxy- d3)-propane (1,2-DMP) have been measured. The conformational energies of these molecules in the gas phase were determined from the observed coupling constants under a three rotational isomeric state model and are compared with the theoretical values from MM2 molecular mechanics and MNDO molecular orbital calculations. The results indicate that gas-phase NMR is useful method for the determination of conformational energies of relatively complex molecules, and that the MNDO results are more reasonable than the MM2 results for molecules containing electronegative atoms such as oxygen.

  8. Conformational study of melectin and antapin antimicrobial peptides in model membrane environments.

    PubMed

    Kocourková, Lucie; Novotná, Pavlína; Čujová, Sabína; Čeřovský, Václav; Urbanová, Marie; Setnička, Vladimír

    2017-01-01

    Antimicrobial peptides have long been considered as promising compounds against drug-resistant pathogens. In this work, we studied the secondary structure of antimicrobial peptides melectin and antapin using electronic (ECD) and vibrational circular dichroism (VCD) spectroscopies that are sensitive to peptide secondary structures. The results from quantitative ECD spectral evaluation by Dichroweb and CDNN program and from the qualitative evaluation of the VCD spectra were compared. The antimicrobial activity of the selected peptides depends on their ability to adopt an amphipathic α-helical conformation on the surface of the bacterial membrane. Hence, solutions of different zwitterionic and negatively charged liposomes and micelles were used to mimic the eukaryotic and bacterial biological membranes. The results show a significant content of α-helical conformation in the solutions of negatively charged liposomes mimicking the bacterial membrane, thus correlating with the antimicrobial activity of the studied peptides. On the other hand in the solutions of zwitterionic liposomes used as models of the eukaryotic membranes, the fraction of α-helical conformation was lower, which corresponds with their moderate hemolytic activity. PMID:27450123

  9. Kinin Peptides Enhance Inflammatory and Oxidative Responses Promoting Apoptosis in a Parkinson's Disease Cellular Model

    PubMed Central

    Kozik, Andrzej

    2016-01-01

    Kinin peptides ubiquitously occur in nervous tissue and participate in inflammatory processes associated with distinct neurological disorders. These substances have also been demonstrated to promote the oxidative stress. On the other hand, the importance of oxidative stress and inflammation has been emphasized in disorders that involve the neurodegenerative processes such as Parkinson's disease (PD). A growing number of reports have demonstrated the increased expression of kinin receptors in neurodegenerative diseases. In this study, the effect of bradykinin and des-Arg10-kallidin, two representative kinin peptides, was analyzed with respect to inflammatory response and induction of oxidative stress in a PD cellular model, obtained after stimulation of differentiated SK-N-SH cells with a neurotoxin, 1-methyl-4-phenylpyridinium. Kinin peptides caused an increased cytokine release and enhanced production of reactive oxygen species and NO by cells. These changes were accompanied by a loss of cell viability and a greater activation of caspases involved in apoptosis progression. Moreover, the neurotoxin and kinin peptides altered the dopamine receptor 2 expression. Kinin receptor expression was also changed by the neurotoxin. These results suggest a mediatory role of kinin peptides in the development of neurodegeneration and may offer new possibilities for its regulation by using specific antagonists of kinin receptors. PMID:27721576

  10. Amyloid-β peptides in interaction with raft-mime model membranes: a neutron reflectivity insight.

    PubMed

    Rondelli, Valeria; Brocca, Paola; Motta, Simona; Messa, Massimo; Colombo, Laura; Salmona, Mario; Fragneto, Giovanna; Cantù, Laura; Del Favero, Elena

    2016-01-01

    The role of first-stage β-amyloid aggregation in the development of the Alzheimer disease, is widely accepted but still unclear. Intimate interaction with the cell membrane is invoked. We designed Neutron Reflectometry experiments to reveal the existence and extent of the interaction between β-amyloid (Aβ) peptides and a lone customized biomimetic membrane, and their dependence on the aggregation state of the peptide. The membrane, asymmetrically containing phospholipids, GM1 and cholesterol in biosimilar proportion, is a model for a raft, a putative site for amyloid-cell membrane interaction. We found that the structured-oligomer of Aβ(1-42), its most acknowledged membrane-active state, is embedded as such into the external leaflet of the membrane. Conversely, the Aβ(1-42) unstructured early-oligomers deeply penetrate the membrane, likely mimicking the interaction at neuronal cell surfaces, when the Aβ(1-42) is cleaved from APP protein and the membrane constitutes a template for its further structural evolution. Moreover, the smaller Aβ(1-6) fragment, the N-terminal portion of Aβ, was also used. Aβ N-terminal is usually considered as involved in oligomer stabilization but not in the peptide-membrane interaction. Instead, it was seen to remove lipids from the bilayer, thus suggesting its role, once in the whole peptide, in membrane leakage, favouring peptide recruitment. PMID:26880066

  11. Dissociative electron attachment to the gas-phase nucleobase hypoxanthine

    NASA Astrophysics Data System (ADS)

    Dawley, M. Michele; Tanzer, Katrin; Carmichael, Ian; Denifl, Stephan; Ptasińska, Sylwia

    2015-06-01

    We present high-resolution measurements of the dissociative electron attachment (DEA) to isolated gas-phase hypoxanthine (C5H4N4O, Hyp), a tRNA purine base. The anion mass spectra and individual ion efficiency curves from Hyp were measured as a function of electron energy below 9 eV. The mass spectra at 1 and 6 eV exhibit the highest anion yields, indicating possible common precursor ions that decay into the detectable anionic fragments. The (Hyp - H) anion (C5H3N4O-) exhibits a sharp resonant peak at 1 eV, which we tentatively assign to a dipole-bound state of the keto-N1H,N9H tautomer in which dehydrogenation occurs at either the N1 or N9 position based upon our quantum chemical computations (B3LYP/6-311+G(d,p) and U(MP2-aug-cc-pVDZ+)) and prior studies with adenine. This closed-shell dehydrogenated anion is the dominant fragment formed upon electron attachment, as with other nucleobases. Seven other anions were also observed including (Hyp - NH)-, C4H3N4-/C4HN3O-, C4H2N3-, C3NO-/HC(HCN)CN-, OCN-, CN-, and O-. Most of these anions exhibit broad but weak resonances between 4 and 8 eV similar to many analogous anions from adenine. The DEA to Hyp involves significant fragmentation, which is relevant to understanding radiation damage of biomolecules.

  12. Gas-Phase Combustion Synthesis of Aluminum Nitride Powder

    NASA Technical Reports Server (NTRS)

    Axelbaum, R. L.; Lottes, C. R.; Huertas, J. I.; Rosen, L. J.

    1996-01-01

    Due to its combined properties of high electrical resistivity and high thermal conductivity aluminum nitride (AlN) is a highly desirable material for electronics applications. Methods are being sought for synthesis of unagglomerated, nanometer-sized powders of this material, prepared in such a way that they can be consolidated into solid compacts having minimal oxygen content. A procedure for synthesizing these powders through gas-phase combustion is described. This novel approach involves reacting AlCl3, NH3, and Na vapors. Equilibrium thermodynamic calculations show that 100% yields can be obtained for these reactants with the products being AlN, NaCl, and H2. The NaCl by-product is used to coat the AlN particles in situ. The coating allows for control of AlN agglomeration and protects the powders from hydrolysis during post-flame handling. On the basis of thermodynamic and kinetic considerations, two different approaches were employed to produce the powder, in co-flow diffusion flame configurations. In the first approach, the three reactants were supplied in separate streams. In the second, the AlCl3 and NH3 were premixed with HCl and then reacted with Na vapor. X-ray diffraction (XRD) spectra of as-produced powders show only NaCl for the first case and NaCl and AlN for the second. After annealing at 775 C tinder dynamic vacuum, the salt was removed and XRD spectra of powders from both approaches show only AlN. Aluminum metal was also produced in the co-flow flame by reacting AlCl3 with Na. XRD spectra of as-produced powders show the products to be only NaCl and elemental aluminum.

  13. Gas-phase chemistry of technetium carbonyl complexes.

    PubMed

    Wang, Yang; Qin, Zhi; Fan, Fang-Li; Haba, Hiromitsu; Komori, Yukiko; Cao, Shi-Wei; Wu, Xiao-Lei; Tan, Cun-Min

    2015-05-28

    Gas-phase chemical behaviors of short-lived technetium carbonyl complexes were studied using a low temperature isothermal chromatograph (IC) coupled with a (252)Cf spontaneous fission (SF) source. Fission products recoiled from the (252)Cf SF source were thermalized in a mixed gas containing CO, and then technetium carbonyl complexes were formed from reactions between CO gas and various technetium isotopes. A gas-jet system was employed to transport the volatile carbonyl complexes from a recoil chamber to the IC. Short IC columns made of Fluorinated Ethylene Propylene (FEP) Teflon and quartz were used to obtain chemical information about the technetium carbonyl complexes. The results for the (104)Tc-(106)Tc carbonyl complexes were found to be strongly influenced by the precursors, and showed the chemical behaviors of (104)Mo-(106)Mo carbonyl complexes, respectively. However, (107)Tc and (108)Tc could represent the chemical information of the element technetium due to their high independent yields and the very short half-lives of their precursors (107)Mo and (108)Mo. An adsorption enthalpy of about ΔHads = -43 kJ mol(-1) was determined for the Tc carbonyl complexes on both the Teflon and quartz surfaces by fitting the breakthrough curves of the (107)Tc and (108)Tc carbonyl complexes with a Monte Carlo simulation program. Chemical yields of around 25% were measured for the Tc carbonyl complexes relative to the transport yields obtained with the gas-jet transport of KCl aerosol particles with Ar carrier gas. Furthermore, the influence of a small amount of O2 gas on the yields of the Mo and Tc carbonyl complexes was studied.

  14. Uptake of Organic Gas Phase Species by 1-Methylnaphthalene

    NASA Astrophysics Data System (ADS)

    Zhang, H.; Xia, J.; Davidovits, P.; Jayne, J. T.; Kolb, C. E.; Worsnop, D. R.

    2002-12-01

    Using a droplet train apparatus, the mass accommodation coefficients (α) on 1-methylnapthalene of gas phase m-xylene, ethylbenzene, butylbenzene, α-pinene, γ-terpinene, and 2-methyl-2-hexanol were measured as a function of temperature (265 K to 296 K). 1-methylnapthalene was selected as a surrogate for hydrophobic and aromatic hydrocarbons found in tropospheric aerosols. The mass accommodation coefficients (α) of all the molecules obtained from these measurements exhibit negative temperature dependence. The upper and lower values of α at 265 K and 296 K respectively are: for m-xylene 0.44 and 0.26; for ethylbenzene 0.37 and 0.22; for butylbenzene 0.47 and 0.31; for α-pinene 0.47 and 0.096; for γ-terpinene 0.39 and 0.12; for 2-methyl-2-hexanol 0.44 and 0.26. The uptake measurements also yielded values for the product HDl1/2 for most of the molecules studied (H = Henry's law constant, Dl = liquid phase diffusion coefficient). Using calculated values of Dl the Henry's law constant is obtained, and expressed in the form ln H (M/atm) = -A + B/T. The A and B values for the molecules studied are listed in Table 1. Table 1: A and B values for the Henry's law constant H expressed as ln H (M/atm) = -A + B/T \\ m-xylene: A=7.20, B=4060\\ethylbenzene: A=5.81, B=3660\\butylbenzene: A=16.95, B=7330α-pinene: A=15.69, B=6360\\2-methyl-2-hexanol: A=9.95, B=4760

  15. IV-VI semiconductor lasers for gas phase biomarker detection

    NASA Astrophysics Data System (ADS)

    McCann, Patrick; Namjou, Khosrow; Roller, Chad; McMillen, Gina; Kamat, Pratyuma

    2007-09-01

    A promising absorption spectroscopy application for mid-IR lasers is exhaled breath analysis where sensitive, selective, and speedy measurement of small gas phase biomarker molecules can be used to diagnose disease and monitor therapies. Many molecules such as nitric oxide, ethane, formaldehyde, acetaldehyde, acetone, carbonyl sulfide, and carbon disulfide have been connected to diseases or conditions such as asthma, oxidative stress, breast cancer, lung cancer, diabetes, organ transplant rejection, and schizophrenia. Measuring these and other, yet to be discovered, biomarker molecules in exhaled breath with mid-IR lasers offers great potential for improving health care since such tests are non-invasive, real-time, and do not require expensive consumables or chemical reagents. Motivated by these potential benefits, mid-IR laser spectrometers equipped with presently available cryogenically-cooled IV-VI lasers mounted in compact Stirling coolers have been developed for clinical research applications. This paper will begin with a description of the development of mid-IR laser instruments and their use in the largest known exhaled breath clinical study ever performed. It will then shift to a description of recent work on the development of new IV-VI semiconductor quantum well materials and laser fabrication methods that offer the promise of low power consumption (i.e. efficient) continuous wave emission at room temperature. Taken together, the demonstration of compelling clinical applications with large market opportunities and the clear identification of a viable pathway to develop low cost mid-IR laser instrumentation can create a renewed focus for future research and development efforts within the mid-IR materials and devices area.

  16. Infrared spectroscopy of ionized corannulene in the gas phase

    NASA Astrophysics Data System (ADS)

    Galué, Héctor Alvaro; Rice, Corey A.; Steill, Jeffrey D.; Oomens, Jos

    2011-02-01

    The gas-phase infrared spectra of radical cationic and protonated corannulene were recorded by infrared multiple-photon dissociation (IRMPD) spectroscopy using the IR free electron laser for infrared experiments. Electrospray ionization was used to generate protonated corannulene and an IRMPD spectrum was recorded in a Fourier-transform ion cyclotron resonance mass spectrometer monitoring H-loss as a function of IR frequency. The radical cation was produced by 193-nm UV photoionization of the vapor of corannulene in a 3D quadrupole trap and IR irradiation produces H, H2, and C2Hx losses. Summing the spectral response of the three fragmentation channels yields the IRMPD spectrum of the radical cation. The spectra were analyzed with the aid of quantum-chemical calculations carried out at various levels of theory. The good agreement of theoretical and experimental spectra for protonated corannulene indicates that protonation occurs on one of the peripheral C-atoms, forming an sp3 hybridized carbon. The spectrum of the radical cation was examined taking into account distortions of the C5v geometry induced by the Jahn-Teller effect as a consequence of the degenerate 2E1 ground electronic state. As indicated by the calculations, the five equivalent Cs minima are separated by marginal barriers, giving rise to a dynamically distorted system. Although in general the character of the various computed vibrational bands appears to be in order, only a qualitative match to the experimental spectrum is found. Along with a general redshift of the calculated frequencies, the IR intensities of modes in the 1000-1250 cm-1 region show the largest discrepancy with the harmonic predictions. In addition to CH "in-plane" bending vibrations, these modes also exhibit substantial deformation of the pentagonal inner ring, which may relate directly to the vibronic interaction in the radical cation.

  17. Gas-phase chemistry of technetium carbonyl complexes.

    PubMed

    Wang, Yang; Qin, Zhi; Fan, Fang-Li; Haba, Hiromitsu; Komori, Yukiko; Cao, Shi-Wei; Wu, Xiao-Lei; Tan, Cun-Min

    2015-05-28

    Gas-phase chemical behaviors of short-lived technetium carbonyl complexes were studied using a low temperature isothermal chromatograph (IC) coupled with a (252)Cf spontaneous fission (SF) source. Fission products recoiled from the (252)Cf SF source were thermalized in a mixed gas containing CO, and then technetium carbonyl complexes were formed from reactions between CO gas and various technetium isotopes. A gas-jet system was employed to transport the volatile carbonyl complexes from a recoil chamber to the IC. Short IC columns made of Fluorinated Ethylene Propylene (FEP) Teflon and quartz were used to obtain chemical information about the technetium carbonyl complexes. The results for the (104)Tc-(106)Tc carbonyl complexes were found to be strongly influenced by the precursors, and showed the chemical behaviors of (104)Mo-(106)Mo carbonyl complexes, respectively. However, (107)Tc and (108)Tc could represent the chemical information of the element technetium due to their high independent yields and the very short half-lives of their precursors (107)Mo and (108)Mo. An adsorption enthalpy of about ΔHads = -43 kJ mol(-1) was determined for the Tc carbonyl complexes on both the Teflon and quartz surfaces by fitting the breakthrough curves of the (107)Tc and (108)Tc carbonyl complexes with a Monte Carlo simulation program. Chemical yields of around 25% were measured for the Tc carbonyl complexes relative to the transport yields obtained with the gas-jet transport of KCl aerosol particles with Ar carrier gas. Furthermore, the influence of a small amount of O2 gas on the yields of the Mo and Tc carbonyl complexes was studied. PMID:25920667

  18. Dissociative electron attachment to the gas-phase nucleobase hypoxanthine

    SciTech Connect

    Dawley, M. Michele; Tanzer, Katrin; Denifl, Stephan E-mail: Sylwia.Ptasinska.1@nd.edu; Carmichael, Ian; Ptasińska, Sylwia E-mail: Sylwia.Ptasinska.1@nd.edu

    2015-06-07

    We present high-resolution measurements of the dissociative electron attachment (DEA) to isolated gas-phase hypoxanthine (C{sub 5}H{sub 4}N{sub 4}O, Hyp), a tRNA purine base. The anion mass spectra and individual ion efficiency curves from Hyp were measured as a function of electron energy below 9 eV. The mass spectra at 1 and 6 eV exhibit the highest anion yields, indicating possible common precursor ions that decay into the detectable anionic fragments. The (Hyp − H) anion (C{sub 5}H{sub 3}N{sub 4}O{sup −}) exhibits a sharp resonant peak at 1 eV, which we tentatively assign to a dipole-bound state of the keto-N1H,N9H tautomer in which dehydrogenation occurs at either the N1 or N9 position based upon our quantum chemical computations (B3LYP/6-311+G(d,p) and U(MP2-aug-cc-pVDZ+)) and prior studies with adenine. This closed-shell dehydrogenated anion is the dominant fragment formed upon electron attachment, as with other nucleobases. Seven other anions were also observed including (Hyp − NH){sup −}, C{sub 4}H{sub 3}N{sub 4}{sup −}/C{sub 4}HN{sub 3}O{sup −}, C{sub 4}H{sub 2}N{sub 3}{sup −}, C{sub 3}NO{sup −}/HC(HCN)CN{sup −}, OCN{sup −}, CN{sup −}, and O{sup −}. Most of these anions exhibit broad but weak resonances between 4 and 8 eV similar to many analogous anions from adenine. The DEA to Hyp involves significant fragmentation, which is relevant to understanding radiation damage of biomolecules.

  19. Measurement of Gas-phase Acids in Diesel Exhaust

    NASA Astrophysics Data System (ADS)

    Wentzell, J. J.; Liggio, J.; Li, S.; Vlasenko, A. L.; Staebler, R. M.; Brook, J.; Lu, G.; Poitras, M.; Chan, T.

    2012-12-01

    Gas-phase acids were measured using chemical ionization mass spectrometry (CIMS) as part of the Diesel Engine Emission Research Experiment (DEERE). The CIMS technique, utilizing acetate ion (CH3COO-) as a reagent ion, proved to be a rapid (measurements on the order of seconds) and sensitive (several counts/pptv) method of quantifying the acid emissions. Diluted diesel exhaust measurements were made from a Constant Volume Sampling dilution tunnel using a light duty (1.9L turbocharged Volkswagen Jetta TDI) diesel engine equipped with an OEM diesel oxidation catalyst and exhaust gas recirculation, mounted on an engine dynamometer. Acids measured included isocyanic, nitrous, nitric, propionic and sum of lactic and oxalic, as well as other unidentified compounds. Complimentary measurements of CO, CO2, Total Hydrocarbon (THC), and NOx, were also performed. Several engine modes (different engine rpm and torque outputs) at steady state were examined to determine their effect on acid emissions. Emission rates with respect to NOx and fuel based emission factors were determined. Measurements of HONO fuel emission factors agree well with real-world measurements within a traffic tunnel.1 The first estimate of isocyanic acid emission factors from a diesel engine is reported, and suggests that the emission of this highly toxic compound in diesel exhaust should not be ignored. 1. Kurtenbach, R., Becker, K. H., Gomes, J. A. G., Kleffmann, J.,Lorzer, J. C., Spittler, M., Wiesen, P., Ackermann, R., Geyer, A.,and Platt, U.: Investigations of emissions and heterogeneous formation of HONO in a road traffic tunnel, Atmos. Environ., 35, 3385-3394, doi:10.1016/S1352-2310(01)00138-8, 2001.

  20. Effective adjunctive therapy by an innate defense regulatory peptide in a preclinical model of severe malaria.

    PubMed

    Achtman, Ariel H; Pilat, Sandra; Law, Charity W; Lynn, David J; Janot, Laure; Mayer, Matt L; Ma, Shuhua; Kindrachuk, Jason; Finlay, B Brett; Brinkman, Fiona S L; Smyth, Gordon K; Hancock, Robert E W; Schofield, Louis

    2012-05-23

    Case fatality rates for severe malaria remain high even in the best clinical settings because antimalarial drugs act against the parasite without alleviating life-threatening inflammation. We assessed the potential for host-directed therapy of severe malaria of a new class of anti-inflammatory drugs, the innate defense regulator (IDR) peptides, based on host defense peptides. The Plasmodium berghei ANKA model of experimental cerebral malaria was adapted to use as a preclinical screen by combining late-stage intervention in established infections with advanced bioinformatic analysis of early transcriptional changes in co-regulated gene sets. Coadministration of IDR-1018 with standard first-line antimalarials increased survival of infected mice while down-regulating key inflammatory networks associated with fatality. Thus, IDR peptides provided host-directed adjunctive therapy for severe disease in combination with antimalarial treatment.

  1. Effects of osmolytes on the helical conformation of model peptide: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Mehrnejad, Faramarz; Ghahremanpour, Mohammad Mehdi; Khadem-Maaref, Mahmoud; Doustdar, Farahnoosh

    2011-01-01

    Co-solvents such as glycerol and sorbitol are small organic molecules solvated in the cellular solutions that can have profound effects on the protein structures. Here, the molecular dynamics simulations and comparative structural analysis of magainin, as a peptide model, in pure water, 2,2,2-trifluoroethanol/water, glycerol/water, and sorbitol/water are reported. Our results show that the peptide NMR structure is largely maintained its native structure in osmolytes-water mixtures. The simulation data indicates that the stabilizing effect of glycerol and sorbitol is induced by preferential accumulation of glycerol and sorbitol molecules around the nonpolar and aromatic residues. Thus, the presence of glycerol and sorbitol molecules decreases the interactions of water molecules with the hydrophobic residues of the peptide, and the alpha helical structure is stabilized.

  2. MINLP models for the synthesis of optimal peptide tags and downstream protein processing.

    PubMed

    Simeonidis, Evangelos; Pinto, Jose M; Lienqueo, M Elena; Tsoka, Sophia; Papageorgiou, Lazaros G

    2005-01-01

    The development of systematic methods for the synthesis of downstream protein processing operations has seen growing interest in recent years, as purification is often the most complex and costly stage in biochemical production plants. The objective of the work presented here is to develop mathematical models based on mixed integer optimization techniques, which integrate the selection of optimal peptide purification tags into an established framework for the synthesis of protein purification processes. Peptide tags are comparatively short sequences of amino acids fused onto the protein product, capable of reducing the required purification steps. The methodology is illustrated through its application on two example protein mixtures involving up to 13 contaminants and a set of 11 candidate chromatographic steps. The results are indicative of the benefits resulting by the appropriate use of peptide tags in purification processes and provide a guideline for both optimal tag design and downstream process synthesis. PMID:15932268

  3. Theoretical modeling of peptide α-helical circular dichroism in aqueous solution.

    PubMed

    Kaminský, Jakub; Kubelka, Jan; Bour, Petr

    2011-03-10

    Reliable modeling of protein and peptide circular dichroism (CD) spectra in the far UV presents a challenge for current theoretical approaches. In this study, the time-dependent density functional theory (TDDFT), configuration interaction with single excitation (CIS), and transition dipole coupling (TDC) were used to assess the most important factors contributing to the CD spectra of the α-helical secondary structure. The dependence on the peptide chain length and also the role of the flexibility and solvent environment were investigated with a model oligopeptide Ac-(Ala)(N)-NH-Me, (N = 1, ..., 18). Both the TDDFT and TDC-like methods suggest that the CD curve typical for the α-helix arises gradually, but its basic characteristic is discernible already for peptides with 4-5 amino acid residues. The calculated dependence was in a qualitative agreement with experimental spectra of short α-helices stabilized by the histidine-metal binding. The TDDFT computations of the CD were found to be unusually sensitive to the basis set and solvent model. Explicit hydration and temperature fluctuations of the peptide geometry, simulated with the aid of molecular dynamics (MD), significantly influenced the CD and absorption spectral shapes. An extensive averaging over MD configurations is thus required to obtain a converged spectral profile in cluster simulations. On the other hand, both the TDDFT and TDC models indicate only a minor influence of the alanine side chains. The CIS and TDC calculations also point toward a relatively small effect of the helix-helix interaction on the CD spectral profiles. For a model system of two helices, the CIS method predicted larger changes in the spectra than TDC. This suggests other than interactions between peptide chains, such as mutual polarization, can have a minor, but measurable, effect on the CD spectrum.

  4. Conformational Preferences in Small Peptide Models: The Relevance of cis/trans-Conformations.

    PubMed

    Jangra, Harish; Haindl, Michael H; Achrainer, Florian; Hioe, Johnny; Gschwind, Ruth M; Zipse, Hendrik

    2016-09-01

    The accurate description of cis/trans peptide structures is of fundamental relevance for the field of protein modeling and protein structure determination. A comprehensive conformational analysis of dipeptide model Ace-Gly-NMe (1) has been carried out by using a combination of theoretical calculations and experimental ((1) H and (13) C NMR and NOESY) spectroscopic measurements to assess the relevance of cis-peptide conformers. NMR measurements in dimethyl sulfoxide (DMSO) solution and calculations employing a continuum solvation model both point to the extended trans,trans conformer C5_tt as the global minimum. The cis-peptide structures C5_ct and C5_tc, with the N- or C-terminal amide group in cis-conformation, are observed separately and located 13.0±2 kJ mol(-1) higher in energy. This is in close agreement with the theoretical prediction of around 12 kJ mol(-1) in DMSO. The ability of common protein force fields to reproduce the energies of the cis-amide conformers C5_ct and C5_tc in 1 is limited, making these methods unsuitable for the description of cis-peptide structures in protein simulations. PMID:27535479

  5. Gas Phase Thz Spectroscopy of Organosulfide and Organophosphorous Compounds Using a Synchrotron Source

    NASA Astrophysics Data System (ADS)

    Cuisset, Arnaud; Smirnova, Irina; Bocquet, Robin; Hindle, Francis; Mouret, Gael; Sadovskii, Dmitrii A.; Pirali, Olivier; Roy, Pascale

    2011-06-01

    This study concerns the gas phase rovibrational spectroscopy of organosulfide and organophosphorous which are considered as non toxic model compounds in the analysis of chemical weapon materials, high pathogenic and mutagenic agents, and other environmentally interesting air-borne species. The coupling of the synchrotron radiation with multipass cells and the FTIR spectrometer allowed to obtain very conclusive results in term of sensitivity and resolution and improved the previous results obtained with classical sources. For DMSO, using an optical path of 150 m the spectra have been recorded at the ultimate resolution of 0.001 Cm-1 allowing to fully resolve the rotational structure of the lowest vibrational modes observed in the THz region. In the 290 - 420 Cm-1 region, the rovibrational spectrum of the "perpendicular" and "parallel" vibrational bands associated with, respectively, the asymmetric ν23 and symmetric ν11 bending modes of DMSO have been recorded with a resolution of 1.5× 10-3 Cm-1. The gas phase vibrational spectra of organophosphorous compounds were measured by FTIR spectroscopy using the vapor pressure of the compounds. Except for TBP, the room temperature vapor pressure was sufficient to detect all active vibrational modes from THz to NIR domain. Contrary to DMSO, the rotational patterns of alkyl phosphates and alkyl phosphonates could not be resolved; only a vibrational analysis may be performed. Nevertheless, the spectral fingerprints observed in the THz region allowed a clear discrimination between the molecules and between the different molecular conformations. A. Cuisset, G. Mouret, O. Pirali, P. Roy, F. Cazier, H. Nouali, J. Demaison, J. Phys. Chem. B, 2008, 112:, 12516-12525 A. Cuisset, L. Nanobashvili, I. Smirnova, R. Bocquet, F. Hindle, G. Mouret, O. Pirali, P. Roy and D. A. Sadovskií, Chem. Phys. Lett., 2010, 492: 30-34 I. Smirnova, A. Cuisset, R. Bocquet, F. Hindle, G. Mouret, O. Pirali, P. Roy, J. Phys. Chem. B, 2010, 114: 16936-16947.

  6. Effect of dimethylamine on the gas phase sulfuric acid concentration measured by Chemical Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Rondo, L.; Ehrhart, S.; Kürten, A.; Adamov, A.; Bianchi, F.; Breitenlechner, M.; Duplissy, J.; Franchin, A.; Dommen, J.; Donahue, N. M.; Dunne, E. M.; Flagan, R. C.; Hakala, J.; Hansel, A.; Keskinen, H.; Kim, J.; Jokinen, T.; Lehtipalo, K.; Leiminger, M.; Praplan, A.; Riccobono, F.; Rissanen, M. P.; Sarnela, N.; Schobesberger, S.; Simon, M.; Sipilä, M.; Smith, J. N.; Tomé, A.; Tröstl, J.; Tsagkogeorgas, G.; Vaattovaara, P.; Winkler, P. M.; Williamson, C.; Wimmer, D.; Baltensperger, U.; Kirkby, J.; Kulmala, M.; Petäjä, T.; Worsnop, D. R.; Curtius, J.

    2016-03-01

    Sulfuric acid is widely recognized as a very important substance driving atmospheric aerosol nucleation. Based on quantum chemical calculations it has been suggested that the quantitative detection of gas phase sulfuric acid (H2SO4) by use of Chemical Ionization Mass Spectrometry (CIMS) could be biased in the presence of gas phase amines such as dimethylamine (DMA). An experiment (CLOUD7 campaign) was set up at the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber to investigate the quantitative detection of H2SO4 in the presence of dimethylamine by CIMS at atmospherically relevant concentrations. For the first time in the CLOUD experiment, the monomer sulfuric acid concentration was measured by a CIMS and by two CI-APi-TOF (Chemical Ionization-Atmospheric Pressure interface-Time Of Flight) mass spectrometers. In addition, neutral sulfuric acid clusters were measured with the CI-APi-TOFs. The CLOUD7 measurements show that in the presence of dimethylamine (<5 to 70 pptv) the sulfuric acid monomer measured by the CIMS represents only a fraction of the total H2SO4, contained in the monomer and the clusters that is available for particle growth. Although it was found that the addition of dimethylamine dramatically changes the H2SO4 cluster distribution compared to binary (H2SO4-H2O) conditions, the CIMS detection efficiency does not seem to depend substantially on whether an individual H2SO4 monomer is clustered with a DMA molecule. The experimental observations are supported by numerical simulations based on A Self-contained Atmospheric chemistry coDe coupled with a molecular process model (Sulfuric Acid Water NUCleation) operated in the kinetic limit.

  7. Effect of dimethylamine on the gas phase sulfuric acid concentration measured by Chemical Ionization Mass Spectrometry

    PubMed Central

    Ehrhart, S.; Kürten, A.; Adamov, A.; Bianchi, F.; Breitenlechner, M.; Duplissy, J.; Franchin, A.; Dommen, J.; Donahue, N. M.; Dunne, E. M.; Flagan, R. C.; Hakala, J.; Hansel, A.; Keskinen, H.; Kim, J.; Jokinen, T.; Lehtipalo, K.; Leiminger, M.; Praplan, A.; Riccobono, F.; Rissanen, M. P.; Sarnela, N.; Schobesberger, S.; Simon, M.; Sipilä, M.; Smith, J. N.; Tomé, A.; Tröstl, J.; Tsagkogeorgas, G.; Vaattovaara, P.; Winkler, P. M.; Williamson, C.; Wimmer, D.; Baltensperger, U.; Kirkby, J.; Kulmala, M.; Petäjä, T.; Worsnop, D. R.; Curtius, J.

    2016-01-01

    Abstract Sulfuric acid is widely recognized as a very important substance driving atmospheric aerosol nucleation. Based on quantum chemical calculations it has been suggested that the quantitative detection of gas phase sulfuric acid (H2SO4) by use of Chemical Ionization Mass Spectrometry (CIMS) could be biased in the presence of gas phase amines such as dimethylamine (DMA). An experiment (CLOUD7 campaign) was set up at the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber to investigate the quantitative detection of H2SO4 in the presence of dimethylamine by CIMS at atmospherically relevant concentrations. For the first time in the CLOUD experiment, the monomer sulfuric acid concentration was measured by a CIMS and by two CI‐APi‐TOF (Chemical Ionization‐Atmospheric Pressure interface‐Time Of Flight) mass spectrometers. In addition, neutral sulfuric acid clusters were measured with the CI‐APi‐TOFs. The CLOUD7 measurements show that in the presence of dimethylamine (<5 to 70 pptv) the sulfuric acid monomer measured by the CIMS represents only a fraction of the total H2SO4, contained in the monomer and the clusters that is available for particle growth. Although it was found that the addition of dimethylamine dramatically changes the H2SO4 cluster distribution compared to binary (H2SO4‐H2O) conditions, the CIMS detection efficiency does not seem to depend substantially on whether an individual H2SO4 monomer is clustered with a DMA molecule. The experimental observations are supported by numerical simulations based on A Self‐contained Atmospheric chemistry coDe coupled with a molecular process model (Sulfuric Acid Water NUCleation) operated in the kinetic limit.

  8. Effect of dimethylamine on the gas phase sulfuric acid concentration measured by Chemical Ionization Mass Spectrometry

    PubMed Central

    Ehrhart, S.; Kürten, A.; Adamov, A.; Bianchi, F.; Breitenlechner, M.; Duplissy, J.; Franchin, A.; Dommen, J.; Donahue, N. M.; Dunne, E. M.; Flagan, R. C.; Hakala, J.; Hansel, A.; Keskinen, H.; Kim, J.; Jokinen, T.; Lehtipalo, K.; Leiminger, M.; Praplan, A.; Riccobono, F.; Rissanen, M. P.; Sarnela, N.; Schobesberger, S.; Simon, M.; Sipilä, M.; Smith, J. N.; Tomé, A.; Tröstl, J.; Tsagkogeorgas, G.; Vaattovaara, P.; Winkler, P. M.; Williamson, C.; Wimmer, D.; Baltensperger, U.; Kirkby, J.; Kulmala, M.; Petäjä, T.; Worsnop, D. R.; Curtius, J.

    2016-01-01

    Abstract Sulfuric acid is widely recognized as a very important substance driving atmospheric aerosol nucleation. Based on quantum chemical calculations it has been suggested that the quantitative detection of gas phase sulfuric acid (H2SO4) by use of Chemical Ionization Mass Spectrometry (CIMS) could be biased in the presence of gas phase amines such as dimethylamine (DMA). An experiment (CLOUD7 campaign) was set up at the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber to investigate the quantitative detection of H2SO4 in the presence of dimethylamine by CIMS at atmospherically relevant concentrations. For the first time in the CLOUD experiment, the monomer sulfuric acid concentration was measured by a CIMS and by two CI‐APi‐TOF (Chemical Ionization‐Atmospheric Pressure interface‐Time Of Flight) mass spectrometers. In addition, neutral sulfuric acid clusters were measured with the CI‐APi‐TOFs. The CLOUD7 measurements show that in the presence of dimethylamine (<5 to 70 pptv) the sulfuric acid monomer measured by the CIMS represents only a fraction of the total H2SO4, contained in the monomer and the clusters that is available for particle growth. Although it was found that the addition of dimethylamine dramatically changes the H2SO4 cluster distribution compared to binary (H2SO4‐H2O) conditions, the CIMS detection efficiency does not seem to depend substantially on whether an individual H2SO4 monomer is clustered with a DMA molecule. The experimental observations are supported by numerical simulations based on A Self‐contained Atmospheric chemistry coDe coupled with a molecular process model (Sulfuric Acid Water NUCleation) operated in the kinetic limit. PMID:27610289

  9. Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling.

    SciTech Connect

    Fang, Bin; Fu, Guoxing; Agniswamy, Johnson; Harrison, Robert W.; Weber, Irene T.

    2009-03-31

    Caspase-3 recognition of various P4 residues in its numerous protein substrates was investigated by crystallography, kinetics, and calculations on model complexes. Asp is the most frequent P4 residue in peptide substrates, although a wide variety of P4 residues are found in the cellular proteins cleaved by caspase-3. The binding of peptidic inhibitors with hydrophobic P4 residues, or no P4 residue, is illustrated by crystal structures of caspase-3 complexes with Ac-IEPD-Cho, Ac-WEHD-Cho, Ac-YVAD-Cho, and Boc-D(OMe)-Fmk at resolutions of 1.9-2.6 {angstrom}. The P4 residues formed favorable hydrophobic interactions in two separate hydrophobic regions of the binding site. The side chains of P4 Ile and Tyr form hydrophobic interactions with caspase-3 residues Trp206 and Trp214 within a non-polar pocket of the S4 subsite, while P4 Trp interacts with Phe250 and Phe252 that can also form the S5 subsite. These interactions of hydrophobic P4 residues are distinct from those for polar P4 Asp, which indicates the adaptability of caspase-3 for binding diverse P4 residues. The predicted trends in peptide binding from molecular models had high correlation with experimental values for peptide inhibitors. Analysis of structural models for the binding of 20 different amino acids at P4 in the aldehyde peptide Ac-XEVD-Cho suggested that the majority of hydrophilic P4 residues interact with Phe250, while hydrophobic residues interact with Trp206, Phe250, and Trp214. Overall, the S4 pocket of caspase-3 exhibits flexible adaptation for different residues and the new structures and models, especially for hydrophobic P4 residues, will be helpful for the design of caspase-3 based drugs.

  10. Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

    1993-01-01

    The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

  11. Implications of Low Volatility SOA and Gas-Phase Fragmentation Reactions on SOA Loadings and their Spatial and Temporal Evolution in the Atmosphere

    SciTech Connect

    Shrivastava, ManishKumar B.; Zelenyuk, Alla; Imre, Dan; Easter, Richard C.; Beranek, Josef; Zaveri, Rahul A.; Fast, Jerome D.

    2013-04-27

    Recent laboratory and field measurements by a number of groups show that secondary organic aerosol (SOA) evaporates orders of magnitude slower than traditional models assume. In addition, chemical transport models using volatility basis set (VBS) SOA schemes neglect gas-phase fragmentation reactions, which are known to be extremely important. In this work, we present modeling studies to investigate the implications of non-evaporating SOA and gas-phase fragmentation reactions. Using the 3-D chemical transport model, WRF-Chem, we show that previous parameterizations, which neglect fragmentation during multi-generational gas-phase chemistry of semi-volatile/inter-mediate volatility organics ("aging SIVOC"), significantly over-predict SOA as compared to aircraft measurements downwind of Mexico City. In sharp contrast, the revised models, which include gas-phase fragmentation, show much better agreement with measurements downwind of Mexico City. We also demonstrate complex differences in spatial SOA distributions when we transform SOA to non-volatile secondary organic aerosol (NVSOA) to account for experimental observations. Using a simple box model, we show that for same amount of SOA precursors, earlier models that do not employ multi-generation gas-phase chemistry of precursors ("non-aging SIVOC"), produce orders of magnitude lower SOA than "aging SIVOC" parameterizations both with and without fragmentation. In addition, traditional absorptive partitioning models predict almost complete SOA evaporation at farther downwind locations for both "non-aging SIVOC" and "aging SIVOC" with fragmentation. In contrast, in our revised approach, SOA transformed to NVSOA implies significantly higher background concentrations as it remains in particle phase even under highly dilute conditions. This work has significant implications on understanding the role of multi-generational chemistry and NVSOA formation on SOA evolution in the atmosphere.

  12. Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results.

    PubMed Central

    Ben-Tal, N; Honig, B; Peitzsch, R M; Denisov, G; McLaughlin, S

    1996-01-01

    We measured directly the binding of Lys3, Lys5, and Lys7 to vesicles containing acidic phospholipids. When the vesicles contain 33% acidic lipids and the aqueous solution contains 100 mM monovalent salt, the standard Gibbs free energy for the binding of these peptides is 3, 5, and 7 kcal/mol, respectively. The binding energies decrease as the mol% of acidic lipids in the membrane decreases and/or as the salt concentration increases. Several lines of evidence suggest that these hydrophilic peptides do not penetrate the polar headgroup region of the membrane and that the binding is mainly due to electrostatic interactions. To calculate the binding energies from classical electrostatics, we applied the nonlinear Poisson-Boltzmann equation to atomic models of the phospholipid bilayers and the basic peptides in aqueous solution. The electrostatic free energy of interaction, which arises from both a long-range coulombic attraction between the positively charged peptide and the negatively charged lipid bilayer, and a short-range Born or image charge repulsion, is a minimum when approximately 2.5 A (i.e., one layer of water) exists between the van der Waals surfaces of the peptide and the lipid bilayer. The calculated molar association constants, K, agree well with the measured values: K is typically about 10-fold smaller than the experimental value (i.e., a difference of about 1.5 kcal/mol in the free energy of binding). The predicted dependence of K (or the binding free energies) on the ionic strength of the solution, the mol% of acidic lipids in the membrane, and the number of basic residues in the peptide agree very well with the experimental measurements. These calculations are relevant to the membrane binding of a number of important proteins that contain clusters of basic residues. Images FIGURE 2 FIGURE 3 PMID:8842196

  13. Gas phase chemistry of bis(pentamethylcyclopentadienyl)samarium

    SciTech Connect

    Marcalo, J.; Matos, A.P. de; Evans, W.

    1996-01-09

    The gas phase chemistry of bis(pentamethylcyclopentadienyl)samarium, (C{sub 5}Me{sub 5}){sub 2}Sm, was studied by Fourier transform ion cyclotron resonance mass spectrometry (FTICR/MS). Positive electron impact (EI) spectra showed the formation of (C{sub 5}Me{sub 5}){sub 2} Sm{sup +}, (C{sub 5}Me{sub 5})Sm{sup +}, and Sm{sup +}. All three ions reacted with (C{sub 5}Me{sub 5}){sub 2}Sm by charge transfer, as verified by double-resonance techniques, and (C{sub 5}Me{sub 5})Sm{sup +} also formed the (C{sub 5}Me{sub 5}){sub 3}Sm{sub 2}{sup +} ion in a condensation reaction with neutral (C{sub 5}Me{sub 5}){sub 2}Sm. The laser desorption/ionization (LDI) spectra showed, in addition to (C{sub 5}Me{sub 5}){sub 2}Sm{sup +}, (C{sub 5}Me{sub 5})Sm{sup +}, and Sm{sup +}, the formation of (C{sub 5}Me{sub 4}H)Sm{sup +} and (C{sub 5}Me{sub 4}CH{sub 2})Sm{sup +}. The latter species most probably involves a tetramethylfulvenide ligand. Access to all of the ionic species cited here could also be obtained by reacting laser-desorbed Sm{sup +} ions with pentamethylcyclopentadiene, C{sub 5}Me{sub 5}H. (C{sub 5}Me{sub 4}CH{sub 2})Sm{sup +}, (C{sub 5}Me{sub 4}H)Sm{sup +}, and (C{sub 5}Me{sub 5})Sm{sup +} were formed as primary products, and the metallocene ion (C{sub 5}Me{sub 5}){sub 2}Sm{sup +} resulted from the rapid addition of C{sub 5}Me{sub 5}H to (C{sub 5}Me{sub 4}CH{sub 2})Sm{sup +}. 34 refs., 4 figs.

  14. Gas-phase lithium cation affinity of glycine.

    PubMed

    Bourcier, Sophie; Chiaa, Ru Xuan; Mimbong, Rosa Ngo Biboum; Bouchoux, Guy

    2015-01-01

    The gas-phase lithium cation binding thermochemistry of glycine has been determined theoretically by quantum chemical calculations at the G4 level and experimentally by the extended kinetic method using electrospray ionization quadrupole time-of-flight tandem mass spectrometry. The lithium cation affinity of glycine, ∆(Li)H°(298)(GLY), i.e. the∆(Li)H°(298) of the reaction GlyLi(+)→ Gly + Li(+)) given by the G4 method is equal to 241.4 kJ.mol(-1) if only the most stable conformer of glycine is considered or to 242.3 kJ.mol(-1) if the 298K equilibrium mixture of neutral conformers is included in the calculation. The ∆(Li)H°(298)(GLY) deduced from the extended kinetic method is obviously dependent on the choice of the Li(+) affinity scale, thus∆(Li)H°(298)(GLY) is equal to 228.7±0.9(2.0) kJ.mol(- 1) if anchored to the recently re-evaluated lithium cation affinity scale but shifted to 235.4±1.0 kJ.mol(-1) if G4 computed lithium cation affinities of the reference molecules is used. This difference of 6.3 kJ.mol(-1) may originate from a compression of the experimental lithium affinity scale in the high ∆(Li)H°(298) region. The entropy change associated with the reaction GlyLi(+)→Gly + Li(+) reveals a gain of approximately 15 J.mol(-) 1.K(-1) with respect to monodentate Li(+) acceptors. The origin of this excess entropy is attributed to the bidentate interaction between the Li(+) cation and both the carbonyl oxygen and the nitrogen atoms of glycine. The computed G4 Gibbs free energy,∆(Li)G°(298)(GLY) is equal to 205.3 kJ.mol(-1), a similar result, 201.0±3.4 kJ.mol(-1), is obtained from the experiment if the∆(Li)G°(298) of the reference molecules is anchored on the G4 results. PMID:26307695

  15. Gas-phase lithium cation affinity of glycine.

    PubMed

    Bourcier, Sophie; Chiaa, Ru Xuan; Mimbong, Rosa Ngo Biboum; Bouchoux, Guy

    2015-01-01

    The gas-phase lithium cation binding thermochemistry of glycine has been determined theoretically by quantum chemical calculations at the G4 level and experimentally by the extended kinetic method using electrospray ionization quadrupole time-of-flight tandem mass spectrometry. The lithium cation affinity of glycine, ∆(Li)H°(298)(GLY), i.e. the∆(Li)H°(298) of the reaction GlyLi(+)→ Gly + Li(+)) given by the G4 method is equal to 241.4 kJ.mol(-1) if only the most stable conformer of glycine is considered or to 242.3 kJ.mol(-1) if the 298K equilibrium mixture of neutral conformers is included in the calculation. The ∆(Li)H°(298)(GLY) deduced from the extended kinetic method is obviously dependent on the choice of the Li(+) affinity scale, thus∆(Li)H°(298)(GLY) is equal to 228.7±0.9(2.0) kJ.mol(- 1) if anchored to the recently re-evaluated lithium cation affinity scale but shifted to 235.4±1.0 kJ.mol(-1) if G4 computed lithium cation affinities of the reference molecules is used. This difference of 6.3 kJ.mol(-1) may originate from a compression of the experimental lithium affinity scale in the high ∆(Li)H°(298) region. The entropy change associated with the reaction GlyLi(+)→Gly + Li(+) reveals a gain of approximately 15 J.mol(-) 1.K(-1) with respect to monodentate Li(+) acceptors. The origin of this excess entropy is attributed to the bidentate interaction between the Li(+) cation and both the carbonyl oxygen and the nitrogen atoms of glycine. The computed G4 Gibbs free energy,∆(Li)G°(298)(GLY) is equal to 205.3 kJ.mol(-1), a similar result, 201.0±3.4 kJ.mol(-1), is obtained from the experiment if the∆(Li)G°(298) of the reference molecules is anchored on the G4 results.

  16. Detection methods for atoms and radicals in the gas phase

    NASA Astrophysics Data System (ADS)

    Hack, W.

    This report lists atoms and free radicals in the gas phase which are of interest for environmental and flame chemistry and have been detected directly. The detection methods which have been used are discussed with respect to their range of application, specificity and sensitivity. In table 1, detection methods for the five atoms of group IV (C, Si, Ge, Sn, Pb) and about 60 radicals containing at least one atom of group IV are summarized (CH, Cd, Cf, CC1, CBr, Cn, Cs, CSe, CH2, CD2, Chf, Cdf, CHC1, CHBr, CF2, CC12, CBr2, CFC1, CFBr, CH3, CD3, CF3, CH2F, CH2C1, CH2Br, CHF2, CHC12, CHBr2, Hco, Fco, CH30, CD30, CH2OH, CH3S, Nco, CH4N, CH302, CF302; C2, C2N, C2H, C20, C2HO, C2H3, C2F3, C2H5, C2HsO, C2H4OH, CH3CO, CD3CO, C2H3O, C2H502, CH3COO2, C2H4N, C2H6N, C3; Si, SiF, SiF2, SiO, SiC, Si2; Ge, GeC, GeO, GeF, GeF2, GeCl2, Sn, SnF, SnO, SnF2, Pb, PbF, PbF2, PbO, PbS). In table 2 detection methods for about 25 other atoms and 60 radicals are listed: (H, D, O, O2, Oh, Od, HO2, DO2, F, Ci, Br, I, Fo, Cio, BrO, Io, FO2, C1O2, Li, Na, K, Rb, Cs, N, N3, Nh, Nd, Nf, Nci, NBr, NH2, ND2, Nhd, Nhf, NF2, NC12, N2H3, No, NO2, NO3, Hno, Dno, P, Ph, Pd, Pf, Pci, PH2, PD2, PF2, Po, As, AsO, AsS, Sb, Bi, S, S2, Sh, Sd, Sf, SF2, So, Hso, Dso, Sn, Se, Te, Se2, SeH, SeD, SeF, SeO, SeS, SeN, TeH, TeO, Bh, BH2, Bo, Bn, B02, Cd, Hg, UF5). The tables also cite some recent kinetic applications of the various methods.

  17. Study of Two Bioactive Peptides in Vacuum and Solvent by Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Yaşar, F.; Demir, K.

    The thermodynamic and structural properties of Tyrosine-Glycine-Leusine-Phenylalanine (YGLF, in a one letter code) and Lysine-Valine-Leusine-Proline-Valine-Proline-Glutamine (KVLPVPQ) peptide sequences were studied by three-dimensional molecular modeling in vacuum and solution. All the three-dimensional conformations of each peptide sequences were obtained by multicanonical simulations with using ECEPP/2 force field and each simulation started from completely random initial conformation. Solvation contributions are included by a term that is proportional to solvent-accessible surface areas of peptides. In the present study, we calculated the average values of total energy, specific heat, fourth-order cumulant and end-to-end distance for two peptide sequences of milk protein as a function of temperature. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of β-turn, γ-turn and helical structures. Although structural predictions of these sequences indicate both the presence of high level of γ-turns and low level of β-turns in vacuum and solvent, it was observed that these probabilities in vacuum were higher than the ones in solvent model.

  18. Mm/submm Study of Gas-Phase Photoproducts from Methanol Interstellar Ice Analogues

    NASA Astrophysics Data System (ADS)

    Mesko, AJ; Smith, Houston Hartwell; Milam, Stefanie N.; Widicus Weaver, Susanna L.

    2016-06-01

    Icy grain reactions have gained quite the popularity in the astrochemistry community to explain the formation of complex organic molecules. Through temperature programmed desorption and photolysis experiments we use rotational spectroscopy to measure the gas-phase products of icy grain reactions. Previous results include testing detection limits of the system by temperature programmed desorption of methanol and water ices, photochemistry of gas-phase methanol, and detection of photodesorbed water from a pure water ice surface. Current work that will be discussed focuses on the detection of gas-phase CO and other photoproducts from an ice surface.

  19. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides.

    PubMed

    Alauddin, Mohammad; Biswal, Himansu S; Gloaguen, Eric; Mons, Michel

    2015-01-21

    Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns. PMID:25482851

  20. Sampling and determination of gas-phase hydrogen peroxide following removal of ozone by gas-phase reaction with nitric oxide

    SciTech Connect

    Tanner, R.L.; Markovits, G.Y.; Ferreri, E.M.; Kelly, T.J.

    1986-01-01

    A method for determination of hydrogen peroxide in the ambient atmosphere is described, using impinger or diffusion scrubber collection of hydrogen peroxide with aqueous-phase analysis by an enzyme-catalyzed fluorescence technique. Interference from ozone at ambient levels is removed by gas-phase titration with excess nitric oxide. The impinger and diffusion scrubber collection techniques are shown to give equivalent results for atmospheric gas-phase hydrogen peroxide with limits of detection of 0.1 ppbv for approximately 60-min and 10-min sampling times, respectively.

  1. Simple off-lattice model to study the folding and aggregation of peptides

    NASA Astrophysics Data System (ADS)

    Combe, Nicolas; Frenkel, Daan

    We present a numerical study of a new protein model. This off-lattice model takes into account both the hydrogen bonds and the amino-acid interactions. It reproduces the folding of a small protein (peptide): morphological analysis of the conformations at low temperature shows two well-known substructures α-helix and β-sheet depending on the chosen sequence. The folding pathway in the scope of this model is studied through a free-energy analysis. We then study the aggregation of proteins. Proteins in the aggregate are mainly bound via hydrogen bonds. Performing a free-energy analysis we show that the addition of a peptide to such an aggregate is not favourable. We qualitatively reproduce the abnormal aggregation of proteins in prion diseases.

  2. Fragmentation Mechanisms of Oxidized Peptides Elucidated by SID, RRKM Modeling and Molecular Dynamics

    SciTech Connect

    Spraggins, Jeffrey M.; Lloyd, Julie A.; Johnston, Murray V.; Laskin, Julia; Ridge, Douglas P.

    2009-09-08

    The gas phase fragmentation reactions of singly charged angiotensin II (AngII, DRVYIHPF) and the ozonolysis products AngII+O (DRVY*IHPF), AngII+3O (DRVYIH*PF), and AngII+4O (DRVY*IH*PF) were studied using SID FT-ICR mass spectrometry and molecular dynamics. Oxidation of Tyr (AngII+O) leads to an additional low-energy charge-remote selective fragmentation channel resulting in the b4 fragment ion. Modification of His leads to a series of new selective dissociation channels. For AngII+3O and AngII+4O, the formation of [MH+3O]+-45 and [MH+3O]+-71 are driven by charge-remote processes while it is suggested that the b5 and [MH+3O]+-88 fragments are a result of charge-directed reactions. Energy-resolved SID experiments and RRKM modeling were able to provide insight into the energetics of the lowest energy fragmentation channel for each of the parent ions. Destabilization of the ozonolysis products was found to be strictly due to entropic effects. Mechanistic details for each of the new dissociation pathways were determined by relating the SID FT-ICR MS results to parent ion conformations samples using molecular dynamics.

  3. Cys-Gly specific dipeptidase Dug1p from S. cerevisiae binds promiscuously to di-, tri-, and tetra-peptides: Peptide-protein interaction, homology modeling, and activity studies reveal a latent promiscuity in substrate recognition.

    PubMed

    Kaur, Hardeep; Datt, Manish; Ekka, Mary Krishna; Mittal, Monica; Singh, Appu Kumar; Kumaran, Sangaralingam

    2011-02-01

    Dug1p is a recently identified novel dipeptidase and plays an important role in glutathione (GSH) degradation. To understand the mechanism of its substrate recognition and specificity towards Cys-Gly dipeptides, we characterized the solution properties of Dug1p and studied the thermodynamics of Dug1p-peptide interactions. In addition, we used homology modeling and ligand docking approaches to get structural insights into Dug1p-peptide interaction. Dug1p exists as dimer and the stoichiometry of peptide-Dug1p complex is 2:1 indicating each monomer in the dimer binds to one peptide. Thermodynamic studies indicate that the free energy change for Dug1p-peptide complex formation is similar (▵G(bind) ∼ -7.0 kcal/mol) for a variety of peptides of different composition and length (22 peptides). Three-dimensional model of Dug1p is constructed and docking of peptides to the modeled structure suggests that hydrogen bonding to active site residues (E172, E171, and D137) lock the N-terminal of the peptide into the binding site. Dug1p recognizes peptides in a metal independent manner and peptide binding is not sensitive to salts (dlogK/dlog[salt] ∼ 0) over a range of [NaCl] (0.02-0.5 M), [ZnCl(2)], and [MnCl(2)] (0-0.5 mM). Our results indicate that promiscuity in peptide binding results from the locking of peptide N-terminus into the active site. These observations were supported by our competitive inhibition activity assays. Dug1p activity towards Cys-Gly peptide is significantly reduced (∼ 70%) in the presence of Glu-Cys-Gly. Therefore, Dug1p can recognize a variety of oligopeptides, but has evolved with post-binding screening potential to hydrolyze Cys-Gly peptides selectively.

  4. Hydrogen-bonded glycine-HCN complexes in gas phase: structure, energetics, electric properties and cooperativity

    NASA Astrophysics Data System (ADS)

    Machado da Silva, Arnaldo; Chakrabarty, Sumana; Chaudhuri, Puspitapallab

    2015-03-01

    Twelve hydrogen-bonded complexes of glycine and hydrogen cyanide have been studied using high-level quantum-chemical calculations in gas phase. In particular, six 1:1 glycine-HCN dimers and six 1:2 glycine-HCN trimers have been considered. Besides the characteristics of the hydrogen bonds and their effect on molecular structure and energetics, several molecular electric properties have been calculated utilising two different models: MP2/6-31++G(d,p) and DFT-B3LYP/6-31++G(d,p). Although the structural parameters calculated by the two models are similar, equilibrium electronic energies of the clusters show model dependence. The lowest energy dimer is same in both the models which is ca. 3.0 kcal/mol more stable than the highest energy dimer. However, the lowest energy trimer is different in two methods. The energetic difference of stability between the highest and lowest trimer is 4.2 kcal/mol (4.4 kcal/mol) at an MP2 (B3LYP) level of calculation. The bond angles of glycine, in particular, are quite sensitive to the hydrogen-bond formation. Four out of six trimers are found to be strongly cooperative in both the models. Significant changes of dipole moments and polarisabilities of isolated glycine and hydrogen cyanide are observed due to the formation of hydrogen bonding. The Rayleigh scattering intensities of all clusters are much larger than those of their constituent monomers.

  5. Peptide binding landscapes: Specificity and homophilicity across sequence space in a lattice model

    NASA Astrophysics Data System (ADS)

    Jeon, Joohyun; Shell, M. Scott

    2016-10-01

    Peptide aggregation frequently involves sequences with strong homophilic binding character, i.e., sequences that self-assemble with like species in a crowded cellular environment, in the face of a multitude of other peptides or proteins as potential heterophilic binding partners. What kinds of sequences display a strong tendency towards homophilic binding and self-assembly, and what are the origins of this behavior? Here, we consider how sequence specificity in oligomerization processes plays out in a simple two-dimensional (2D) lattice statistical-thermodynamic peptide model that permits exhaustive examination of the entire sequence and configurational landscapes. We find that sequences with strong self-specificities have either alternating hydrophobic and hydrophilic residues or short patches of hydrophobic residues, both which minimize intramolecular hydrophobic interactions in part due to the constraints of the 2D lattice. We also find that these specificities are highly sensitive to entropic and free energetic features of the unbound conformational state, such that direct binding interaction energies alone do not capture the complete behavior. These results suggest that the ability of particular peptide sequences to self-assemble and aggregate in a many-protein environment reflects a precise balance of direct binding interactions and behavior in the unbound (monomeric) state.

  6. TFP5/TP5 peptide provides neuroprotection in the MPTP model of Parkinson's disease

    PubMed Central

    Binukumar, BK; Pant, Harish C.

    2016-01-01

    Cyclin-dependent kinase 5 (Cdk5) is a member of the serine-threonine kinase family of cyclin-dependent kinases. Cdk5 is critical to normal mammalian nervous system development and plays important regulatory roles in multiple cellular functions. Recent evidence indicates that Cdk5 is inappropriately activated in several neurodegenerative conditions, including Parkinson's disease (PD). PD is a chronic neurodegenerative disorder characterized by the loss of dopamine neurons in the substantia nigra, decreased striatal dopamine levels, and consequent extrapyramidal motor dysfunction. During neurotoxicity, p35 is cleaved to form p25. Binding of p25 with Cdk5 leads deregulation of Cdk5 resulting in number of neurodegenerative pathologies. To date, strategies to specifically inhibit Cdk5 hyperactivity have not been successful without affecting normal Cdk5 activity. Here we show that inhibition of p25/Cdk5 hyperactivation through TFP5/TP5, truncated 24-aa peptide derived from the Cdk5 activator p35 rescues nigrostriatal dopaminergic neurodegeneration induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP/MPP+) in a mouse model of PD. TP5 peptide treatment also blocked dopamine depletion in the striatum and improved gait dysfunction after MPTP administration. The neuroprotective effect of TFP5/TP5 peptide is also associated with marked reduction in neuroinflammation and apoptosis. Here we show inhibition of Cdk5/p25-hyperactivation by TFP5/TP5 peptide, which identifies Cdk5/p25 as a potential therapeutic target to reduce neurodegeneration in PD. PMID:27335538

  7. Effects of Gas-Phase Radiation and Detailed Kinetics on the Burning and Extinction of a Solid Fuel

    NASA Technical Reports Server (NTRS)

    Rhatigan, Jennifer L.

    2001-01-01

    This is the first attempt to analyze both radiation and detailed kinetics on the burning and extinction of a solid fuel in a stagnation-point diffusion flame. We present a detailed and comparatively accurate computational model of a solid fuel flame along with a quantitative study of the kinetics mechanism, radiation interactions, and the extinction limits of the flame. A detailed kinetics model for the burning of solid trioxane (a trimer of formaldehyde) is coupled with a narrowband radiation model, with carbon dioxide, carbon monoxide, and water vapor as the gas-phase participating media. The solution of the solid trioxane diffusion flame over the flammable regime is presented in some detail, as this is the first solution of a heterogeneous trioxane flame. We identify high-temperature and low-temperature reaction paths for the heterogeneous trioxane flame. We then compare the adiabatic solution to solutions that include Surface radiation only and gas-phase and surface radiation using a black surface model. The analysis includes discussion of detailed flame chemistry over the flammable regime and, in particular, at the low stretch extinction limit. We emphasize the low stretch regime of the radiatively participating flame, since this is the region representative of microgravity flames. When only surface radiation is included, two extinction limits exist (the blow-off limit, and the low stretch radiative limit), and the burning rate and maximum flame temperatures are lower, as expected. With the inclusion of surface and gas-phase radiation, results show that, while flame temperatures are lower, the burning rate of the trioxane diffusion flame may actually increase at low stretch rate due to radiative feedback from the flame to the surface.

  8. Identification of gas-phase dimethyl sulfate and monomethyl hydrogen sulfate in the Los Angeles atmosphere

    SciTech Connect

    Eatough, D.J.; White, V.F.; Hansen, L.D.; Eatough, N.L.; Cheney, J.L.

    1986-09-01

    Gas-phase dimethyl sulfate and monomethyl hydrogen sulfate have been identified in the atmosphere in Los Angeles. Gas-phase concentrations of these two alkyl sulfates were determined by using analytical methods based on the collection of the compounds before collection of particles using diffusion denuders and after collection of particles using resin beds or sorption filters, and specific analysis of the collected alkyl sulfates by ion chromatography. The data show the dimethyl sulfate is present in both particles and the gas phase. The concentration of total gas-phase methyl sulfates was found to vary from 34 to 178 nmol/m/sup 3/ during the smog episode studied. These species constituted a significant fraction of the total sulfur budget in the Los Angeles basin during the sampling period.

  9. Identification of gas-phase dimethyl sulfate and monomethyl hydrogen sulfate in the Los Angeles atmosphere

    SciTech Connect

    Eatough, D.J.; White, V.F.; Hansen, L.D.; Eatough, N.L.; Cheney, J.L.

    1986-01-01

    Analytical techniques were developed for the collection and determination of gas-phase dimethyl sulfate and monomethyl sulfuric acid based on collection of the alkyl sulfate compounds with both denuder tubes and resin sorption beds and analysis of the collected material by ion chromatography. Gas-phase dimethyl sulfate and monomethyl sulfuric acid were identified in Los Angeles using these techniques. The data indicate that dimethyl sulfate is present in both particles and in the gas phase. The concentration of gas-phase methyl sulfates was found to be several micrograms/cu m. These species thus account for a significant fraction of the total sulfur budget in the Los Angeles Basin during the sample period.

  10. Gas-phase water-mediated equilibrium between methylglyoxal and its geminal diol.

    PubMed

    Axson, Jessica L; Takahashi, Kaito; De Haan, David O; Vaida, Veronica

    2010-04-13

    In aqueous solution, aldehydes, and to a lesser extent ketones, hydrate to form geminal diols. We investigate the hydration of methylglyoxal (MG) in the gas phase, a process not previously considered to occur in water-restricted environments. In this study, we spectroscopically identified methylglyoxal diol (MGD) and obtained the gas-phase partial pressures of MG and MGD. These results, in conjunction with the relative humidity, were used to obtain the equilibrium constant, K(P), for the water-mediated hydration of MG in the gas phase. The Gibbs free energy for this process, DeltaG(o), obtained as a result, suggests a larger than expected gas-phase diol concentration. This may have significant implications for understanding the role of organics in atmospheric chemistry.

  11. Simulation and Numerical Modeling of the Self-assembly of an Optoelectronic Peptide

    NASA Astrophysics Data System (ADS)

    Mansbach, Rachael; Ferguson, Andrew

    We report molecular dynamics simulations of the self-assembly of synthetic π-conjugated oligopeptides into optoelectronic nanostructures. The electronic properties provide the basis for an array of organic electronic devices, such as light-emitting diodes, field-effect transistors, and solar cells. Control of the structure, stability, and kinetics of self-assembled organic electronics by tuning monomer chemistry and environmental conditions presents a powerful route to the fabrication of biocompatible ``designer materials.'' We have performed coarse-grained simulations of the self-assembly of several hundred peptides over microsecond time scales to probe the morphology and kinetics of aggregation with molecular-level detail. We have subsequently used this simulation data to parameterize a kinetic aggregation model based on Smoluchowski coagulation theory to enable prediction of aggregation dynamics on millisecond time scales. These numerical models are now being integrated into a multi-physics model of peptide aggregation in a microfluidic flow cell developed by our experimental collaborators to model the self-assembly of diverse peptide architectures under tailored flow-fields for the fabrication of biocompatible assemblies with defined morphology and optoelectronic function.

  12. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall,G.E.; Sears, T.J.

    2009-04-03

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.

  13. Chemical Nuclear Polarization of Biradicals Created by Photolysis of Cyclic Aliphatic Ketones in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Obynochnyia, A. A.; Purtovb, P. A.; Salikhova, K. M.

    2008-02-01

    Chemical nuclear polarization (CNP) of short-lived biradicals created in the photolysis of cyclic ketones in the gas phase with a buffer gas of CDCl3 molecules was studied theoretically and experimentally. The magnetoresonance and kinetic parameters were proposed for the biradicals. The experimental fact that the CNP of cycloundecanone in the gas phase and liquid was the strongest was confirmed by calculations. The computational results agree well with the experiment for both gas and liquid phases.

  14. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall, G.E.

    2011-05-31

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  15. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall G. E.; Goncharov, V.

    2012-05-29

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  16. Ultrafast electronic relaxation of excited state vitamin B 12 in the gas phase

    NASA Astrophysics Data System (ADS)

    Shafizadeh, Niloufar; Poisson, Lionel; Soep, Benoıˆt

    2008-06-01

    The time evolution of electronically excited vitamin B 12 (cyanocobalamin) has been observed for the first time in the gas phase. It reveals an ultrafast decay to a state corresponding to metal excitation. This decay is interpreted as resulting from a ring to metal electron transfer. This opens the observation of the excited state of other complex biomimetic systems in the gas phase, the key to the characterisation of their complex evolution through excited electronic states.

  17. An atmospheric pressure flow reactor: Gas phase kinetics and mechanism in tropospheric conditions without wall effects

    NASA Technical Reports Server (NTRS)

    Koontz, Steven L.; Davis, Dennis D.; Hansen, Merrill

    1988-01-01

    A new type of gas phase flow reactor, designed to permit the study of gas phase reactions near 1 atm of pressure, is described. A general solution to the flow/diffusion/reaction equations describing reactor performance under pseudo-first-order kinetic conditions is presented along with a discussion of critical reactor parameters and reactor limitations. The results of numerical simulations of the reactions of ozone with monomethylhydrazine and hydrazine are discussed, and performance data from a prototype flow reactor are presented.

  18. The peptide agonist-binding site of the glucagon-like peptide-1 (GLP-1) receptor based on site-directed mutagenesis and knowledge-based modelling

    PubMed Central

    Dods, Rachel L.; Donnelly, Dan

    2015-01-01

    Glucagon-like peptide-1 (7–36)amide (GLP-1) plays a central role in regulating blood sugar levels and its receptor, GLP-1R, is a target for anti-diabetic agents such as the peptide agonist drugs exenatide and liraglutide. In order to understand the molecular nature of the peptide–receptor interaction, we used site-directed mutagenesis and pharmacological profiling to highlight nine sites as being important for peptide agonist binding and/or activation. Using a knowledge-based approach, we constructed a 3D model of agonist-bound GLP-1R, basing the conformation of the N-terminal region on that of the receptor-bound NMR structure of the related peptide pituitary adenylate cyclase-activating protein (PACAP21). The relative position of the extracellular to the transmembrane (TM) domain, as well as the molecular details of the agonist-binding site itself, were found to be different from the model that was published alongside the crystal structure of the TM domain of the glucagon receptor, but were nevertheless more compatible with published mutagenesis data. Furthermore, the NMR-determined structure of a high-potency cyclic conformationally-constrained 11-residue analogue of GLP-1 was also docked into the receptor-binding site. Despite having a different main chain conformation to that seen in the PACAP21 structure, four conserved residues (equivalent to His-7, Glu-9, Ser-14 and Asp-15 in GLP-1) could be structurally aligned and made similar interactions with the receptor as their equivalents in the GLP-1-docked model, suggesting the basis of a pharmacophore for GLP-1R peptide agonists. In this way, the model not only explains current mutagenesis and molecular pharmacological data but also provides a basis for further experimental design. PMID:26598711

  19. Non-stationary filtration mode during chemical reactions with the gas phase

    NASA Astrophysics Data System (ADS)

    Zavialov, Ivan; Konyukhov, Andrey; Negodyaev, Sergey

    2015-04-01

    An experimental and numerical study of filtration accompanied by chemical reactions between displacing fluid and solid skeleton is considered. Glass balls (400-500 μm in diameter) were placed in 1 cm gap between two glass sheets and were used as model porous medium. The baking soda was added to the glass balls. The 70% solution of acetic acid was used as the displacer. The modeling porous medium was saturated with a mineral oil, and then 70% solution of colored acetic acid was pumped through the medium. The glass balls and a mineral oil have a similar refractive index, so the model porous medium was optically transparent. During the filtration, the gas phase was generated by the chemical reactions between the baking soda and acetic acid, and time-dependent displacement of the chemical reaction front was observed. The front of the chemical reaction was associated with the most intensive gas separation. The front moved, stopped, and then moved again to the area where it had been already. We called this process a secondary oxidation wave. To describe this effect, we added to the balance equations a term associated with the formation and disappearance of phases due to chemical reactions. The equations were supplemented by Darcy's law for multiphase filtration. Nonstationarity front propagation of the chemical reaction in the numerical experiment was observed at Damköhler numbers greater than 100. The mathematical modelling was agreed well with the experimental results.

  20. Structure activity relationship modelling of milk protein-derived peptides with dipeptidyl peptidase IV (DPP-IV) inhibitory activity.

    PubMed

    Nongonierma, Alice B; FitzGerald, Richard J

    2016-05-01

    Quantitative structure activity type models were developed in an attempt to predict the key features of peptide sequences having dipeptidyl peptidase IV (DPP-IV) inhibitory activity. The models were then employed to help predict the potential of peptides, which are currently reported in the literature to be present in the intestinal tract of humans following milk/dairy product ingestion, to act as inhibitors of DPP-IV. Two models (z- and v-scale) for short (2-5 amino acid residues) bovine milk peptides, behaving as competitive inhibitors of DPP-IV, were developed. The z- and the v-scale models (p<0.05, R(2) of 0.829 and 0.815, respectively) were then applied to 56 milk protein-derived peptides previously reported in the literature to be found in the intestinal tract of humans which possessed a structural feature of DPP-IV inhibitory peptides (P at the N2 position). Ten of these peptides were synthetized and tested for their in vitro DPP-IV inhibitory properties. There was no agreement between the predicted and experimentally determined DPP-IV half maximal inhibitory concentrations (IC50) for the competitive peptide inhibitors. However, the ranking for DPP-IV inhibitory potency of the competitive peptide inhibitors was conserved. Furthermore, potent in vitro DPP-IV inhibitory activity was observed with two peptides, LPVPQ (IC50=43.8±8.8μM) and IPM (IC50=69.5±8.7μM). Peptides present within the gastrointestinal tract of human may have promise for the development of natural DPP-IV inhibitors for the management of serum glucose.

  1. Interaction of the antimicrobial peptide gomesin with model membranes: a calorimetric study.

    PubMed

    Domingues, Tatiana M; Mattei, Bruno; Seelig, Joachim; Perez, Katia R; Miranda, Antonio; Riske, Karin A

    2013-07-01

    Gomesin is a potent cationic antimicrobial peptide (z = +6) isolated from the Brazilian spider Acanthoscurria gomesiana . The interaction of gomesin with large unilamellar vesicles composed of a 1:1 mixture of zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) phospholipids is studied with isothermal titration calorimetry (ITC). In parallel, light scattering and optical microscopy are used to assess peptide-induced vesicle aggregation. The ability of gomesin to permeabilize the membrane is examined with fluorescence spectroscopy of the leakage of 5,6-carboxyfluorescein (CF). Vesicles coated with 3 mol % 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (PE-PEG) lipids are also investigated to assess the influence of peptide-induced vesicle aggregation in the activity of gomesin. The ITC and light scattering titrations are done in two ways: lipid into peptide and peptide into lipid injections. Although some differences arise between the two setups, the basic interaction of gomesin with anionic vesicles is preserved. A surface partition model combined with the Gouy-Chapman theory is put forward to fit the ITC results. The intrinsic binding constant of gomesin is found to be K ≈ 10(3) M(-1). The interaction of gomesin with anionic membranes is highly exothermic and enthalpy-driven. Binding of gomesin is virtually always accompanied by vesicle aggregation and changes in membrane permeability, leading to CF leakage. Addition of PE-PEG to the membrane strongly attenuates vesicle aggregation but does not significantly change the mode of action of gomesin. The results point to a strong interaction of gomesin with the membrane surface, causing membrane rupture without a deep penetration into the bilayer core.

  2. CS-AMPPred: An Updated SVM Model for Antimicrobial Activity Prediction in Cysteine-Stabilized Peptides

    PubMed Central

    Porto, William F.; Pires, Állan S.; Franco, Octavio L.

    2012-01-01

    The antimicrobial peptides (AMP) have been proposed as an alternative to control resistant pathogens. However, due to multifunctional properties of several AMP classes, until now there has been no way to perform efficient AMP identification, except through in vitro and in vivo tests. Nevertheless, an indication of activity can be provided by prediction methods. In order to contribute to the AMP prediction field, the CS-AMPPred (Cysteine-Stabilized Antimicrobial Peptides Predictor) is presented here, consisting of an updated version of the Support Vector Machine (SVM) model for antimicrobial activity prediction in cysteine-stabilized peptides. The CS-AMPPred is based on five sequence descriptors: indexes of (i) α-helix and (ii) loop formation; and averages of (iii) net charge, (iv) hydrophobicity and (v) flexibility. CS-AMPPred was based on 310 cysteine-stabilized AMPs and 310 sequences extracted from PDB. The polynomial kernel achieves the best accuracy on 5-fold cross validation (85.81%), while the radial and linear kernels achieve 84.19%. Testing in a blind data set, the polynomial and radial kernels achieve an accuracy of 90.00%, while the linear model achieves 89.33%. The three models reach higher accuracies than previously described methods. A standalone version of CS-AMPPred is available for download at and runs on any Linux machine. PMID:23240023

  3. Vibrational infrared conformational studies of model peptides representing the semicrystalline domains of Bombyx mori silk fibroin.

    PubMed

    Taddei, Paola; Monti, Patrizia

    2005-08-01

    The structural organization of Bombyx mori silk fibroin was investigated by infrared (IR) spectroscopy. To this aim, (AG)15 and other model peptides of varying chain length, containing tyrosine (Y), valine (V), and serine (S) in the basic (AG)n sequence were synthesized by the solid phase method and their spectroscopic properties were determined. Both the position and the relative content of Y, V, and S residues in the (AG)n model system appeared critical in determining the preferred conformation, i.e., silk I, silk II, and unordered structures. Curve fitting analysis in the amide I range showed that the model peptides with prevailing silk II structure displayed different beta-sheet content, which was dependent on the degree of interruption of the (AG)n sequence. In this regard, the bands at about 1000 and 980 cm(-1), specifically assigned to the AG sequence of the B. mori silk fibroin chain, were identified as marker of the degree of interruption of the (AG)n sequence.A stable silk I structure was observed only when the Y residue was located near the chain terminus, while a silk I --> silk II conformational transition occurred when it was positioned in the central region of the peptide. Analysis of the second-derivative spectra in the amide I range allowed us to identify a band at 1639 cm(-1) (4 --> 1 hydrogen-bonded type II beta-turns), which is characteristic of the silk I conformation.

  4. Peptide identification

    DOEpatents

    Jarman, Kristin H [Richland, WA; Cannon, William R [Richland, WA; Jarman, Kenneth D [Richland, WA; Heredia-Langner, Alejandro [Richland, WA

    2011-07-12

    Peptides are identified from a list of candidates using collision-induced dissociation tandem mass spectrometry data. A probabilistic model for the occurrence of spectral peaks corresponding to frequently observed partial peptide fragment ions is applied. As part of the identification procedure, a probability score is produced that indicates the likelihood of any given candidate being the correct match. The statistical significance of the score is known without necessarily having reference to the actual identity of the peptide. In one form of the invention, a genetic algorithm is applied to candidate peptides using an objective function that takes into account the number of shifted peaks appearing in the candidate spectrum relative to the test spectrum.

  5. Simulation of gas phase transport of carbon-14 at Yucca Mountain, Nevada, USA

    USGS Publications Warehouse

    Lu, N.; Ross, B.

    1994-01-01

    We have simulated gas phase transport of Carbon-14 at Yucca Mountain, Nevada. Three models were established to calculate travel time of Carbon-14 from the potential repository to the mountain surface: a geochemical model for retardation factors, a coupled gas-flow and heat transfer model for temperature and gas flow fields, and a particle tracker for travel time calculation. The simulations used three parallel, east-west cross-sections that were taken from the Sandia National Laboratories Interactive Graphics Information System (IGIS). Assuming that the repository is filled with 30- year-old waste at an initial areal power density of 57 kw/acre, we found that repository temperatures remain above 60??C for more than 10,000 years. For a tuff permeability of 10-7 cm2, Carbon-14 travel times to the surface are mostly less than 1,000 years, for particles starting at any time within the first 10,000 years. If the tuff permeability is 10-8 cm2, however, Carbon- 14 travel times to the surface range from 3,000 to 12,000 years, for particle starting within the 10,000 years.

  6. [Calculation of flammability limits of gas phases with ethylene oxide in sterilisers].

    PubMed

    Askar, Enis; Schröder, Volkmar; Acikalin, Aydan; Steinbach, Jörg

    2008-12-01

    A calculation method for flammability limits of gas phases with ethylene oxide in sterilisers was developed. Using the Software GasEq and the newly developed Makro "SterEx" for MS-Excel, flammability limits of mixtures with ethylene oxide, air and inert gases at temperatures between 20 degrees C and 100 degrees C and pressures between 0.4 bar and 1.0 bar can be calculated. This method can be used to easily determine safe operating conditions. The used semi-empirical model is based upon the assumption of constant flame temperature profiles at the flammability limits subject to the EO-concentration for different mixtures. To collect model parameters and to validate the model, several experiments with mixtures of ethylene oxide, nitrogen, carbon dioxide, water vapour and air were carried out to determine flammability limits. To simulate the structural conditions of sterilisers, the experiments were conducted in accordance to DIN EN 1839-B in a closed autoclave with temperatures and pressures relevant for sterilisation processes. The calculation of flammability limits of process gas mixtures with "SterEx" provides good agreement with flammability limits that were determined in experiments. PMID:19037868

  7. Development of a sarcoidosis murine lung granuloma model using Mycobacterium superoxide dismutase A peptide.

    PubMed

    Swaisgood, Carmen M; Oswald-Richter, Kyra; Moeller, Stephen D; Klemenc, Jennifer M; Ruple, Lisa M; Farver, Carol F; Drake, John M; Culver, Daniel A; Drake, Wonder P

    2011-02-01

    Sarcoidosis is characterized by noncaseating granulomas containing CD4(+) T cells with a Th1 immunophenotype. Although the causative antigens remain unknown, independent studies noted molecular and immunologic evidence of mycobacterial virulence factors in sarcoidosis specimens. A major limiting factor in discovering new insights into the pathogenesis of sarcoidosis is the lack of an animal model. Using a distinct superoxide dismutase A peptide (sodA) associated with sarcoidosis granulomas, we developed a pulmonary model of sarcoidosis granulomatous inflammation. Mice were sensitized by a subcutaneous injection of sodA, incorporated in incomplete Freund's adjuvant (IFA). Control subjects consisted of mice with no sensitization (ConNS), sensitized with IFA only (ConIFA), or with Schistosoma mansoni eggs. Fourteen days later, sensitized mice were challenged by tail-vein injection of naked beads, covalently coupled to sodA peptides or to schistosome egg antigens (SEA). Histologic analysis revealed hilar lymphadenopathy and noncaseating granulomas in the lungs of sodA-treated or SEA-treated mice. Flow cytometry of bronchoalveolar lavage (BAL) demonstrated CD4(+) T-cell responses against sodA peptide in the sodA-sensitized mice only. Cytometric bead analysis revealed significant differences in IL-2 and IFN-γ secretion in the BAL fluid of sodA-treated mice, compared with mice that received SEA or naked beads (P = 0.008, Wilcoxon rank sum test). ConNS and ConIFA mice demonstrated no significant formation of granuloma, and no Th1 immunophenotype. The use of microbial peptides distinct for sarcoidosis reveals a histologic and immunologic profile in the murine model that correlates well with those profiles noted in human sarcoidosis, providing the framework to investigate the molecular basis for the progression or resolution of sarcoidosis. PMID:20348207

  8. Temperature dependence of the particle/gas partition coefficient: An application to predict indoor gas-phase concentrations of semi-volatile organic compounds.

    PubMed

    Wei, Wenjuan; Mandin, Corinne; Blanchard, Olivier; Mercier, Fabien; Pelletier, Maud; Le Bot, Barbara; Glorennec, Philippe; Ramalho, Olivier

    2016-09-01

    The indoor gas-phase concentrations of semi-volatile organic compounds (SVOCs) can be predicted from their respective concentrations in airborne particles by applying the particle/gas partitioning equilibrium. The temperature used for partitioning is often set to 25°C. However, indoor temperatures frequently differ from this reference value. This assumption may result in errors in the predicted equilibrium gas-phase SVOC concentrations. To improve the prediction model, the temperature dependence of the particle/gas partition coefficient must be addressed. In this paper, a theoretical relationship between the particle/gas partition coefficient and temperature was developed based on the SVOC absorptive mechanism. The SVOC particle/gas partition coefficients predicted by employing the derived theoretical relationship agree well with the experimental data retrieved from the literature (R>0.93). The influence of temperature on the equilibrium gas-phase SVOC concentration was quantified by a dimensionless analysis of the derived relationship between the SVOC particle/gas partition coefficient and temperature. The predicted equilibrium gas-phase SVOC concentration decreased by between 31% and 53% when the temperature was lowered by 6°C, while it increased by up to 750% when the indoor temperature increased from 15°C to 30°C.

  9. Temperature dependence of the particle/gas partition coefficient: An application to predict indoor gas-phase concentrations of semi-volatile organic compounds.

    PubMed

    Wei, Wenjuan; Mandin, Corinne; Blanchard, Olivier; Mercier, Fabien; Pelletier, Maud; Le Bot, Barbara; Glorennec, Philippe; Ramalho, Olivier

    2016-09-01

    The indoor gas-phase concentrations of semi-volatile organic compounds (SVOCs) can be predicted from their respective concentrations in airborne particles by applying the particle/gas partitioning equilibrium. The temperature used for partitioning is often set to 25°C. However, indoor temperatures frequently differ from this reference value. This assumption may result in errors in the predicted equilibrium gas-phase SVOC concentrations. To improve the prediction model, the temperature dependence of the particle/gas partition coefficient must be addressed. In this paper, a theoretical relationship between the particle/gas partition coefficient and temperature was developed based on the SVOC absorptive mechanism. The SVOC particle/gas partition coefficients predicted by employing the derived theoretical relationship agree well with the experimental data retrieved from the literature (R>0.93). The influence of temperature on the equilibrium gas-phase SVOC concentration was quantified by a dimensionless analysis of the derived relationship between the SVOC particle/gas partition coefficient and temperature. The predicted equilibrium gas-phase SVOC concentration decreased by between 31% and 53% when the temperature was lowered by 6°C, while it increased by up to 750% when the indoor temperature increased from 15°C to 30°C. PMID:27152992

  10. General aspects of peptide selectivity towards lipid bilayers and cell membranes studied by variation of the structural parameters of amphipathic helical model peptides.

    PubMed

    Dathe, Margitta; Meyer, Jana; Beyermann, Michael; Maul, Björn; Hoischen, Christian; Bienert, Michael

    2002-02-01

    Model compounds of modified hydrophobicity (Eta), hydrophobic moment (mu) and angle subtended by charged residues (Phi) were synthesized to define the general roles of structural motifs of cationic helical peptides for membrane activity and selectivity. The peptide sets were based on a highly hydrophobic, non-selective KLA model peptide with high antimicrobial and hemolytic activity. Variation of the investigated parameters was found to be a suitable method for modifying peptide selectivity towards either neutral or highly negatively charged lipid bilayers. Eta and mu influenced selectivity preferentially via modification of activity on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) bilayers, while the size of the polar/hydrophobic angle affected the activity against 1-palmitoyl-2-oleoylphosphatidyl-DL-glycerol (POPG). The influence of the parameters on the activity determining step was modest in both lipid systems and the activity profiles were the result of the parameters' influence on the second less pronounced permeabilization step. Thus, the activity towards POPC vesicles was determined by the high permeabilizing efficiency, however, changes in the structural parameters preferentially influenced the relatively moderate affinity. In contrast, intensive peptide accumulation via electrostatic interactions was sufficient for the destabilization of highly negatively charged POPG lipid membranes, but changes in the activity profile, as revealed by the modification of Phi, seem to be preferentially caused by variation of the low permeabilizing efficiency. The parameters proved very effective also in modifying antimicrobial and hemolytic activity. However, their influence on cell selectivity was limited. A threshold value of hydrophobicity seems to exist which restricted the activity modifying potential of mu and Phi on both lipid bilayers and cell membranes.

  11. Aggregation of peptides in the tube model with correlated sidechain orientations

    NASA Astrophysics Data System (ADS)

    Hung, Nguyen Ba; Hoang, Trinh Xuan

    2015-06-01

    The ability of proteins and peptides to aggregate and form toxic amyloid fibrils is associated with a range of diseases including BSE (or mad cow), Alzheimer's and Parkinson's Diseases. In this study, we investigate the the role of amino acid sequence in the aggregation propensity by using a modified tube model with a new procedure for hydrophobic interaction. In this model, the amino acid sidechains are not considered explicitly, but their orientations are taken into account in the formation of hydrophobic contact. Extensive Monte Carlo simulations for systems of short peptides are carried out with the use of parallel tempering technique. Our results show that the propensity to form and the structures of the aggregates strongly depend on the amino acid sequence and the number of peptides. Some sequences may not aggregate at all at a presumable physiological temperature while other can easily form fibril-like, β-sheet struture. Our study provides an insight into the principles of how the formation of amyloid can be governed by amino acid sequence.

  12. Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model

    NASA Astrophysics Data System (ADS)

    Koga, Shogo; Williams, David S.; Perriman, Adam W.; Mann, Stephen

    2011-09-01

    Although phospholipid bilayers are ubiquitous in modern cells, their impermeability, lack of dynamic properties, and synthetic complexity are difficult to reconcile with plausible pathways of proto-metabolism, growth and division. Here, we present an alternative membrane-free model, which demonstrates that low-molecular-weight mononucleotides and simple cationic peptides spontaneously accumulate in water into microdroplets that are stable to changes in temperature and salt concentration, undergo pH-induced cycles of growth and decay, and promote α-helical peptide secondary structure. Moreover, the microdroplets selectively sequester porphyrins, inorganic nanoparticles and enzymes to generate supramolecular stacked arrays of light-harvesting molecules, nanoparticle-mediated oxidase activity, and enhanced rates of glucose phosphorylation, respectively. Taken together, our results suggest that peptide-nucleotide microdroplets can be considered as a new type of protocell model that could be used to develop novel bioreactors, primitive artificial cells and plausible pathways to prebiotic organization before the emergence of lipid-based compartmentalization on the early Earth.

  13. Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model.

    PubMed

    Koga, Shogo; Williams, David S; Perriman, Adam W; Mann, Stephen

    2011-09-01

    Although phospholipid bilayers are ubiquitous in modern cells, their impermeability, lack of dynamic properties, and synthetic complexity are difficult to reconcile with plausible pathways of proto-metabolism, growth and division. Here, we present an alternative membrane-free model, which demonstrates that low-molecular-weight mononucleotides and simple cationic peptides spontaneously accumulate in water into microdroplets that are stable to changes in temperature and salt concentration, undergo pH-induced cycles of growth and decay, and promote α-helical peptide secondary structure. Moreover, the microdroplets selectively sequester porphyrins, inorganic nanoparticles and enzymes to generate supramolecular stacked arrays of light-harvesting molecules, nanoparticle-mediated oxidase activity, and enhanced rates of glucose phosphorylation, respectively. Taken together, our results suggest that peptide-nucleotide microdroplets can be considered as a new type of protocell model that could be used to develop novel bioreactors, primitive artificial cells and plausible pathways to prebiotic organization before the emergence of lipid-based compartmentalization on the early Earth. PMID:21860462

  14. Computational modelling of H+-coupled peptide transport via human PEPT1.

    PubMed

    Irie, Megumi; Terada, Tomohiro; Katsura, Toshiya; Matsuoka, Satoshi; Inui, Ken-ichi

    2005-06-01

    H+-coupled peptide transporter 1 (PEPT1) mediates the transport of small peptides and peptide-like drugs in a pH- and voltage-dependent manner. Here, we investigated the transport mechanisms of PEPT1 for neutral and charged substrates by experimental studies and computational simulation. Uptake studies revealed that the Michaelis-Menten constant (Km) of glycylsarcosine (Gly-Sar), a neutral substrate, decreased with a fall in pH from 7.4 to 5.5, but at pH 5.0, the Km increased again. In contrast, the Km value of an anionic substrate, ceftibuten, declined steadily with decreasing pH. Based on these findings and information from the literature, we hypothesized the transport mechanisms in which (1) H+ binds to not only the H+-binding site, but also the substrate-binding site; and (2) H+ at the substrate-binding site inhibits the interaction of neutral and cationic substrates, but is necessary for that of anionic substrates. To validate these hypotheses, a computational model was constructed and various properties of substrate transport by PEPT1 were simulated. Our model reproduced the voltage dependence, hyperbolic saturation and bell-shaped pH-profile of Gly-Sar transport. Moreover, the various transport properties of negatively and positively charged substrates were also reconstructed. These findings indicated that the inferred mechanisms are able to sufficiently interpret the transport of both neutral and charged substrates by PEPT1. PMID:15802293

  15. Modeling of the Binding of Peptide Blockers to Voltage-Gated Potassium Channels: Approaches and Evidence

    PubMed Central

    Novoseletsky, V. N.; Volyntseva, A. D.; Shaitan, K. V.; Kirpichnikov, M. P.; Feofanov, A. V.

    2016-01-01

    Modeling of the structure of voltage-gated potassium (KV) channels bound to peptide blockers aims to identify the key amino acid residues dictating affinity and provide insights into the toxin-channel interface. Computational approaches open up possibilities for in silico rational design of selective blockers, new molecular tools to study the cellular distribution and functional roles of potassium channels. It is anticipated that optimized blockers will advance the development of drugs that reduce over activation of potassium channels and attenuate the associated malfunction. Starting with an overview of the recent advances in computational simulation strategies to predict the bound state orientations of peptide pore blockers relative to KV-channels, we go on to review algorithms for the analysis of intermolecular interactions, and then take a look at the results of their application. PMID:27437138

  16. Describing the Mechanism of Antimicrobial Peptide Action with the Interfacial Activity Model

    PubMed Central

    Wimley, William C.

    2010-01-01

    Antimicrobial peptides (AMPs) have been studied for three decades, and yet a molecular understanding of their mechanism of action is still lacking. Here we summarize current knowledge for both synthetic vesicle experiments and microbe experiments, with a focus on comparisons between the two. Microbial experiments are done at peptide:lipid ratios that are at least 4 orders of magnitude higher than vesicle-based experiments. To close the gap between the two concentration regimes, we propose an “interfacial activity model”, which is based on an experimentally testable molecular image of AMP-membrane interactions. The interfacial activity model may be useful in driving engineering and design of novel AMPs. PMID:20698568

  17. Kinetics of interaction of vanillin with amino acids and peptides in model systems.

    PubMed

    Chobpattana, W; Jeon, I J; Smith, J S

    2000-09-01

    Model systems were used to study the reaction kinetics of vanillin and pentalysine, lysine, glutathione, cysteine, aspartame, or phenylalanine (molar ratio 1:1) in phosphate buffer. The buffer pH was adjusted to the pK(a)(2) of the available alpha-amino group of each amino acid or peptide. Reductions of vanillin followed first-order kinetics at 55, 65, and 75 degrees C in the presence of each of the amino acids or peptides used. The reaction rates were accelerated as the temperature increased. The rate constants were highest for pentalysine followed by lysine, phenylalanine, glutathione/cysteine, and aspartame. The reduction of phenylalanine followed first-order kinetics, whereas the formation of its reaction product followed zero-order kinetics. The activation energy (E(a)) for the reaction ranged from 5.6 to 14.5 kcal/mol.

  18. Gas-phase and transpiration-driven mechanisms for volatilization through wetland macrophytes.

    PubMed

    Reid, Matthew C; Jaffé, Peter R

    2012-05-15

    Natural and constructed wetlands have gained attention as potential tools for remediation of shallow sediments and groundwater contaminated with volatile organic compounds (VOCs). Wetland macrophytes are known to enhance rates of contaminant removal via volatilization, but the magnitude of different volatilization mechanisms, and the relationship between volatilization rates and contaminant physiochemical properties, remain poorly understood. Greenhouse mesocosm experiments using the volatile tracer sulfur hexafluoride were conducted to determine the relative magnitudes of gas-phase and transpiration-driven volatilization mechanisms. A numerical model for vegetation-mediated volatilization was developed, calibrated with tracer measurements, and used to predict plant-mediated volatilization of common VOCs as well as quantify the contribution of different volatilization pathways. Model simulations agree with conclusions from previous work that transpiration is the main driver for volatilization of VOCs, but also demonstrate that vapor-phase transport in wetland plants is significant, and can represent up to 50% of the total flux for compounds with greater volatility like vinyl chloride.

  19. Elementary reactions and their role in gas-phase prebiotic chemistry.

    PubMed

    Balucani, Nadia

    2009-05-01

    The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided to the system. After that groundbreaking experiment, gas-phase prebiotic molecules have been observed in a wide variety of extraterrestrial objects (including interstellar clouds, comets and planetary atmospheres) where the physical conditions vary widely. A thorough characterization of the chemical evolution of those objects relies on a multi-disciplinary approach: 1) observations allow us to identify the molecules and their number densities as they are nowadays; 2) the chemistry which lies behind their formation starting from atoms and simple molecules is accounted for by complex reaction networks; 3) for a realistic modeling of such networks, a number of experimental parameters are needed and, therefore, the relevant molecular processes should be fully characterized in laboratory experiments. A survey of the available literature reveals, however, that much information is still lacking if it is true that only a small percentage of the elementary reactions considered in the models have been characterized in laboratory experiments. New experimental approaches to characterize the relevant elementary reactions in laboratory are presented and the implications of the results are discussed.

  20. Mechanism And Kinetics Of Silylation Of Resist Layers From The Gas Phase

    NASA Astrophysics Data System (ADS)

    Visser, Robert-Jan; Schellekens, Jack P. W.; Reuhman-Huisken, Marian E.

    1987-09-01

    The silylation from the gas phase of photoresists based on diazoquinone and novolac or polyvinylphenol, which can be used in dry developable systems has been investigated. It is shown that the phenolic hydroxyl groups are almost completely silylated. The kinetics of the reaction have been followed by gravimetry, IR spectroscopy and Rutherford backscattering spectrometry. During the reaction a completely silylated, swollen layer is formed with a sharp front separating it from the unreacted resin. The rate control-ling processes are the relaxation of the polymer and the diffusion of the reagent. When the relaxation is slow with respect to diffusion, linear reaction kinetics as in Case II diffusion are observed. When the relaxation is fast the reaction proceeds with the square root of time. The increase of the reaction rate with UV exposure of the resist is attributed to an increase in the relaxation rate of the resist. A model explains the higher photoselectivity of the reaction at elevated temperatures. Results with a number of model resists indicate that some diazoquinones can act as physical crosslinks between polymer chains via the formation of hydrogen bonds whereas the corresponding in-denecarboxylic acids cannot. Due to the high content of silicon after the treatment these resists become highly etch-resistant towards oxygen plasmas.

  1. Elementary Reactions and Their Role in Gas-Phase Prebiotic Chemistry

    PubMed Central

    Balucani, Nadia

    2009-01-01

    The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided to the system. After that groundbreaking experiment, gas-phase prebiotic molecules have been observed in a wide variety of extraterrestrial objects (including interstellar clouds, comets and planetary atmospheres) where the physical conditions vary widely. A thorough characterization of the chemical evolution of those objects relies on a multi-disciplinary approach: 1) observations allow us to identify the molecules and their number densities as they are nowadays; 2) the chemistry which lies behind their formation starting from atoms and simple molecules is accounted for by complex reaction networks; 3) for a realistic modeling of such networks, a number of experimental parameters are needed and, therefore, the relevant molecular processes should be fully characterized in laboratory experiments. A survey of the available literature reveals, however, that much information is still lacking if it is true that only a small percentage of the elementary reactions considered in the models have been characterized in laboratory experiments. New experimental approaches to characterize the relevant elementary reactions in laboratory are presented and the implications of the results are discussed. PMID:19564951

  2. Selective removal of alkali metal cations from multiply-charged ions via gas-phase ion/ion reactions using weakly coordinating anions.

    PubMed

    Luongo, Carl A; Bu, Jiexun; Burke, Nicole L; Gilbert, Joshua D; Prentice, Boone M; Cummings, Steven; Reed, Christopher A; McLuckey, Scott A

    2015-03-01

    Selective removal of alkali metal cations from mixed cation multiply-charged peptide ions is demonstrated here using gas-phase ion/ion reactions with a series of weakly coordinating anions (WCAs), including hexafluorophosphate (PF6 (-)), tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (BARF), tetrakis(pentafluorophenyl)borate (TPPB), and carborane (CHB11Cl11 (-)). In all cases, a long-lived complex is generated by dication/anion condensation followed by ion activation to compare proton transfer with alkali ion transfer from the peptide to the anion. The carborane anion was the only anion studied to undergo dissociation exclusively through loss of the metallated anion, regardless of the studied metal adduct. All other anions studied yield varying abundances of protonated and metallated peptide depending on the peptide sequence and the metal identity. Density functional theory calculations suggest that for the WCAs studied, metal ion transfer is most strongly favored thermodynamically, which is consistent with the experimental results. The carborane anion is demonstrated to be a robust reagent for the selective removal of alkali metal cations from peptide cations with mixtures of excess protons and metal cations. PMID:25560986

  3. Selective Removal of Alkali Metal Cations from Multiply-Charged Ions via Gas-Phase Ion/Ion Reactions Using Weakly Coordinating Anions

    NASA Astrophysics Data System (ADS)

    Luongo, Carl A.; Bu, Jiexun; Burke, Nicole L.; Gilbert, Joshua D.; Prentice, Boone M.; Cummings, Steven; Reed, Christopher A.; McLuckey, Scott A.

    2015-03-01

    Selective removal of alkali metal cations from mixed cation multiply-charged peptide ions is demonstrated here using gas-phase ion/ion reactions with a series of weakly coordinating anions (WCAs), including hexafluorophosphate (PF6 -), tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (BARF), tetrakis(pentafluorophenyl)borate (TPPB), and carborane (CHB11Cl11 -). In all cases, a long-lived complex is generated by dication/anion condensation followed by ion activation to compare proton transfer with alkali ion transfer from the peptide to the anion. The carborane anion was the only anion studied to undergo dissociation exclusively through loss of the metallated anion, regardless of the studied metal adduct. All other anions studied yield varying abundances of protonated and metallated peptide depending on the peptide sequence and the metal identity. Density functional theory calculations suggest that for the WCAs studied, metal ion transfer is most strongly favored thermodynamically, which is consistent with the experimental results. The carborane anion is demonstrated to be a robust reagent for the selective removal of alkali metal cations from peptide cations with mixtures of excess protons and metal cations.

  4. Competitive threshold collision-induced dissociation: Gas-phase acidities and bond dissociation energies for a series of alcohols

    SciTech Connect

    DeTuri, V.F.; Ervin, K.M.

    1999-09-02

    Energy-resolved competitive collision-induced dissociation methods are used to measure the gas-phase acidities of a series of alcohols (methanol, ethanol, 2-propanol, and 2-methyl-2-propanol). The competitive dissociation reactions of fluoride-alcohol, [F{sup {minus}}{center{underscore}dot}HOR], alkoxide-water, [RO{sup {minus}}{center{underscore}dot}HOH], and alkoxide-methanol [RO{+-}{center{underscore}dot}HOCH{sub 3}] proton-bound complexes are studied using a guided ion beam tandem mass spectrometer. The reaction cross sections and product branching fractions to the two proton transfer channels are measured as a function of collision energy. The enthalpy difference between the two product channels is found by modeling the reaction cross sections near threshold using RRKM theory to account for the energy-dependent product branching ratio and kinetic shift. From the enthalpy difference, the alcohol gas-phase acidities are determined relative to the well-known values of HF and H{sub 2}O. The measured gas-phase acidities are {Delta}{sub acid}H{sub 298}(CH{sub 3}OH) = 1599 {+-} 3 kJ/mol, {Delta}{sub acid}H{sub 298}(CH{sub 3}CH{sub 2}OH) = 1586 {+-} 5 kJ/mol, {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 2}CHOH) = 1576 {+-} 4 kJ/mol, and {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 3}COH) = 1573 {+-} 3 kJ/mol.

  5. Gas-phase CO2, C2H2, and HCN toward Orion-KL

    NASA Astrophysics Data System (ADS)

    Boonman, A. M. S.; van Dishoeck, E. F.; Lahuis, F.; Doty, S. D.; Wright, C. M.; Rosenthal, D.

    2003-03-01

    The infrared spectra toward Orion-IRc2, Peak 1 and Peak 2 in the 13.5-15.5 mu m wavelength range are presented, obtained with the Short Wavelength Spectrometer on board the Infrared Space Observatory. The spectra show absorption and emission features of the vibration-rotation bands of gas-phase CO2, HCN, and C2H2, respectively. Toward the deeply embedded massive young stellar object IRc2 all three bands appear in absorption, while toward the shocked region Peak 2 CO2, HCN, and C2H2 are seen in emission. Toward Peak 1 only CO2 has been detected in emission. Analysis of these bands shows that the absorption features toward IRc2 are characterized by excitation temperatures of ~ 175-275 K, which can be explained by an origin in the shocked plateau gas. HCN and C2H2 are only seen in absorption in the direction of IRc2, whereas the CO2 absorption is probably more widespread. The CO2 emission toward Peak 1 and 2 is best explained with excitation by infrared radiation from dust mixed with the gas in the warm component of the shock. The similarity of the CO2 emission and absorption line shapes toward IRc2, Peak 1 and Peak 2 suggests that the CO2 is located in the warm component of the shock (T ~ 200 K) toward all three positions. The CO2 abundances of ~ 10-8 for Peak 1 and 2, and of a few times 10-7 toward IRc2 can be explained by grain mantle evaporation and/or reformation in the gas-phase after destruction by the shock. The HCN and C2H2 emission detected toward Peak 2 is narrower (T ~ 50-150 K) and originates either in the warm component of the shock or in the extended ridge. In the case of an origin in the warm component of the shock, the low HCN and C2H2 abundances of ~ 10-9 suggest that they are destroyed by the shock or have only been in the warm gas for a short time (t <~ 104 yr). In the case of an origin in the extended ridge, the inferred abundances are much higher and do not agree with predictions from current chemical models at low temperatures. Based on

  6. Synthetic peptides.

    PubMed

    Francis, M J

    1996-01-01

    Efforts to produce more stable and defined vaccines have concentrated on studying, in detail, the immune response to many infectious diseases in order to identify the antigenic sites on the pathogens that are involved in stimulating protective immumty. Armed with this knowledge, it is possible to mimic such sites by producing short chains of amino acids (peptides) and to use these as the basis for novel vaccines. The earliest documented work on peptide immunization is actually for a plant virus, tobacco mosaic virus. In 1963, Anderer (1) demonstrated that rabbit antibodies to an isolated hexapeptide fragment from the virus-coat protein coupled to bovine serum albumm would neutralize the infectious vn-us in culture. Two years later, he used a synthetically produced copy of the same peptide to confirm this observation. This was pioneering work, and it was over 10 years before the next example of a peptide that elicited antivirus antibody appeared following work by Sela and his colleagues (2) on a virus, MS2 bacteriophage, which infects bacteria. The emergence of more accessible techniques for sequencing proteins in 1977, coupled with the ability to synthesize readily peptides already developed in 1963, heralded a decade of intensive research into experimental peptide vaccines. The first demonstration that peptides could elicit protective immunity in vivo, in addition to neutralizing activity in vitro, was obtained using a peptide from the VP1 coat protein of foot-and-mouth disease virus (FMDV) in 1982, with the guinea pig as a laboratory animal model (3, 4). PMID:21359696

  7. Reaction mechanisms in the radiolysis of peptides, polypeptides, and proteins. I. Reactions of the peptide main-chain in model systems

    SciTech Connect

    Garrison, W.M.

    1982-08-01

    The object of this review is to bring together and to correlate our present knowledge of products and mechanisms in the radiolysis of peptides, polypeptides and proteins in both aqueous and solid-state systems. Results obtained with various experimental techniques such as product analysis, competition kinetics, ESR spectroscopy and pulse radiolysis are included. Here in part I the emphasis is on the various radiation-induced reactions of the peptide main-chain in model systems. In part II the emphasis is on the radiation chemistry of side-chain loci of the aliphatic, sulfur-containing, aromatic and other unsaturated amino acid residues in similar systems. And, in part III this information on model systems is used in interpreting the mechanisms of chemical change in the radiolysis of proteins in aqueous solution and in the solid state. 60 references.

  8. Bayesian Nonparametric Model for the Validation of Peptide Identification in Shotgun Proteomics*S⃞

    PubMed Central

    Zhang, Jiyang; Ma, Jie; Dou, Lei; Wu, Songfeng; Qian, Xiaohong; Xie, Hongwei; Zhu, Yunping; He, Fuchu

    2009-01-01

    Tandem mass spectrometry combined with database searching allows high throughput identification of peptides in shotgun proteomics. However, validating database search results, a problem with a lot of solutions proposed, is still advancing in some aspects, such as the sensitivity, specificity, and generalizability of the validation algorithms. Here a Bayesian nonparametric (BNP) model for the validation of database search results was developed that incorporates several popular techniques in statistical learning, including the compression of feature space with a linear discriminant function, the flexible nonparametric probability density function estimation for the variable probability structure in complex problem, and the Bayesian method to calculate the posterior probability. Importantly the BNP model is compatible with the popular target-decoy database search strategy naturally. We tested the BNP model on standard proteins and real, complex sample data sets from multiple MS platforms and compared it with PeptideProphet, the cutoff-based method, and a simple nonparametric method (proposed by us previously). The performance of the BNP model was shown to be superior for all data sets searched on sensitivity and generalizability. Some high quality matches that had been filtered out by other methods were detected and assigned with high probability by the BNP model. Thus, the BNP model could be able to validate the database search results effectively and extract more information from MS/MS data. PMID:19005226

  9. From solution to the gas phase: factors that influence kinetic trapping of substance P in the gas phase.

    PubMed

    Fort, Kyle L; Silveira, Joshua A; Pierson, Nicholas A; Servage, Kelly A; Clemmer, David E; Russell, David H

    2014-12-11

    Substance P (RPKPQQFFGLM-NH2) [M + 3H](3+) ions have been shown to exist as two conformers: one that is kinetically trapped and one that is thermodynamically more stable and therefore energetically preferred. Molecular dynamics (MD) simulations suggested that the kinetically trapped population is stabilized by interactions between the charge sites and the polar side chains of glutamine (Q) located at positions 5 and 6 and phenylalanine (F) located at positions 7 and 8. Here, the individual contributions of these specific intramolecular interactions are systematically probed through site-directed alanine mutations of the native amino acid sequence. Ion mobility spectrometry data for the mutant peptide ions confirm that interactions between the charge sites and glutamine/phenylalanine (Q/F) side chains afford stabilization of the kinetically trapped ion population. In addition, experimental data for proline-to-alanine mutations at positions 2 and 4 clearly show that interactions involving the charge sites and the Q/F side chains are altered by the cis/trans orientations of the proline residues and that mutation of glycine to proline at position 9 supports results from MD simulations suggesting that the C-terminus also provides stabilization of the kinetically trapped conformation.

  10. Some Fundamental Experiments on Apparent Dissolution Rate of Gas Phase in the Groundwater Recovery Processes of the Geological Disposal System - 12146

    SciTech Connect

    Yoshii, Taiki; Niibori, Yuichi; Mimura, Hitoshi

    2012-07-01

    The apparent dissolution rates of gas phase in the co-presence of solid phase were examined by in-room experiments in this study. The apparent dissolution rate of gas phase q (mol/m{sup 3}.s) was generally defined by q=aK{sub L}(γP{sub g}-c), where a (1/m) is specific surface area of the interface between gas and liquid phases, K{sub L} (m/s) is overall mass transfer coefficient, γ (mol/(Pa.m{sup 3})) is reciprocal number of Henry constant, P{sub g} (Pa) is partial pressure of gas phase, and c (mol/m{sup 3}) is the concentration of gas component in liquid phase. As a model gas, CO{sub 2} gas was used. For evaluating the values of K{sub L}, this study monitored pH or the migration rate of the interface between water/gas phases, using some experiments such as the packed beds and the micro channel consisting of granite chip and rubber sheet including a slit. In the results, the values of K{sub L} were distributed in the range from 5.0x10{sup -6} m/s to 5.0x10{sup -7} m/s. These values were small, in comparison with that (7.8x10{sup -4} m/s) obtained from the bubbling test where gas phase was continually injected into deionized water without solid phase. This means that the solid phase limits the local mixing of water phase near gas-liquid interfaces. (authors)

  11. Use of model peptide reactions for the characterization of kinetically controlled ligation.

    PubMed

    Lee, Joongoo; Kwon, Yoonjin; Pentelute, Brad L; Bang, Duhee

    2011-08-17

    Since the introduction of kinetically controlled ligation (KCL), a chemoselective reaction between a peptide-(α)thioarylester and a Cys-peptide-(α)thioalkylester, KCL has been utilized for the total chemical synthesis of large proteins (i.e., lysozyme and HIV-protease) by providing fully convergent synthetic routes. Although KCL has the potential to become an important chemistry for protein synthesis, the principle of KCL is not fully characterized. In particular, prior work on KCL has focused on the reactivity difference of the two different -(α)thioester forms-alkyl vs aryl. Another equally important feature of KCL, Xaa-Cys ligation sites, has not been investigated. The work reported here describes combinatorial KCL reactions using model peptides to dissect the interplay of the Xaa(1), Xaa(2), -(α)thioarylester, and -(α)thioalkylester. Results from these studies provide fundamental insights into the KCL reaction, and will lead to the optimal synthetic route for the routine chemical synthesis of large target protein molecules.

  12. Investigating the inclusion properties of aromatic amino acids complexing beta-cyclodextrins in model peptides.

    PubMed

    Caso, Jolanda Valentina; Russo, Luigi; Palmieri, Maddalena; Malgieri, Gaetano; Galdiero, Stefania; Falanga, Annarita; Isernia, Carla; Iacovino, Rosa

    2015-10-01

    Cyclodextrins are commonly used as complexing agents in biological, pharmaceutical, and industrial applications since they have an effect on protein thermal and proteolytic stability, refolding yields, solubility, and taste masking. β-cyclodextrins (β-CD), because of their cavity size are a perfectly suited complexing agent for many common guest moieties. In the case of peptide-cyclodextrin and protein-cyclodextrin host-guest complexes the aromatic amino acids are reported to be the principal responsible of the interaction. For these reasons, we have investigated the inclusion properties of nine designed tripeptides, obtained permuting the position of two L-alanines (Ala, A) with that of one L-tryptophan (Trp, W), L-phenylalanine (Phe, F), or L-tyrosine (Tyr, Y), respectively. Interestingly, the position of the aromatic side-chain in the sequence appears to modulate the β-CD:peptide binding constants, determined via UV-Vis and NMR spectroscopy, which in turn assumes values higher than those reported for the single amino acid. The tripeptides containing a tyrosine showed the highest binding constants, with the central position in the Ac-AYA-NH2 peptide becoming the most favorite for the interaction. A combined NMR and Molecular Docking approach permitted to build detailed complex models, highlighting the stabilizing interactions of the neighboring amino acids backbone atoms with the upper rim of the β-CD.

  13. Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results.

    PubMed

    Azoia, Nuno G; Fernandes, Margarida M; Micaêlo, Nuno M; Soares, Cláudio M; Cavaco-Paulo, Artur

    2012-05-01

    Molecular dynamics simulations of a keratin/peptide complex have been conducted to predict the binding affinity of four different peptides toward human hair. Free energy calculations on the peptides' interaction with the keratin model demonstrated that electrostatic interactions are believed to be the main driving force stabilizing the complex. The molecular mechanics-Poisson-Boltzmann surface area methodology used for the free energy calculations demonstrated that the dielectric constant in the protein's interior plays a major role in the free energy calculations, and the only way to obtain accordance between the free energy calculations and the experimental binding results was to use the average dielectric constant.

  14. Ion channel models based on self-assembling cyclic peptide nanotubes

    PubMed Central

    Montenegro, Javier

    2013-01-01

    CONSPECTUS Compartmentalization and isolation from external media facilitates the sophisticated functionality and connectivity of all the different biological processes accomplished by living entities. The lipid bilayer membranes are the dynamic structural motifs selected by Nature to individualize cells and keep ions, proteins, biopolymers and metabolites confined in the appropriate location. However, cellular interaction with the exterior and the regulation of its internal environment requires the assistance of minimal energy short cuts for the transport of molecules across membranes. Ion channels and pores stand out from all other possible transport mechanisms due to their high selectivity and efficiency in discriminating and transporting ions or molecules across membrane barriers. Nevertheless, the complexity of these smart “membrane holes” has been a significant driving force to develop artificial structures with comparable performance to the natural systems. The emergence of the broad range of supramolecular interactions as efficient tools for the rational design and preparation of stable 3D superstructures has boosted the possibilities and stimulated the creativity of chemists to design synthetic mimics of natural active macromolecules and even to develop artificial functions and properties. In this account we highlight results from our laboratories on the construction of artificial ion channel models that exploit the self-assembling of flat cyclic peptides into supramolecular nanotubes. The straightforward synthesis of the cyclic peptide monomers and the complete control over the internal diameter and external surface properties of the resulting hollow tubular suprastructure make CPs the optimal candidates for the fabrication of ion channels. Ion channel activities and selective transport of small molecules are examples of the huge potential of cyclic peptide nanotubes for the construction of functional transmembrane ion channels or pores. Our

  15. Ion channel models based on self-assembling cyclic peptide nanotubes.

    PubMed

    Montenegro, Javier; Ghadiri, M Reza; Granja, Juan R

    2013-12-17

    The lipid bilayer membranes are Nature's dynamic structural motifs that individualize cells and keep ions, proteins, biopolymers and metabolites confined in the appropriate location. The compartmentalization and isolation of these molecules from the external media facilitate the sophisticated functions and connections between the different biological processes accomplished by living organisms. However, cells require assistance from minimal energy shortcuts for the transport of molecules across membranes so that they can interact with the exterior and regulate their internal environments. Ion channels and pores stand out from all other possible transport mechanisms due to their high selectivity and efficiency in discriminating and transporting ions or molecules across membrane barriers. Nevertheless, the complexity of these smart "membrane holes" has driven researchers to develop simpler artificial structures with comparable performance to the natural systems. As a broad range of supramolecular interactions have emerged as efficient tools for the rational design and preparation of stable 3D superstructures, these results have stimulated the creativity of chemists to design synthetic mimics of natural active macromolecules and even to develop artificial structures with functions and properties. In this Account, we highlight results from our laboratories on the construction of artificial ion channel models that exploit the self-assembly of conformationally flat cyclic peptides (CPs) into supramolecular nanotubes. Because of the straightforward synthesis of the cyclic peptide monomers and the complete control over the internal diameter and external surface properties of the resulting hollow tubular suprastructure, CPs are the optimal candidates for the fabrication of ion channels. The ion channel activity and selective transport of small molecules by these structures are examples of the great potential that cyclic peptide nanotubes show for the construction of

  16. Ion channel models based on self-assembling cyclic peptide nanotubes.

    PubMed

    Montenegro, Javier; Ghadiri, M Reza; Granja, Juan R

    2013-12-17

    The lipid bilayer membranes are Nature's dynamic structural motifs that individualize cells and keep ions, proteins, biopolymers and metabolites confined in the appropriate location. The compartmentalization and isolation of these molecules from the external media facilitate the sophisticated functions and connections between the different biological processes accomplished by living organisms. However, cells require assistance from minimal energy shortcuts for the transport of molecules across membranes so that they can interact with the exterior and regulate their internal environments. Ion channels and pores stand out from all other possible transport mechanisms due to their high selectivity and efficiency in discriminating and transporting ions or molecules across membrane barriers. Nevertheless, the complexity of these smart "membrane holes" has driven researchers to develop simpler artificial structures with comparable performance to the natural systems. As a broad range of supramolecular interactions have emerged as efficient tools for the rational design and preparation of stable 3D superstructures, these results have stimulated the creativity of chemists to design synthetic mimics of natural active macromolecules and even to develop artificial structures with functions and properties. In this Account, we highlight results from our laboratories on the construction of artificial ion channel models that exploit the self-assembly of conformationally flat cyclic peptides (CPs) into supramolecular nanotubes. Because of the straightforward synthesis of the cyclic peptide monomers and the complete control over the internal diameter and external surface properties of the resulting hollow tubular suprastructure, CPs are the optimal candidates for the fabrication of ion channels. The ion channel activity and selective transport of small molecules by these structures are examples of the great potential that cyclic peptide nanotubes show for the construction of

  17. Gas-Phase Retinal Spectroscopy: Temperature Effects Are But a Mirage.

    PubMed

    Valsson, Omar; Filippi, Claudia

    2012-04-01

    We employ state-of-the-art first-principle approaches to investigate whether temperature effects are responsible for the unusually broad and flat spectrum of protonated Schiff base retinal observed in photodissociation spectroscopy, as has recently been proposed. We first carefully calibrate how to construct a realistic geometrical model of retinal and show that the exchange-correlation M06-2X functional yields an accurate description while the commonly used complete active space self-consistent field method (CASSCF) is not adequate. Using modern multiconfigurational perturbative methods (NEVPT2) to compute the excitations, we then demonstrate that conformations with different orientations of the β-ionone ring are characterized by similar excitations. Moreover, other degrees of freedom identified as active in room-temperature molecular dynamics simulations do not yield the shift required to explain the anomalous spectral shape. Our findings indicate that photodissociation experiments are not representative of the optical spectrum of retinal in the gas phase and call for further experimental characterization of the dissociation spectra. PMID:26286419

  18. Gas-phase hydrolysis of triplet SO2: A possible direct route to atmospheric acid formation.

    PubMed

    Donaldson, D James; Kroll, Jay A; Vaida, Veronica

    2016-07-15

    Sulfur chemistry is of great interest to the atmospheric chemistry of several planets. In the presence of water, oxidized sulfur can lead to new particle formation, influencing climate in significant ways. Observations of sulfur compounds in planetary atmospheres when compared with model results suggest that there are missing chemical mechanisms. Here we propose a novel mechanism for the formation of sulfurous acid, which may act as a seed for new particle formation. In this proposed mechanism, the lowest triplet state of SO2 ((3)B1), which may be accessed by near-UV solar excitation of SO2 to its excited (1)B1 state followed by rapid intersystem crossing, reacts directly with water to form H2SO3 in the gas phase. For ground state SO2, this reaction is endothermic and has a very high activation barrier; our quantum chemical calculations point to a facile reaction being possible in the triplet state of SO2. This hygroscopic H2SO3 molecule may act as a condensation nucleus for water, giving rise to facile new particle formation (NPF).

  19. Gas-phase hydrolysis of triplet SO2: A possible direct route to atmospheric acid formation

    NASA Astrophysics Data System (ADS)

    Donaldson, D. James; Kroll, Jay A.; Vaida, Veronica

    2016-07-01

    Sulfur chemistry is of great interest to the atmospheric chemistry of several planets. In the presence of water, oxidized sulfur can lead to new particle formation, influencing climate in significant ways. Observations of sulfur compounds in planetary atmospheres when compared with model results suggest that there are missing chemical mechanisms. Here we propose a novel mechanism for the formation of sulfurous acid, which may act as a seed for new particle formation. In this proposed mechanism, the lowest triplet state of SO2 (3B1), which may be accessed by near-UV solar excitation of SO2 to its excited 1B1 state followed by rapid intersystem crossing, reacts directly with water to form H2SO3 in the gas phase. For ground state SO2, this reaction is endothermic and has a very high activation barrier; our quantum chemical calculations point to a facile reaction being possible in the triplet state of SO2. This hygroscopic H2SO3 molecule may act as a condensation nucleus for water, giving rise to facile new particle formation (NPF).

  20. Gas-phase hydrolysis of triplet SO2: A possible direct route to atmospheric acid formation

    PubMed Central

    Donaldson, D. James; Kroll, Jay A.; Vaida, Veronica

    2016-01-01

    Sulfur chemistry is of great interest to the atmospheric chemistry of several planets. In the presence of water, oxidized sulfur can lead to new particle formation, influencing climate in significant ways. Observations of sulfur compounds in planetary atmospheres when compared with model results suggest that there are missing chemical mechanisms. Here we propose a novel mechanism for the formation of sulfurous acid, which may act as a seed for new particle formation. In this proposed mechanism, the lowest triplet state of SO2 (3B1), which may be accessed by near-UV solar excitation of SO2 to its excited 1B1 state followed by rapid intersystem crossing, reacts directly with water to form H2SO3 in the gas phase. For ground state SO2, this reaction is endothermic and has a very high activation barrier; our quantum chemical calculations point to a facile reaction being possible in the triplet state of SO2. This hygroscopic H2SO3 molecule may act as a condensation nucleus for water, giving rise to facile new particle formation (NPF). PMID:27417675

  1. Gas-phase hydrolysis of triplet SO2: A possible direct route to atmospheric acid formation.

    PubMed

    Donaldson, D James; Kroll, Jay A; Vaida, Veronica

    2016-01-01

    Sulfur chemistry is of great interest to the atmospheric chemistry of several planets. In the presence of water, oxidized sulfur can lead to new particle formation, influencing climate in significant ways. Observations of sulfur compounds in planetary atmospheres when compared with model results suggest that there are missing chemical mechanisms. Here we propose a novel mechanism for the formation of sulfurous acid, which may act as a seed for new particle formation. In this proposed mechanism, the lowest triplet state of SO2 ((3)B1), which may be accessed by near-UV solar excitation of SO2 to its excited (1)B1 state followed by rapid intersystem crossing, reacts directly with water to form H2SO3 in the gas phase. For ground state SO2, this reaction is endothermic and has a very high activation barrier; our quantum chemical calculations point to a facile reaction being possible in the triplet state of SO2. This hygroscopic H2SO3 molecule may act as a condensation nucleus for water, giving rise to facile new particle formation (NPF). PMID:27417675

  2. [Kinetics of degradation of hexane in the gas phase by photocatalysis and combined photocatalysis and ozone].

    PubMed

    Liu, Juan; Zhang, Peng-yi; Yu, Gang; Zhu, Wan-peng; Liang, Fu-yan

    2004-01-01

    The degradations of trace hexane under high flow rate (5 L/min-17 L/min) in the gas phase by TiO2/UV, O3/UV and O3/TiO2/UV were studied. The kinetic effects of the inlet concentration of hexane, flow rate, water concentration and ozone dosage on the conversion of hexane in the three processes were examined respectively. The experimental results showed that the addition of ozone to the photocatalysis process increased the conversion of hexane significantly. The O3/TiO2/UV process was more efficient than the TiO2/UV in decomposing hexane. The degradation rate increased with increasing the initial concentration of hexane in the processes of TiO2/UV and O3/TiO2/UV. They matched well with the Langmuir-Hinshelwood (L-H) kinetic model. In the range of flow rate studied, the degradation rate increased with an increasing flow rate in both processes of TiO2/UV and O3/TiO2/UV, while was not affected in the process of O3/UV. The degradation rate in the three processes was affected by water concentration. The degradation rate of the two processes O3/UV and O3/TiO2/UV increased almost linearly with the increase of ozone dosage.

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

    PubMed

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

    2016-07-28

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

  4. Secondary Organic Aerosol formation from the gas-phase reaction of catechol with ozone

    NASA Astrophysics Data System (ADS)

    Coeur-Tourneur, C.; Tomas, A.; Guilloteau, A.; Henry, F.; Ledoux, F.; Visez, N.; Riffault, V.; Wenger, J. C.; Bedjanian, Y.; Foulon, V.

    2009-04-01

    The formation of secondary organic aerosol from the gas-phase reaction of catechol (1,2-dihydroxybenzene) with ozone has been studied in two smog chambers (at the LPCA in France and at the CRAC in Ireland). Aerosol production was monitored using a scanning mobility particle sizer. The overall organic aerosol yield (Y) was determined as the ratio of the suspended aerosol mass corrected for wall losses (Mo) to the total reacted catechol concentrations, assuming a particle density of 1.4 g cm-3. Analysis of the data clearly shows that Y is a strong function of Mo and that secondary organic aerosol formation can be expressed by a one-product gas/particle partitioning absorption model. The aerosol formation is affected by the initial catechol concentration, which leads to aerosol yields ranging from 17% to 86%. The aerosol yields determined in the LPCA and CRAC smog chambers were comparable and were also in accordance with those determined in a previous study performed in EUPHORE (EUropean PHOto REactor, Spain).

  5. Theoretical study on the properties of linear and cyclic amides in gas phase and water solution.

    PubMed

    Aparicio-Martínez, S; Hall, K R; Balbuena, P B

    2006-07-27

    The structural and energetic properties of a group of selected amides, of well-known importance for the design of efficient clathrate inhibitors, are calculated with Hartree-Fock and density functional theory, B3LYP, theoretical levels, and a 6-311++g** basis set in the gas phase and a water solution. The conformational behavior of the molecules is studied through the scanning of the torsional potential energy surfaces and by the analysis of the differences in the energetic and structural properties between the isomers. The properties of the amides in water solution are determined within a self-consistent reaction field approach with a polarizable continuum model that allows the calculation of the different contributions to the free energy of solvation. The calculated barriers to rotation are in good agreement with the available experimental data and the comparison of the gas and water results shows the strong effect of the solute polarization. The properties of different amide-water complexes are calculated and compared with available experimental information.

  6. Doppler indices of gas phase formation in hypobaric environments: Time-intensity analysis

    NASA Technical Reports Server (NTRS)

    Powell, Michael R.

    1991-01-01

    A semi-quantitative method to analyze decompression data is described. It possesses the advantage that it allows a graded response to decompression rather than the dichotomous response generally employed. A generalized critical volume (C-V), or stoichiometric time-dependent equilibrium model is examined that relates the constant of the equation P sub i equals m P sub f plus b to variable tissue supersaturation and gas washout terms. The effects of the tissue ratio on gas phase formation indicate that a decreased ratio yields fewer individuals with Doppler detectable gas bubbles, but those individuals still present with Spencer Grade 3 or 4. This might indicate a local collapse of tissue saturation. The individuals with Grade 3 or 4 could be at risk for type 2 decompression sickness by transpulmonic arterialization. The primary regulator of the problems of decompression sickness is the reduction of local supersaturation, presumably governed by the presence and number of gas micronuclei. It is postulated that a reduction in these nuclei will favor a low incidence of decompression sickness in microgravity secondary to hypokinesia and adynamia.

  7. Evaluation of the potentials of humic acid removal in water by gas phase surface discharge plasma.

    PubMed

    Wang, Tiecheng; Qu, Guangzhou; Ren, Jingyu; Yan, Qiuhe; Sun, Qiuhong; Liang, Dongli; Hu, Shibin

    2016-02-01

    Degradation of humic acid (HA), a predominant type of natural organic matter in ground water and surface waters, was conducted using a gas phase surface discharge plasma system. HA standard and two surface waters (Wetland, and Weihe River) were selected as the targets. The experimental results showed that about 90.9% of standard HA was smoothly removed within 40 min's discharge plasma treatment at discharge voltage 23.0 kV, and the removal process fitted the first-order kinetic model. Roles of some active species in HA removal were studied by evaluating the effects of solution pH and OH radical scavenger; and the results presented that O3 and OH radical played significant roles in HA removal. Scanning electron microscope (SEM) and FTIR analysis showed that HA surface topography and molecular structure were changed during discharge plasma process. The mineralization of HA was analyzed by UV-Vis spectrum, dissolved organic carbon (DOC), specific UV absorbance (SUVA), UV absorption ratios, and excitation-emission matrix (EEM) fluorescence. The formation of disinfection by-products during HA sample chlorination was also identified, and CHCl3 was detected as the main disinfection by-product, but discharge plasma treatment could suppress its formation to a certain extent. In addition, approximately 82.3% and 67.9% of UV254 were removed for the Weihe River water and the Wetland water after 40 min of discharge plasma treatment.

  8. Gas phase synthesis of organophosphorus compounds and the atmosphere of the giant planets

    NASA Astrophysics Data System (ADS)

    Bossard, A. R.; Kamga, R.; Raulin, F.

    1986-08-01

    Spark discharge and UV irradiation experiments were performed to investigate the interactions of CH4 and PH3 and the chemical evolution of PH3-H2O-NH3-CH4 mixtures in the upper atmospheres of the giant planets. The spark discharges were performed with various combinations of CH4-PH3, CH-PH3-H2, C2H6-PH3, and CH3PH2-CH4. PH3 alone and CH4-PH3 were exposed to 147 nm UV light. Sparks released into the hydrocarbon-phosphine mixtures induced the formation of alkylphosphines. The main products were H2, C2H6 and CH3PH2 when the initial mole fraction of PH3 was low. If the fraction of PH3 was high, the main products were He, CH3PH2 and P2H4. A gas phase chemical reaction model was defined for the formation reaction of methylphosphine. UV irradiation of CH4-PH3 usually produced a solid deposit and the constituents H2 and P2H4. The stability of the various reaction products in the Saturn and Jupiter atmospheres is discussed.

  9. Decomposition of gas-phase diphenylether at 473 K by electron beam generated plasma

    NASA Astrophysics Data System (ADS)

    Kim, Hyun-Ha; Hakoda, Teruyuki; Kojima, Takuji

    2003-03-01

    Decomposition of gas-phase diphenylether (DPE) in the order of several parts per million by volume (ppmv) was studied as a model compound of dioxin using a flow-type electron-beam reactor at an elevated temperature of 473 K. The ground state oxygen (3P) atoms played an important role in the decomposition of DPE resulting in the formation of 1,4-hydroquinone (HQ) as a major ring retaining product. The high yield of hydroquinone indicated that the breakage of ether bond (C-O) is important in the initial step of DPE decomposition. Ring cleavage products were CO and CO2, and NO2 was also produced from background N2-O2. The sum of the yields of HQ, CO2 and CO accounts for over 90% of the removed DPE. Hydroxyl radicals (OH) were less important in the dilute DPE decomposition at a high water content, and were mostly consumed by recombination reactions to form hydrogen peroxide. The smaller the initial DPE concentrations, the higher the decomposition efficiency and the lower the yields of primary products. NO scavenges oxygen atoms and decreases the DPE decomposition, while the addition of n-butane causes positive effect on the decomposition of DPE due to the several secondary radicals (HO2, alkyl and alkoxy radicals) produced during the decomposition of n-butane.

  10. Methods, fluxes and sources of gas phase alkyl nitrates in the coastal air.

    PubMed

    Dirtu, Alin C; Buczyńska, Anna J; Godoi, Ana F L; Favoreto, Rodrigo; Bencs, László; Potgieter-Vermaak, Sanja S; Godoi, Ricardo H M; Van Grieken, René; Van Vaeck, Luc

    2014-10-01

    The daily and seasonal atmospheric concentrations, deposition fluxes and emission sources of a few C3-C9 gaseous alkyl nitrates (ANs) at the Belgian coast (De Haan) on the Southern North Sea were determined. An adapted sampler design for low- and high-volume air-sampling, optimized sample extraction and clean-up, as well as identification and quantification of ANs in air samples by means of gas chromatography mass spectrometry, are reported. The total concentrations of ANs ranged from 0.03 to 85 pptv and consisted primarily of the nitro-butane and nitro-pentane isomers. Air mass backward trajectories were calculated by the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model to determine the influence of main air masses on AN levels in the air. The shorter chain ANs have been the most abundant in the Atlantic/Channel/UK air masses, while longer chain ANs prevailed in continental air. The overall mean N fluxes of the ANs were slightly higher for summer than those for winter-spring, although their contributions to the total nitrogen flux were low. High correlations between AN and HNO₂ levels were observed during winter/spring. During summer, the shorter chain ANs correlated well with precipitation. Source apportionment by means of principal component analysis indicated that most of the gas phase ANs could be attributed to traffic/combustion, secondary photochemical formation and biomass burning, although marine sources may also have been present and a contributing factor. PMID:24952420

  11. Methods, fluxes and sources of gas phase alkyl nitrates in the coastal air.

    PubMed

    Dirtu, Alin C; Buczyńska, Anna J; Godoi, Ana F L; Favoreto, Rodrigo; Bencs, László; Potgieter-Vermaak, Sanja S; Godoi, Ricardo H M; Van Grieken, René; Van Vaeck, Luc

    2014-10-01

    The daily and seasonal atmospheric concentrations, deposition fluxes and emission sources of a few C3-C9 gaseous alkyl nitrates (ANs) at the Belgian coast (De Haan) on the Southern North Sea were determined. An adapted sampler design for low- and high-volume air-sampling, optimized sample extraction and clean-up, as well as identification and quantification of ANs in air samples by means of gas chromatography mass spectrometry, are reported. The total concentrations of ANs ranged from 0.03 to 85 pptv and consisted primarily of the nitro-butane and nitro-pentane isomers. Air mass backward trajectories were calculated by the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model to determine the influence of main air masses on AN levels in the air. The shorter chain ANs have been the most abundant in the Atlantic/Channel/UK air masses, while longer chain ANs prevailed in continental air. The overall mean N fluxes of the ANs were slightly higher for summer than those for winter-spring, although their contributions to the total nitrogen flux were low. High correlations between AN and HNO₂ levels were observed during winter/spring. During summer, the shorter chain ANs correlated well with precipitation. Source apportionment by means of principal component analysis indicated that most of the gas phase ANs could be attributed to traffic/combustion, secondary photochemical formation and biomass burning, although marine sources may also have been present and a contributing factor.

  12. Toward industrial scale synthesis of ultrapure singlet nanoparticles with controllable sizes in a continuous gas-phase process

    NASA Astrophysics Data System (ADS)

    Feng, Jicheng; Biskos, George; Schmidt-Ott, Andreas

    2015-10-01

    Continuous gas-phase synthesis of nanoparticles is associated with rapid agglomeration, which can be a limiting factor for numerous applications. In this report, we challenge this paradigm by providing experimental evidence to support that gas-phase methods can be used to produce ultrapure non-agglomerated “singlet” nanoparticles having tunable sizes at room temperature. By controlling the temperature in the particle growth zone to guarantee complete coalescence of colliding entities, the size of singlets in principle can be regulated from that of single atoms to any desired value. We assess our results in the context of a simple analytical model to explore the dependence of singlet size on the operating conditions. Agreement of the model with experimental measurements shows that these methods can be effectively used for producing singlets that can be processed further by many alternative approaches. Combined with the capabilities of up-scaling and unlimited mixing that spark ablation enables, this study provides an easy-to-use concept for producing the key building blocks for low-cost industrial-scale nanofabrication of advanced materials.

  13. Toward industrial scale synthesis of ultrapure singlet nanoparticles with controllable sizes in a continuous gas-phase process

    PubMed Central

    Feng, Jicheng; Biskos, George; Schmidt-Ott, Andreas

    2015-01-01

    Continuous gas-phase synthesis of nanoparticles is associated with rapid agglomeration, which can be a limiting factor for numerous applications. In this report, we challenge this paradigm by providing experimental evidence to support that gas-phase methods can be used to produce ultrapure non-agglomerated “singlet” nanoparticles having tunable sizes at room temperature. By controlling the temperature in the particle growth zone to guarantee complete coalescence of colliding entities, the size of singlets in principle can be regulated from that of single atoms to any desired value. We assess our results in the context of a simple analytical model to explore the dependence of singlet size on the operating conditions. Agreement of the model with experimental measurements shows that these methods can be effectively used for producing singlets that can be processed further by many alternative approaches. Combined with the capabilities of up-scaling and unlimited mixing that spark ablation enables, this study provides an easy-to-use concept for producing the key building blocks for low-cost industrial-scale nanofabrication of advanced materials. PMID:26511290

  14. Toward industrial scale synthesis of ultrapure singlet nanoparticles with controllable sizes in a continuous gas-phase process.

    PubMed

    Feng, Jicheng; Biskos, George; Schmidt-Ott, Andreas

    2015-01-01

    Continuous gas-phase synthesis of nanoparticles is associated with rapid agglomeration, which can be a limiting factor for numerous applications. In this report, we challenge this paradigm by providing experimental evidence to support that gas-phase methods can be used to produce ultrapure non-agglomerated "singlet" nanoparticles having tunable sizes at room temperature. By controlling the temperature in the particle growth zone to guarantee complete coalescence of colliding entities, the size of singlets in principle can be regulated from that of single atoms to any desired value. We assess our results in the context of a simple analytical model to explore the dependence of singlet size on the operating conditions. Agreement of the model with experimental measurements shows that these methods can be effectively used for producing singlets that can be processed further by many alternative approaches. Combined with the capabilities of up-scaling and unlimited mixing that spark ablation enables, this study provides an easy-to-use concept for producing the key building blocks for low-cost industrial-scale nanofabrication of advanced materials. PMID:26511290

  15. Toward industrial scale synthesis of ultrapure singlet nanoparticles with controllable sizes in a continuous gas-phase process.

    PubMed

    Feng, Jicheng; Biskos, George; Schmidt-Ott, Andreas

    2015-10-29

    Continuous gas-phase synthesis of nanoparticles is associated with rapid agglomeration, which can be a limiting factor for numerous applications. In this report, we challenge this paradigm by providing experimental evidence to support that gas-phase methods can be used to produce ultrapure non-agglomerated "singlet" nanoparticles having tunable sizes at room temperature. By controlling the temperature in the particle growth zone to guarantee complete coalescence of colliding entities, the size of singlets in principle can be regulated from that of single atoms to any desired value. We assess our results in the context of a simple analytical model to explore the dependence of singlet size on the operating conditions. Agreement of the model with experimental measurements shows that these methods can be effectively used for producing singlets that can be processed further by many alternative approaches. Combined with the capabilities of up-scaling and unlimited mixing that spark ablation enables, this study provides an easy-to-use concept for producing the key building blocks for low-cost industrial-scale nanofabrication of advanced materials.

  16. Models of Self-Peptide Sampling by Developing T Cells Identify Candidate Mechanisms of Thymic Selection

    PubMed Central

    Bains, Iren; van Santen, Hisse M.; Seddon, Benedict; Yates, Andrew J.

    2013-01-01

    Conventional and regulatory T cells develop in the thymus where they are exposed to samples of self-peptide MHC (pMHC) ligands. This probabilistic process selects for cells within a range of responsiveness that allows the detection of foreign antigen without excessive responses to self. Regulatory T cells are thought to lie at the higher end of the spectrum of acceptable self-reactivity and play a crucial role in the control of autoimmunity and tolerance to innocuous antigens. While many studies have elucidated key elements influencing lineage commitment, we still lack a full understanding of how thymocytes integrate signals obtained by sampling self-peptides to make fate decisions. To address this problem, we apply stochastic models of signal integration by T cells to data from a study quantifying the development of the two lineages using controllable levels of agonist peptide in the thymus. We find two models are able to explain the observations; one in which T cells continually re-assess fate decisions on the basis of multiple summed proximal signals from TCR-pMHC interactions; and another in which TCR sensitivity is modulated over time, such that contact with the same pMHC ligand may lead to divergent outcomes at different stages of development. Neither model requires that T and T are differentially susceptible to deletion or that the two lineages need qualitatively different signals for development, as have been proposed. We find additional support for the variable-sensitivity model, which is able to explain apparently paradoxical observations regarding the effect of partial and strong agonists on T and T development. PMID:23935465

  17. Modeling the endosomal escape of cell-penetrating peptides: transmembrane pH gradient driven translocation across phospholipid bilayers.

    PubMed

    Magzoub, Mazin; Pramanik, Aladdin; Gräslund, Astrid

    2005-11-15

    Cell-penetrating peptides (CPPs) are able to mediate the efficient cellular uptake of a wide range of cargoes. Internalization of a number of CPPs requires uptake by endocytosis, initiated by binding to anionic cell surface heparan sulfate (HS), followed by escape from endosomes. To elucidate the endosomal escape mechanism, we have modeled the process for two CPPs: penetratin (pAntp) and the N-terminal signal peptide of the unprocessed bovine prion protein (bPrPp). Large unilamellar phospholipid vesicles (LUVs) were produced encapsulating either peptide, and an ionophore, nigericin, was used to create a transmembrane pH gradient (DeltapH(mem), inside acidic) similar to the one arising in endosomes in vivo. In the absence of DeltapH(mem), no pAntp escape from the LUVs is observed, while a fraction of bPrPp escapes. In the presence of DeltapH(mem), a significant amount of pAntp escapes and an even higher degree of bPrPp escape takes place. These results, together with the differences in kinetics of escape, indicate different escape mechanisms for the two peptides. A minimum threshold peptide concentration exists for the escape of both peptides. Coupling of the peptides to a cargo reduces the fraction escaping, while complexation with HS significantly hinders the escape. Fluorescence correlation spectroscopy results show that during the escape process the LUVs are intact. Taken together, these results suggest a model for endosomal escape of CPPs: DeltapH(mem)-mediated mechanism, following dissociation from HS of the peptides, above a minimum threshold peptide concentration, in a process that does not involve lysis of the vesicles.

  18. The topology of lysine-containing amphipathic peptides in bilayers by circular dichroism, solid-state NMR, and molecular modeling.

    PubMed Central

    Vogt, B; Ducarme, P; Schinzel, S; Brasseur, R; Bechinger, B

    2000-01-01

    In order to better understand the driving forces that determine the alignment of amphipathic helical polypeptides with respect to the surface of phospholipid bilayers, lysine-containing peptide sequences were designed, prepared by solid-phase chemical synthesis, and reconstituted into membranes. CD spectroscopy indicates that all peptides exhibit a high degree of helicity in the presence of SDS micelles or POPC small unilamellar vesicles. Proton-decoupled (31)P-NMR solid-state NMR spectroscopy demonstrates that in the presence of peptides liquid crystalline phosphatidylcholine membranes orient well along glass surfaces. The orientational distribution and dynamics of peptides labeled with (15)N at selected sites were investigated by proton-decoupled (15)N solid-state NMR spectroscopy. Polypeptides with a single lysine residue adopt a transmembrane orientation, thereby locating this polar amino acid within the core region of the bilayer. In contrast, peptides with > or = 3 lysines reside along the surface of the membrane. With 2 lysines in the center of an otherwise hydrophobic amino acid sequence the peptides assume a broad orientational distribution. The energy of lysine discharge, hydrophobic, polar, and all other interactions are estimated to quantitatively describe the polypeptide topologies observed. Furthermore, a molecular modeling algorithm based on the hydrophobicities of atoms in a continuous hydrophilic-hydrophobic-hydrophilic potential describes the experimentally observed peptide topologies well. PMID:11053137

  19. Device for two-dimensional gas-phase separation and characterization of ion mixtures

    DOEpatents

    Tang, Keqi; Shvartsburg, Alexandre A.; Smith, Richard D.

    2006-12-12

    The present invention relates to a device for separation and characterization of gas-phase ions. The device incorporates an ion source, a field asymmetric waveform ion mobility spectrometry (FAIMS) analyzer, an ion mobility spectrometry (IMS) drift tube, and an ion detector. In one aspect of the invention, FAIMS operating voltages are electrically floated on top of the IMS drift voltage. In the other aspect, the FAIMS/IMS interface is implemented employing an electrodynamic ion funnel, including in particular an hourglass ion funnel. The present invention improves the efficiency (peak capacity) and sensitivity of gas-phase separations; the online FAIMS/IMS coupling creates a fundamentally novel two-dimensional gas-phase separation technology with high peak capacity, specificity, and exceptional throughput.

  20. Multiscale Computational Analysis of Nitrogen and Oxygen Gas-Phase Thermochemistry in Hypersonic Flows

    NASA Astrophysics Data System (ADS)

    Bender, Jason D.

    Understanding hypersonic aerodynamics is important for the design of next-generation aerospace vehicles for space exploration, national security, and other applications. Ground-level experimental studies of hypersonic flows are difficult and expensive; thus, computational science plays a crucial role in this field. Computational fluid dynamics (CFD) simulations of extremely high-speed flows require models of chemical and thermal nonequilibrium processes, such as dissociation of diatomic molecules and vibrational energy relaxation. Current models are outdated and inadequate for advanced applications. We describe a multiscale computational study of gas-phase thermochemical processes in hypersonic flows, starting at the atomic scale and building systematically up to the continuum scale. The project was part of a larger effort centered on collaborations between aerospace scientists and computational chemists. We discuss the construction of potential energy surfaces for the N4, N2O2, and O4 systems, focusing especially on the multi-dimensional fitting problem. A new local fitting method named L-IMLS-G2 is presented and compared with a global fitting method. Then, we describe the theory of the quasiclassical trajectory (QCT) approach for modeling molecular collisions. We explain how we implemented the approach in a new parallel code for high-performance computing platforms. Results from billions of QCT simulations of high-energy N2 + N2, N2 + N, and N2 + O2 collisions are reported and analyzed. Reaction rate constants are calculated and sets of reactive trajectories are characterized at both thermal equilibrium and nonequilibrium conditions. The data shed light on fundamental mechanisms of dissociation and exchange reactions -- and their coupling to internal energy transfer processes -- in thermal environments typical of hypersonic flows. We discuss how the outcomes of this investigation and other related studies lay a rigorous foundation for new macroscopic models for

  1. Towards the chemometric dissection of peptide--HLA-A*0201 binding affinity: comparison of local and global QSAR models.

    PubMed

    Doytchinova, Irini A; Walshe, Valerie; Borrow, Persephone; Flower, Darren R

    2005-03-01

    The affinities of 177 nonameric peptides binding to the HLA-A*0201 molecule were measured using a FACS-based MHC stabilisation assay and analysed using chemometrics. Their structures were described by global and local descriptors, QSAR models were derived by genetic algorithm, stepwise regression and PLS. The global molecular descriptors included molecular connectivity chi indices, kappa shape indices, E-state indices, molecular properties like molecular weight and log P, and three-dimensional descriptors like polarizability, surface area and volume. The local descriptors were of two types. The first used a binary string to indicate the presence of each amino acid type at each position of the peptide. The second was also position-dependent but used five z-scales to describe the main physicochemical properties of the amino acids forming the peptides. The models were developed using a representative training set of 131 peptides and validated using an independent test set of 46 peptides. It was found that the global descriptors could not explain the variance in the training set nor predict the affinities of the test set accurately. Both types of local descriptors gave QSAR models with better explained variance and predictive ability. The results suggest that, in their interactions with the MHC molecule, the peptide acts as a complicated ensemble of multiple amino acids mutually potentiating each other. PMID:16059672

  2. Amphipols Outperform Dodecylmaltoside Micelles in Stabilizing Membrane Protein Structure in the Gas Phase

    PubMed Central

    2014-01-01

    Noncovalent mass spectrometry (MS) is emerging as an invaluable technique to probe the structure, interactions, and dynamics of membrane proteins (MPs). However, maintaining native-like MP conformations in the gas phase using detergent solubilized proteins is often challenging and may limit structural analysis. Amphipols, such as the well characterized A8-35, are alternative reagents able to maintain the solubility of MPs in detergent-free solution. In this work, the ability of A8-35 to retain the structural integrity of MPs for interrogation by electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is compared systematically with the commonly used detergent dodecylmaltoside. MPs from the two major structural classes were selected for analysis, including two β-barrel outer MPs, PagP and OmpT (20.2 and 33.5 kDa, respectively), and two α-helical proteins, Mhp1 and GalP (54.6 and 51.7 kDa, respectively). Evaluation of the rotationally averaged collision cross sections of the observed ions revealed that the native structures of detergent solubilized MPs were not always retained in the gas phase, with both collapsed and unfolded species being detected. In contrast, ESI-IMS-MS analysis of the amphipol solubilized MPs studied resulted in charge state distributions consistent with less gas phase induced unfolding, and the presence of lowly charged ions which exhibit collision cross sections comparable with those calculated from high resolution structural data. The data demonstrate that A8-35 can be more effective than dodecylmaltoside at maintaining native MP structure and interactions in the gas phase, permitting noncovalent ESI-IMS-MS analysis of MPs from the two major structural classes, while gas phase dissociation from dodecylmaltoside micelles leads to significant gas phase unfolding, especially for the α-helical MPs studied. PMID:25495802

  3. Enantiomer-selective photolysis of cold gas-phase tryptophan in L-serine clusters with linearly polarized light.

    PubMed

    Fujihara, Akimasa; Maeda, Naoto; Hayakawa, Shigeo

    2014-04-01

    Photostability of cold gas-phase tryptophan (Trp) enantiomers in L-serine (L-Ser) clusters at 8 K as a model for interstellar molecular clouds was examined using a tandem mass spectrometer containing a cold ion trap to investigate the hypothesis that homochirality in gas-phase Ser clusters promotes the enantiomeric enrichment of other amino acids via enantiomer-selective photolysis with linearly polarized light. In the UV excitation of heterochiral H(+) (L-Ser) 3(D-Trp), the CO2-eliminated product in the cluster was observed. In contrast, the photodissociation mass spectrum of homochiral H(+)(L-Ser)3(L-Trp) showed that photolysis of amino acids in the cluster did not occur due to the evaporation of L-Ser molecules. In the spectra of the homochiral H(+)(L-Ser) (L-Trp) and heterochiral H(+)(L-Ser) (D-Trp), the evaporation of L-Ser was the primary reaction pathway, and no difference between the L- and D-enantiomers was observed. The findings confirm that when 3 L-Ser units are present in the cluster, the photolytic decomposition of Trp is enantiomerically selective.

  4. Real-Time Optical Monitoring of Flow Kinetics and Gas Phase Reactions Under High-Pressure OMCVD Conditions

    NASA Technical Reports Server (NTRS)

    Dietz, N.; McCall, S.; Bachmann, K. J.

    2001-01-01

    This contribution addresses the real-time optical characterization of gas flow and gas phase reactions as they play a crucial role for chemical vapor phase depositions utilizing elevated and high pressure chemical vapor deposition (HPCVD) conditions. The objectives of these experiments are to validate on the basis of results on real-time optical diagnostics process models simulation codes, and provide input parameter sets needed for analysis and control of chemical vapor deposition at elevated pressures. Access to microgravity is required to retain high pressure conditions of laminar flow, which is essential for successful acquisition and interpretation of the optical data. In this contribution, we describe the design and construction of the HPCVD system, which include access ports for various optical methods of real-time process monitoring and to analyze the initial stages of heteroepitaxy and steady-state growth in the different pressure ranges. To analyze the onset of turbulence, provisions are made for implementation of experimental methods for in-situ characterization of the nature of flow. This knowledge will be the basis for the design definition of experiments under microgravity, where gas flow conditions, gas phase and surface chemistry, might be analyzed by remote controlled real-time diagnostics tools, developed in this research project.

  5. Continuous stirred-tank-reactor investigation of the gas-phase reaction of hydroxyl radicals and toluene

    SciTech Connect

    Gery, M.W.; Fox, D.L.; Jeffries, H.E.; Stockburger, L.; Weathers, W.S.

    1985-01-01

    A continuous stirred-tank reactor (CSTR) was used to study the gas-phase reaction between HO and toluene. HO was generated by the in situ photolysis of nitrous acid. Flow-reactor operation at steady-state conditions with a residence time of 20 minutes allowed investigation of primary and very rapid secondary reactions. CSTR and batch-reactor experiments were also performed with selected products. Both gas-phase and aerosol products were identified by chromatography and mass spectroscopy, with total product yields between 55 and 75% of reacted carbon. Toluene reaction products included cresols, nitrocresols, nitrotoluenes, 3,5-dinitrotoluene, benzaldehyde, benzyl nitrate, nitrophenols, methyl-p-benzoquinone, methylglyoxal, glyoxal, formaldehyde, methyl nitrate, PAN, and CO. The fraction of HO methyl hydrogen abstraction was calculated to be 0.13 + or - 0.04. The ratio of reaction rate constants for nitrotoluene versus cresol formation from the HO adduct was calculated to be about 3.3 x 10,000. Also, the ratio of cresol formation versus O2 addition to the HO adduct was estimated to be > or = 0.55. Comparisons of these measurements with previous values and the implications with respect to photochemical kinetics modeling of the atmosphere are discussed.

  6. Laser-induced carbon plasma emission spectroscopic measurements on solid targets and in gas-phase optical breakdown.

    PubMed

    Nemes, László; Keszler, Anna M; Hornkohl, James O; Parigger, Christian G

    2005-06-20

    We report measurements of time- and spatially averaged spontaneous-emission spectra following laser-induced breakdown on a solid graphite/ambient gas interface and on solid graphite in vacuum, and also emission spectra from gas-phase optical breakdown in allene C3H4 and helium, and in CO2 and helium mixtures. These emission spectra were dominated by CII (singly ionized carbon), CIII (doubly ionized carbon), hydrogen Balmer beta (Hbeta), and Swan C2 band features. Using the local thermodynamic equilibrium and thin plasma assumptions, we derived electron number density and electron temperature estimates. The former was in the 10(16) cm(-3) range, while the latter was found to be near 20000 K. In addition, the vibration-rotation temperature of the Swan bands of the C2 radical was determined to be between 4500 and 7000 K, using an exact theoretical model for simulating diatomic emission spectra. This temperature range is probably caused by the spatial inhomogeneity of the laser-induced plasma plume. Differences are pointed out in the role of ambient CO2 in a solid graphite target and in gas-phase breakdown plasma.

  7. Laser-induced carbon plasma emission spectroscopic measurements on solid targets and in gas-phase optical breakdown

    SciTech Connect

    Nemes, Laszlo; Keszler, Anna M.; Hornkohl, James O.; Parigger, Christian

    2005-06-20

    We report measurements of time- and spatially averaged spontaneous-emission spectra following laser-induced breakdown on a solid graphite/ambient gas interface and on solid graphite in vacuum, and also emission spectra from gas-phase optical breakdown in allene C3H4 and helium, and in CO2 and helium mixtures. These emission spectra were dominated by CII (singly ionized carbon), CIII (doubly ionized carbon), hydrogen Balmer beta (H{sub b}eta), and Swan C2 band features. Using the local thermodynamic equilibrium and thin plasma assumptions, we derived electron number density and electron temperature estimates. The former was in the 1016 cm{sup -3} range, while the latter was found to be near 20000 K. In addition, the vibration-rotation temperature of the Swan bands of the C2 radical was determined to be between 4500 and 7000 K, using an exact theoretical model for simulating diatomic emission spectra. This temperature range is probably caused by the spatial inhomogeneity of the laser-induced plasma plume. Differences are pointed out in the role of ambient CO2 in a solid graphite target and in gas-phase breakdown plasma.

  8. Gas-phase thermal dissociation of uranium hexafluoride: Investigation by the technique of laser-powered homogeneous pyrolysis

    SciTech Connect

    Bostick, W.D.; McCulla, W.H.; Trowbridge, L.D.

    1987-04-01

    In the gas-phase, uranium hexafluoride decomposes thermally in a quasi-unimolecular reaction to yield uranium pentafluoride and atomic fluorine. We have investigated this reaction using the relatively new technique of laser-powered homogeneous pyrolysis, in which a megawatt infrared laser is used to generate short pulses of high gas temperatures under strictly homogeneous conditions. In our investigation, SiF/sub 4/ is used as the sensitizer to absorb energy from a pulsed CO/sub 2/ laser and to transfer this energy by collisions with the reactant gas. Ethyl chloride is used as an external standard ''thermometer'' gas to permit estimation of the unimolecular reaction rate constants by a relative rate approach. When UF/sub 6/ is the reactant, CF/sub 3/Cl is used as reagent to trap atomic fluorine reaction product, forming CF/sub 4/ as a stable indicator which is easily detected by infrared spectroscopy. Using these techniques, we estimate the UF/sub 6/ unimolecular reaction rate constant near the high-pressure limit. In the Appendix, we describe a computer program, written for the IBM PC, which predicts unimolecular rate constants based on the Rice-Ramsperger-Kassel theory. Parameterization of the theoretical model is discussed, and recommendations are made for ''appropriate'' input parameters for use in predicting the gas-phase unimolecular reaction rate for UF/sub 6/ as a function of temperature and gas composition and total pressure. 85 refs., 17 figs., 14 tabs.

  9. Computational study of the Sonogashira cross-coupling reaction in the gas phase and in dichloromethane solution.

    PubMed

    Sikk, Lauri; Tammiku-Taul, Jaana; Burk, Peeter; Kotschy, András

    2012-07-01

    The Sonogashira cross-couplig reaction, consisting of oxidative addition, cis-trans isomerization, transmetalation, and reductive elimination, was computationally modeled using the DFT B3LYP/cc-pVDZ method for reaction between bromobenzene and phenylacetylene. Palladium diphosphane was used as a catalyst, copper(I) bromide as a co-catalyst and trimethylamine as a base. The reaction mechanism was studied both in the gas phase and in dichloromethane solution using PCM method. The complete catalytic cycle is thermodynamically strongly shifted toward products (diphenylacetylene and regenerated palladium catalyst) and is exothermic being in accordance with experimental data. The rate-determining step is the oxidative addition, since the highest point on the Gibbs energy graph of the complete reaction is the transition state of this step. This conclusion is also supported by recent experimental data. The computed energy profile suggests that the transmetalation step is initiated by the dissociation of neutral ligand, while the activation Gibbs energy of this step is 0.1 kcal mol(-1) in the gas phase. PMID:22160651

  10. Study of Hind Limb Tissue Gas Phase Formation in Response to Suspended Adynamia and Hypokinesia

    NASA Technical Reports Server (NTRS)

    Butler, Bruce D.

    1996-01-01

    The purpose of this study was to investigate the hypothesis that reduced joint/muscle activity (hypo kinesia) as well as reduced or null loading of limbs (adynamia) in gravity would result in reduced decompression-induced gas phase and symptoms of decompression sickness (DCS). Finding a correlation between the two phenomena would correspond to the proposed reduction in tissue gas phase formation in astronauts undergoing decompression during extravehicular activity (EVA) in microgravity. The observation may further explain the reported low incidence of DCS in space.

  11. Spray characterization and gas phase interaction downstream of a simplified atomizer

    NASA Astrophysics Data System (ADS)

    Hebrard, P.; Trichet, P.; Millan, P.

    1992-07-01

    A detailed study of the flowfield produced by a simplified airblast atomizer was performed. This atomizer consists of an annular liquid sheet introduced into coflowing nonswirling and swirling air flow fields. Droplet size and velocity were measured in the resultant spray using a two components Phase/Doppler Particle Analyzer. A complete set of measurements was obtained at axial locations from 8 mm to 150 mm downstream from the nozzle. Laser velocimetry was also employed to measure the gas phase properties. The effect of swirl on droplet transport process is examined for this type of airblast atomizer and the results demonstrate the strong influence the spray has on the gas phase.

  12. Direct gas-phase epoxidation of propylene to propylene oxide through radical reactions: A theoretical study

    NASA Astrophysics Data System (ADS)

    Kizilkaya, Ali Can; Fellah, Mehmet Ferdi; Onal, Isik

    2010-03-01

    The gas-phase radical chain reactions which utilize O 2 as the oxidant to produce propylene oxide (PO) are investigated through theoretical calculations. The transition states and energy profiles were obtained for each path. The rate constants were also calculated. The energetics for the competing pathways indicate that PO can be formed selectively due to its relatively low activation barrier (9.3 kcal/mol) which is in a good agreement with the experimental value (11 kcal/mol) of gas-phase propylene epoxidation. The formation of the acrolein and combustion products have relatively high activation barriers and are not favored. These results also support the recent experimental findings.

  13. Atmospheric chemistry of gas-phase polycyclic aromatic hydrocarbons: formation of atmospheric mutagens.

    PubMed Central

    Atkinson, R; Arey, J

    1994-01-01

    The atmospheric chemistry of the 2- to 4-ring polycyclic aromatic hydrocarbons (PAH), which exist mainly in the gas phase in the atmosphere, is discussed. The dominant loss process for the gas-phase PAH is by reaction with the hydroxyl radical, resulting in calculated lifetimes in the atmosphere of generally less than one day. The hydroxyl (OH) radical-initiated reactions and nitrate (NO3) radical-initiated reactions often lead to the formation of mutagenic nitro-PAH and other nitropolycyclic aromatic compounds, including nitrodibenzopyranones. These atmospheric reactions have a significant effect on ambient mutagenic activity, indicating that health risk assessments of combustion emissions should include atmospheric transformation products. PMID:7821285

  14. Gas Phase Spectra and Structural Determination of Glucose 6 Phosphate Using Cryogenic Ion Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kregel, Steven J.; Voss, Jonathan; Marsh, Brett; Garand, Etienne

    2014-06-01

    Glucose-6-Phosphate (G6P) is one member of a class of simple phosphorylated sugars that are relevant in biological processes. We have acquired a gas phase infrared spectrum of G6P- using cryogenic ion vibrational spectroscopy (CIVS) in a home-built spectrometer. The experimental spectrum was compared with calculated vibrational spectra from a systematic conformer search. For both of the α and β anomers, results show that only the lowest energy conformers are present in the gas phase. If spectral signatures for similar sugars could be cataloged, it would allow for conformer-specific determination of mixture composition, for example, for glycolyzation processes.

  15. Control of gas phase nanoparticle shape and its effect on MRI relaxivity

    NASA Astrophysics Data System (ADS)

    Aktaş, Sıtkı; Thornton, Stuart C.; Binns, Chris; Lari, Leonardo; Pratt, Andrew; Kröger, Roland; Horsfield, Mark A.

    2015-03-01

    We have used a sputtering gas aggregation source to produce Fe@FeO nanoparticles with different shapes, by annealing them at different temperatures in the gas phase. Without annealing, the most common shape found for the nanoparticles is cubic but annealing the nanoparticles at 1129 °C transforms the cubes into cuboctahedra. Measurements of the MRI relaxivity show that the cubic nanoparticles have a higher performance by a factor of two, which is attributed to a higher saturation magnetization for this shape. This indicates that the shape-control enabled by gas-phase synthesis is important for obtaining optimal performance in applications.

  16. Time-dependent gas phase kinetics in a hydrogen diluted silane plasma

    SciTech Connect

    Nunomura, S.; Kondo, M.; Yoshida, I.

    2009-02-16

    The gas phase kinetics in a high-pressure hydrogen diluted silane plasma has been studied at time scales of 10{sup -2}-6x10{sup 2} s. The time-resolved gas phase composition shows the following kinetics at different time scales: silane decomposition and polysilane generation in < or approx. 2x10{sup -1} s, nanoparticle formation and plasma density reduction in 10{sup -1}-10{sup 0} s, polysilane accumulation in 10{sup 0}-10{sup 2} s, and silane depletion and electrode heating in > or approx. 10{sup 1} s. Disilane radicals are implied to be the dominant film precursors in addition to silyl radicals.

  17. A pressure cell for nonresonant inelastic x-ray scattering studies of gas phases

    SciTech Connect

    Minzer, M.; Bradley, J. A.; Musgrave, R.; Seidler, G. T.; Skilton, A.

    2008-08-15

    We report the design and performance of a gas-phase sample cell for measurements of momentum transfer (q) dependent nonresonant inelastic x-ray scattering (NRIXS). NRIXS measurements from He gas at 2 MPa (20 bars) readily demonstrate dipole-allowed and dipole-forbidden final states for two-electron excitations. Direct comparison of gas-phase NRIXS measurements with the corresponding nonresonant electron energy loss spectroscopy results (EELS) will be a valuable method for characterizing systematic errors in either technique for studies that require absolute normalization of the double differential cross section.

  18. Antimicrobial Peptide, Lumbricusin, Ameliorates Motor Dysfunction and Dopaminergic Neurodegeneration in a Mouse Model of Parkinson's Disease.

    PubMed

    Kim, Dae Hong; Lee, Ik Hwan; Nam, Seung Taek; Hong, Ji; Zhang, Peng; Lu, Li Fang; Hwang, Jae Sam; Park, Ki Cheol; Kim, Ho

    2015-10-01

    We recently reported that the antimicrobial peptide Lumbricusin (NH2-RNRRWCIDQQA), isolated from the earthworm, increases cell proliferation in neuroblastoma SH-SY5Y cells. Here, we investigated whether Lumbricusin has neurotropic activity in mouse neural stem cells (MNSCs) and a protective effect in a mouse model of Parkinson's disease (PD). In MNSCs isolated from mouse brains, Lumbricusin treatment significantly increased cell proliferation (up to 12%) and reduced the protein expression of p27(Kip1) through proteasomal protein degradation but not transcriptional regulation. Lumbricusin inhibited the 6-OHDA-induced apoptosis of MNSCs, and also showed neuroprotective effects in a mouse PD model, ameliorating the motor impairments seen in the pole, elevated body swing, and rotation tests. These results suggest that the Lumbricusin-induced promotion of neural cell proliferation via p27(Kip1) degradation has a protective effect in an experimental PD model. Thus, the antimicrobial peptide Lumbricusin could possibly be developed as a potential therapeutic agent for the treatment of PD. PMID:26215270

  19. A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices.

    PubMed Central

    Efremov, R G; Nolde, D E; Vergoten, G; Arseniev, A S

    1999-01-01

    We describe application of the implicit solvation model (see the first paper of this series), to Monte Carlo simulations of several peptides in bilayer- and water-mimetic environments, and in vacuum. The membrane-bound peptides chosen were transmembrane segments A and B of bacteriorhodopsin, the hydrophobic segment of surfactant lipoprotein, and magainin2. Their conformations in membrane-like media are known from the experiments. Also, molecular dynamics study of surfactant lipoprotein with different explicit solvents has been reported (Kovacs, H., A. E. Mark, J. Johansson, and W. F. van Gunsteren. 1995. J. Mol. Biol. 247:808-822). The principal goal of this work is to compare the results obtained in the framework of our solvation model with available experimental and computational data. The findings could be summarized as follows: 1) structural and energetic properties of studied molecules strongly depend on the solvent; membrane-mimetic media significantly promote formation of alpha-helices capable of traversing the bilayer, whereas a polar environment destabilizes alpha-helical conformation via reduction of solvent-exposed surface area and packing; 2) the structures calculated in a membrane-like environment agree with the experimental ones; 3) noticeable differences in conformation of surfactant lipoprotein assessed via Monte Carlo simulation with implicit solvent (this work) and molecular dynamics in explicit solvent were observed; 4) in vacuo simulations do not correctly reproduce protein-membrane interactions, and hence should be avoided in modeling membrane proteins. PMID:10233063

  20. Modeling the Interaction between Integrin-Binding Peptide (RGD) and Rutile Surface: The Effect of Na+ on Peptide Adsorption

    SciTech Connect

    Wu, Chunya; Skelton, Adam; Chen, Mingjun; Vlcek, Lukas; Cummings, Peter T

    2011-01-01

    The dynamics of a single tripeptide Arg-Gly-Asp (RGD) adsorbing onto negatively charged hydroxylated rutile (110) surface in aqueous solution was studied using molecular dynamics (MD) simulations. The results indicate that the adsorbed Na{sup +} ions play an important role in determining the binding geometry of RGD. With an initial 'horseshoe' configuration, the charged side groups (COO{sup -} and NH{sub 2}) of the peptide are able to interact with the surface through direct hydrogen bonds (H bonds) in the very early stage of adsorption. The Na{sup +} ions approach the positively charged Arg side chain, competing with the Arg side chain for adsorption to the negatively charged hydroxyl oxygen. In coordination with the structural adjustment of the peptide, the Arg residue is driven to detach from the rutile surface. In contrast, the Na+ ions in close proximity to the negatively charged Asp side chain contribute to the binding of the COO{sup -} group on the surface, helping the carboxyl oxygen not involved in COO{sup -}-surface H bonds to orientate toward the hydroxyl hydrogens. Once both carboxyl oxygens form enough H bonds with the hydroxyl hydrogens, the redundant ions move toward a more favorable adsorption site.

  1. Real-Time Gas-Phase Imaging over a Pd(110) Catalyst during CO Oxidation by Means of Planar Laser-Induced Fluorescence

    PubMed Central

    2015-01-01

    The gas composition surrounding a catalytic sample has direct impact on its surface structure, which is essential when in situ investigations of model catalysts are performed. Herein a study of the gas phase close to a Pd(110) surface during CO oxidation under semirealistic conditions is presented. Images of the gas phase, provided by planar laser-induced fluorescence, clearly visualize the formation of a boundary layer with a significantly lower CO partial pressure close to the catalytically active surface, in comparison to the overall concentration as detected by mass spectrometry. The CO partial pressure variation within the boundary layer will have a profound effect on the catalysts’ surface structure and function and needs to be taken into consideration for in situ model catalysis studies. PMID:25893136

  2. Full membrane spanning self-assembled monolayers as model systems for UHV-based studies of cell-penetrating peptides

    SciTech Connect

    Franz, Johannes; Graham, Daniel J.; Baio, Joe E.; Lelle, Marco; Peneva, Kalina; Müllen, Klaus; Castner, David G.; Weidner, Tobias

    2015-03-01

    Biophysical studies of the interaction of peptides with model membranes provide a simple yet effective approach to understand the transport of peptides and peptide based drug carriers across the cell membrane. Therein, the authors discuss the use of self-assembled monolayers fabricated from the full membrane-spanning thiol (FMST) 3-((14-((4'-((5-methyl-1-phenyl-35-(phytanyl)oxy-6,9,12,15,18,21,24,27,30,33,37-undecaoxa-2,3-dithiahenpentacontan-51-yl)oxy)-[1,1'-biphenyl]-4-yl)oxy)tetradecyl)oxy)-2-(phytanyl)oxy glycerol for ultrahigh vacuum (UHV) based experiments. UHV-based methods such as electron spectroscopy and mass spectrometry can provide important information about how peptides bind and interact with membranes, especially with the hydrophobic core of a lipid bilayer. Moreover, near-edge x-ray absorption fine structure spectra and x-ray photoelectron spectroscopy (XPS) data showed that FMST forms UHV-stable and ordered films on gold. XPS and time of flight secondary ion mass spectrometry depth profiles indicated that a proline-rich amphipathic cell-penetrating peptide, known as sweet arrow peptide is located at the outer perimeter of the model membrane.

  3. Polymerization in the gas phase, in clusters, and on nanoparticle surfaces.

    PubMed

    El-Shall, M Samy

    2008-07-01

    Gas phase and cluster experiments provide unique opportunities to quantitatively study the effects of initiators, solvents, chain transfer agents, and inhibitors on the mechanisms of polymerization. Furthermore, a number of important phenomena, unique structures, and novel properties may exist during gas-phase and cluster polymerization. In this regime, the structure of the growing polymer may change dramatically and the rate coefficient may vary significantly upon the addition of a single molecule of the monomer. These changes would be reflected in the properties of the oligomers deposited from the gas phase. At low pressures, cationic and radical cationic polymerizations may proceed in the gas phase through elimination reactions. In the same systems at high pressure, however, the ionic intermediates may be stabilized, and addition without elimination may occur. In isolated van der Waals clusters of monomer molecules, sequential polymerization with several condensation steps can occur on a time scale of a few microseconds following the ionization of the gas-phase cluster. The cluster reactions, which bridge gas-phase and condensed-phase chemistry, allow examination of the effects of controlled states of aggregation. This Account describes several examples of gas-phase and cluster polymerization studies where the most significant results can be summarized as follows: (1) The carbocation polymerization of isobutene shows slower rates with increasing polymerization steps resulting from entropy barriers, which could explain the need for low temperatures for the efficient propagation of high molecular weight polymers. (2) Radical cation polymerization of propene can be initiated by partial charge transfer from an ionized aromatic molecule such as benzene coupled with covalent condensation of the associated propene molecules. This novel mechanism leads exclusively to the formation of propene oligomer ions and avoids other competitive products. (3) Structural information

  4. Polymerization in the gas phase, in clusters, and on nanoparticle surfaces.

    PubMed

    El-Shall, M Samy

    2008-07-01

    Gas phase and cluster experiments provide unique opportunities to quantitatively study the effects of initiators, solvents, chain transfer agents, and inhibitors on the mechanisms of polymerization. Furthermore, a number of important phenomena, unique structures, and novel properties may exist during gas-phase and cluster polymerization. In this regime, the structure of the growing polymer may change dramatically and the rate coefficient may vary significantly upon the addition of a single molecule of the monomer. These changes would be reflected in the properties of the oligomers deposited from the gas phase. At low pressures, cationic and radical cationic polymerizations may proceed in the gas phase through elimination reactions. In the same systems at high pressure, however, the ionic intermediates may be stabilized, and addition without elimination may occur. In isolated van der Waals clusters of monomer molecules, sequential polymerization with several condensation steps can occur on a time scale of a few microseconds following the ionization of the gas-phase cluster. The cluster reactions, which bridge gas-phase and condensed-phase chemistry, allow examination of the effects of controlled states of aggregation. This Account describes several examples of gas-phase and cluster polymerization studies where the most significant results can be summarized as follows: (1) The carbocation polymerization of isobutene shows slower rates with increasing polymerization steps resulting from entropy barriers, which could explain the need for low temperatures for the efficient propagation of high molecular weight polymers. (2) Radical cation polymerization of propene can be initiated by partial charge transfer from an ionized aromatic molecule such as benzene coupled with covalent condensation of the associated propene molecules. This novel mechanism leads exclusively to the formation of propene oligomer ions and avoids other competitive products. (3) Structural information

  5. A model of the peptide triazole entry inhibitor binding to HIV-1 gp120 and mechanism of bridging sheet disruption

    PubMed Central

    Emileh, Ali; Tuzer, Ferit; Yeh, Herman; Umashankara, Muddegowda; Moreira, Diogo R. M.; LaLonde, Judith M.; Bewley, Carole A.; Abrams, Cameron F.; Chaiken, Irwin M.

    2013-01-01

    Peptide-triazole (PT) entry inhibitors prevent HIV-1 infection by blocking viral gp120 binding to both HIV-1 receptor and coreceptor on target cells. Here, we used all-atom explicit solvent molecular dynamics (MD) to propose a model for the encounter complex of the peptide-triazoles with gp120. Saturation Transfer Difference NMR (STD NMR) and single-site mutagenesis experiments were performed to test the simulation results. We found that docking of the peptide to a conserved patch of residues lining the “F43 pocket” of gp120 in a bridging sheet naïve gp120 conformation of the glycoprotein, led to a stable complex. This pose prevents formation of the bridging sheet minidomain, which is required for receptor/coreceptor binding, providing a mechanistic basis for dual-site antagonism of this class of inhibitors. Burial of the peptide triazole at gp120 inner/outer domain interface significantly contributed to complex stability and rationalizes the significant contribution of hydrophobic triazole groups to peptide potency. Both the simulation model and STD NMR experiments suggest that the I-X-W (where X=(2S, 4S)-4-(4-phenyl-1H-1, 2, 3-triazol-1-yl) pyrrolidine) tripartite hydrophobic motif in the peptide is the major contributor of contacts at the gp120/PT interface. Since the model predicts that the peptide Trp side chain hydrogen bonding with gp120 S375 contributes to stability of the PT/gp120 complex, we tested this prediction through analysis of peptide binding to gp120 mutant S375A. The results showed that a peptide triazole KR21 inhibits S375A with 20-fold less potency versus WT, consistent with predictions of the model. Overall, the PT/gp120 model provides a starting point for both rational design of higher affinity peptide triazoles and development of structure-minimized entry inhibitors that can trap gp120 into an inactive conformation and prevent infection. PMID:23470147

  6. Gas-Phase Protein Inner-Shell Spectroscopy by Coupling an Ion Trap with a Soft X-ray Beamline.

    PubMed

    Milosavljević, Aleksandar R; Canon, Francis; Nicolas, Christophe; Miron, Catalin; Nahon, Laurent; Giuliani, Alexandre

    2012-05-01

    C, N, and O near-edge ion yield spectroscopy of 8+ selected electrosprayed cations of cytochrome c protein (12 kDa) has been performed by coupling a linear quadrupole ion trap with a soft X-ray beamline. The photoactivation tandem mass spectra were recorded as a function of the photon energy. Photoionization of the precursor, accompanied by CO2 loss, is the dominant relaxation process, showing high photoion stability following direct or resonant photoionization. The partial ion yields extracted from recorded mass spectra show significantly different behaviors for single and double ionization channels, which can be qualitatively explained by different Auger decay mechanisms. However, the single ionization spectra reveal characteristic structures when compared to existing near-edge X-ray absorption fine structure (NEXAFS) spectra from thin films of peptides and proteins. Therefore, the present experiment opens up new avenues for near-edge X-ray spectroscopy of macromolecules in the gas phase, overcoming the radiation damage issue or the environmental effects as due to the surface, intermolecular interactions, and solvent.

  7. Capture of gas-phase arsenic oxide by lime: kinetic and mechanistic studies.

    PubMed

    Jadhav, R A; Fan, L S

    2001-02-15

    Trace metal emission from coal combustion is a major concern for coal-burning utilities. Toxic compounds such as arsenic species are difficult to control because of their high volatility. Mineral sorbents such as lime and hydrated lime have been shown to be effective in capturing arsenic from the gas phase over a wide temperature range. In this study, the mechanism of interaction between arsenic oxide (As2O3) and lime (CaO) is studied over the range of 300-1000 degrees C. The interaction between these two components is found to depend on the temperature; tricalcium orthoarsenate (Ca3As2O8) is found to be the product of the reaction below 600 degrees C, whereas dicalcium pyroarsenate (Ca2As2O7) is found to be the reaction product in the range of 700-900 degrees C. Maximum capture of arsenic oxide is found to occur in the range of 500-600 degrees C. At 500 degrees C, a high reactivity calcium carbonate is found to capture arsenic oxide by a combination of physical and chemical adsorption. Intrinsic kinetics of the reaction between calcium oxide and arsenic oxide in the medium-temperature range of 300-500 degrees C is studied in a differential bed flow-through reactor. Using the shrinking core model, the order of reaction with respect to arsenic oxide concentration is found to be about 1, and the activation energy is calculated to be 5.1 kcal/mol. The effect of initial surface area of CaO sorbent is studied over a range of 2.7-45 m2/g using the grain model. The effect of other major acidic flue gas species (SO2 and HCl) on arsenic capture is found to be minimal under the conditions of the experiment. PMID:11349294

  8. A Theoretical Study on Gas-Phase Coating of Aerosol Particles

    PubMed

    Jain; Fotou; Kodas

    1997-01-01

    In situ coating of aerosol particles by gas-phase and surface reaction in a flow reactor is modeled accounting for scavenging (capture of small particles by large particles) and simultaneous surface reaction along with the finite sintering rate of the scavenged particles. A log-normal size distribution is assumed for the host and coating particles to describe coagulation and a monodisperse size distribution is used for the coating particles to describe sintering. As an example, coating of titania particles with silica in a continuous flow hot-wall reactor was modeled. High temperatures, low reactant concentrations, and large host particle surface areas favored smoother coatings in the parameter range: temperature 1700-1800 K, host particle number concentration 1 x 10(5)-1 x 10(7) #/cm3, average host particle size 1 &mgr;m, inlet coating reactant concentration (SiCl4) 2 x 10(-7)-2 x 10(-10) mol/cm3, and various surface reaction rates. The fraction of silica deposited on the TiO2 particles decreased by more than seven times with a hundredfold increase in SiCl4 inlet concentration because of the resulted increase in the average SiO2 particle size under the assumed coating conditions. Increasing the TiO2 particle number concentration resulted in higher scavenging efficiency of SiO2. In the TiO2/SiO2 system it is likely that surface reaction as well as scavenging play important roles in the coating process. The results agree qualitatively with experimental observations of TiO2 particles coated in situ with silica.

  9. Gas phase dispersion in a small rotary kiln

    SciTech Connect

    Spencer, B.B.

    1981-07-01

    A study was made of nonideal flow of gas in a rotary kiln reactor. A rotating tube 0.165 m in diameter by 2.17 m long, with internal lifting flights, was operated at room temperature. Rotational speeds from 2.0 to 7.0 rpm, air flow rates from 0.351 to 4.178 m/sup 3//h, and solid contents of 0.0, 5.1, and 15.3% of tube volume were studied. Residence time distribution of the gas was measured by means of the pulse injection technique using a helium tracer. A model was developed based on dispersive flow that exchanges with a deadwater region. Two parameters, a dispersion number describing bulk gas flow and an interchange factor describing exchange between the flow region and the gas trapped in the solids bed, were sufficient to correlate the data, but these parameters are sensitive to experimental error. The model is applicable to analysis of other flow systems, such as packed beds.