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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. Structural exploration and Frster theory modeling for the interpretation of gas-phase FRET measurements: Chromophore-grafted amyloid-? 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 Frster theory (Frster 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-? 12-28 fragments, known to be involved in amyloid plaque formation connected to Alzheimer's disease. We sample structures of the peptides that are grafted with 5-carboxyrhodamine 575 (Rh575) and QSY-7 chromophores by means of replica-exchange molecular dynamics simulations upon an Amber-type forcefield parametrization as a function of the charge state. The generated ensembles provide chromophore-distance and -orientation distributions which are used with the spectral parameters of the Rh575/QSY-7 chromophores to model FRET-efficiencies for the systems. The theoretical values agree with the experimental average "action"-FRET efficiencies and motivate to use the herein reported parametrization, sampling, and FRET-modeling technique in future studies on the structural properties and aggregation-behavior of related systems. PMID:26178129

  3. Modelling peptide-metal dication interactions: formamide-Ca2+ reactions in the gas phase.

    PubMed

    Eizaguirre, Ane; Mó, Otilia; Yáñez, Manuel; Salpin, Jean-Yves; Tortajada, Jeanine

    2012-10-01

    The collision induced dissociation of formamide-Ca(2+) complexes produced in the gas phase through nanoelectrospray ionization yields as main products ions [CaOH](+), [HCNH](+), [Ca(NH(2))](+), HCO(+) and [Ca(NH(3))](2+) and possibly [Ca(H(2)O)](2+) and [C,O,Ca](2+), the latter being rather minor. The mechanisms behind these fragmentation processes have been established by analyzing the topology of the potential energy surface by means of B3LYP calculations carried out with a core-correlated cc-pWCVTZ basis set. The Ca(2+) complexes formed by formamide itself and formimidic acid play a fundamental role. The former undergoes a charge separation reaction yielding [Ca(NH(2))](+) + HCO(+), and the latter undergoes the most favorable Coulomb explosion yielding [Ca-OH](+) + [HCNH](+) and is the origin of a multistep mechanism which accounts for the observed loss of water and HCN. Conversely, the other isomer of formamide, amino(hydroxyl)carbene, does not play any significant role in the unimolecular reactivity of the doubly charged molecular cation. PMID:22892540

  4. 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.

  5. Photosynthesis of a combinatorial peptide library in the gas phase.

    PubMed

    Lee, Sunyoung; Glover, Matthew S; Reilly, James P; Clemmer, David E

    2015-09-15

    A strategy for generating large numbers of peptides from a relatively small number of precursors based on photosynthetic combination in the gas phase is presented. In this approach, electrospray ionization is used to create a combination of proton-bound dimers from a specified set of peptides present in solution. The dimers are then accumulated and isolated in an ion trap mass spectrometer. Photoexcitation (at 157 nm) leads to water elimination and the formation of larger peptide sequences that are characterized by subsequent isolation and collision-induced dissociation. The method is illustrated by using a set of four enkephalin-related and acetylated peptides to generate 12 larger peptide sequences. The ability to synthesize, isolate, and characterize many amino acid sequences from only a few precursors provides a fast and efficient means of characterizing properties of such species (e.g., dissociation patterns and reactivities). PMID:26285100

  6. 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.

  7. 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

  8. Improved machine learning method for analysis of gas phase chemistry of peptides

    PubMed Central

    Gehrke, Allison; Sun, Shaojun; Kurgan, Lukasz; Ahn, Natalie; Resing, Katheryn; Kafadar, Karen; Cios, Krzysztof

    2008-01-01

    Background Accurate peptide identification is important to high-throughput proteomics analyses that use mass spectrometry. Search programs compare fragmentation spectra (MS/MS) of peptides from complex digests with theoretically derived spectra from a database of protein sequences. Improved discrimination is achieved with theoretical spectra that are based on simulating gas phase chemistry of the peptides, but the limited understanding of those processes affects the accuracy of predictions from theoretical spectra. Results We employed a robust data mining strategy using new feature annotation functions of MAE software, which revealed under-prediction of the frequency of occurrence in fragmentation of the second peptide bond. We applied methods of exploratory data analysis to pre-process the information in the MS/MS spectra, including data normalization and attribute selection, to reduce the attributes to a smaller, less correlated set for machine learning studies. We then compared our rule building machine learning program, DataSqueezer, with commonly used association rules and decision tree algorithms. All used machine learning algorithms produced similar results that were consistent with expected properties for a second gas phase mechanism at the second peptide bond. Conclusion The results provide compelling evidence that we have identified underlying chemical properties in the data that suggest the existence of an additional gas phase mechanism for the second peptide bond. Thus, the methods described in this study provide a valuable approach for analyses of this kind in the future. PMID:19055745

  9. 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.

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

    PubMed

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

    2016-04-01

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

  11. 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

    2016-01-01

    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.

  12. Factors that Influence Competitive Intermolecular Solvation of Protonated Groups in Peptides and Proteins in the Gas Phase

    PubMed Central

    Tao, Yuanqi; Julian, Ryan R.

    2013-01-01

    The ability of 18-crown-6 (18C6) to form noncovalent complexes with cationic groups in the gas phase has been leveraged in numerous, largely orthogonal mass spectrometry-based applications. Although the fundamental interaction between 18C6 and a charged group in the gas phase is quite strong, the strength of attachment of 18C6 to large molecules is more difficult to predict because intramolecular binding of the cation can be competitive. Herein, we demonstrate in experiments with model peptides that 18C6 adducts are not strongly attached to flexible molecules with numerous potential hydrogen bonding sites. 18C6 adduct stability is increased if intramolecular charge complexation is inhibited by sterics or competitive binding. It is demonstrated with molecular mechanics that significant structural changes occur upon loss of 18C6 in model peptides. Examination of the loss of 18C6 adducts from proteins following collisional activation reveals that lower charge states lose the most 18C6. The degree of 18C6 adduct stability may reflect the degree of structural reorganization that occurs following collisional activation, suggesting that lower charge states represent structures that are not similar to gas phase idealized states. In this regard, 18C6 may serve the function of protecting solution phase protein structure. Collisional activation of holomyoglobin with 18C6 adducts attached reveals that heme loss occurs primarily after 18C6 loss, further supporting the notion that 18C6 protects native structure by solvating charged sites. PMID:23836378

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

    PubMed

    Litinas, Iraklis; Koutselos, Andreas D

    2015-12-31

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

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

    SciTech Connect

    Webb, S.W.

    1998-09-01

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

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

    PubMed

    Baldauf, Carsten; Rossi, Mariana

    2015-12-16

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

  16. 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.

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

    PubMed

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

    2016-04-01

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

  18. 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.

  19. Model of boron diffusion from gas phase in silicon carbide

    SciTech Connect

    Aleksandrov, O. V.; Mokhov, E. N.

    2011-06-15

    Boron diffusion from the gas phase in silicon carbide is described on the basis of a two-component model. 'Shallow' boron, i.e., boron at silicon sites, is a slow component with a high surface concentration. Its diffusivity is proportional to the concentration of positively charged intrinsic point defects, which are presumably interstitial silicon atoms. 'Deep' boron, i.e., impurity-defect pairs of boron-carbon vacancy, is a fast component with lower surface concentration. The ratio between the surface concentrations of the components depends on the pressure of silicon or carbon vapors in the gas phase. The diffusion and interaction of components are described by the set of diffusion-reaction equations. The diffusion retardation observed on the concentration-profile tail is related to the capture of impurity-defect pairs and excess vacancies by traps of background impurities and defects.

  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. Gas-Phase Chemical Models of Interstellar Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Lee, Ho-Hsin

    A large gas-phase chemical model of interstellar molecular clouds containing almost 4,000 gas-phase reactions involving 409 species are developed. The calculated results are in excellent agreement with observed abundances in TMC1. The effects of rapid neutral-neutral reactions in the gas phase on the synthesis of complex species is studied via a series of model calculations. Reactions between O or N atoms and carbon clusters C n are critical in hindering the synthesis of complex species. Neutral-neutral reactions involving molecular hydrogen (HAARs) are shown to aid molecular synthesis. Bistability in large gas-phase chemical networks of dense clouds is examined. The dependence of bistability on the parameter ζn H for a wide range of elemental depletions is investigated. We confirm that bistability can exist at steady-state for a range of ζn H, and the range of bistability is dependent on elemental depletions and networks utilized. The steady-state results for a variety of molecules in both the HIP and LIP solutions at a high density near 3 104 cm-3 with a standard cosmic ionization rate are also present. A model of time-dependent gas-phase chemistry in a spatially inhomogeneous cloud which is exposed on one side to an isotropic radiation field is presented. Shielding due to H2, CO and dust particles are fully considered. The cloud hydrogen number density is a function of cloud depth varying as (1-cr)-2 where r is the depth into the cloud. The cloud temperature is kept constant at 30 K. The cloud is divided into 43 slabs, which are defined so that the photodissociation rate of CO is halved as one proceeds to the next slab. Models with three different sets of initial conditions regarding hydrogen are presented here. The first model starts with atomic hydrogen in all slabs, the second starts with molecular hydrogen, and the third utilizes an H/H2 fraction with larger value in the outer slabs. The fractional abundance profiles and integrated column densities for selected species as functions of cloud depth at different times are discussed. A comparison between fractional abundances with observations in TMC1 is given. Total integrated column densities obtained via a weighting procedure are designed for unresolved distant sources.

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

    PubMed

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

    2016-03-17

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

  3. On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions

    PubMed Central

    Marchese, Roberto; Grandori, Rita; Carloni, Paolo; Raugei, Simone

    2010-01-01

    Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation. PMID:20463874

  4. 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 ordre de grandeur mais la méthode donne également correctement les autres caractéristiques ; par exemple l'ordre des processus en traçant simplement la courbe des données expérimentales.

  5. 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).

  6. Gas-Phase Fragmentation of Oligoproline Peptide Ions Lacking Easily Mobilizable Protons

    NASA Astrophysics Data System (ADS)

    Rudowska, Magdalena; Wieczorek, Robert; Kluczyk, Alicja; Stefanowicz, Piotr; Szewczuk, Zbigniew

    2013-06-01

    The fragmentation of peptides containing quaternary ammonium group, but lacking easily mobilizable protons, was examined with the aid of deuterium-labeled analogs and quantum-chemical modeling. The fragmentation of oligoproline containing quaternary ammonium group involves the mobilization of hydrogens localized at α- and γ- or δ-carbon atoms in the pyrrolidine ring of proline. The study of the dissociation pattern highlights the unusual proline residue behavior during MS/MS experiments of peptides.

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

    PubMed Central

    Prentice, Boone M.

    2013-01-01

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

  8. 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.

  9. Energetics and Dynamics of Electron Transfer and Proton Transfer in Dissociation of Metal III (salen)-Peptide Complexes in the Gas Phase

    SciTech Connect

    Laskin, Julia; Yang, Zhibo; Chu, Ivan K.

    2008-03-12

    Time- and collision energy-resolved surface-induced dissociation (SID) of ternary complexes of CoIII(salen)+, FeIII(salen)+, and MnIII(salen)+ with several angiotensin peptide analogs was studied using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Time-resolved fragmentation efficiency curves (TFECs) were modeled using an RRKM-based approach developed in our laboratory. The approach utilizes a very flexible analytical expression for the internal energy deposition function that is capable of reproducing both single-collision and multiple-collision activation in the gas phase and excitation by collisions with a surface. The energetics and dynamics of competing dissociation pathways obtained from the modeling provides important insight on the competition between proton transfer, electron transfer, loss of neutral peptide ligand, and other processes that determine gas-phase fragmentation of these model systems. Similar fragmentation behavior was obtained for various CoIII(salen)-peptide systems of different angiotensin analogs. In contrast, dissociation pathways and relative stabilities of the complexes changed dramatically when cobalt was replaced with trivalent iron or manganese. We demonstrate that the electron transfer efficiency is correlated with redox properties of the metalIII(salen) complexes (Co > Fe > Mn), while differences in the types of fragments formed from the complexes reflect differences in the modes of binding between the metal-salen complex and the peptide ligand. RRKM modeling of time- and collision energy-resolved SID data suggests that the competition between proton transfer and electron transfer during dissociation of CoIII(salen)-peptide complexes is mainly determined by differences in entropy effects while the energetics of these two pathways are very similar.

  10. 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. PMID:24863621

  11. Probing peptide cation-radicals by near-UV photodissociation in the gas phase. Structure elucidation of histidine radical chromophores formed by electron transfer reduction.

    PubMed

    Nguyen, Huong T H; Shaffer, Christopher J; Tureček, František

    2015-03-12

    Electron transfer reduction of gas-phase ions generated from histidine-containing peptides forms stable cation-radicals that absorb light at 355 nm, as studied for AAHAR, AAHAK, DSHAK, FHEK, HHGYK, and HHSHR. Laser photodissociation of mass-selected cation-radicals chiefly resulted in loss of H atoms, contrasting dissociations induced by slow collisional heating. The 355 nm absorption was due to new chromophores created by electron transfer and radical rearrangements in the cation-radicals. The chromophores were identified by time-dependent density functional theory calculations as 2H,3H-imidazoline and 2H-dihydrophenol radicals, formed by hydrogen atom transfer to the histidine and tyrosine side chain groups, respectively. These radicals undergo facile C-H bond dissociations upon photon absorption. In contrast, dissociations of histidine peptide cation-radicals containing the 1H,3H-imidazoline ring prefer loss of 4-methylimidazole via a multistep reaction pathway. The isomeric cation-radicals can be distinguished by a combination of collision-induced dissociation and near-UV photodissociation. The TD-DFT excitation energies in model imidazoline radicals were benchmarked on EOM-CCSD energies, and a satisfactory agreement was found for the M06-2X and ωB97XD functionals. The combination of electron transfer, photodissociation, collisional activation, and theory is presented as a powerful tool for studying structures and electronic properties of peptide cation-radicals in the gas phase. PMID:25688483

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

    PubMed Central

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

    2005-01-01

    The ion/ion reactions of several dozen reagent anions with triply protonated cations of the model peptide KGAILKGAILR have been examined to evaluate predictions of a LandauZener-based model for the likelihood for electron transfer. Evidence for electron transfer was provided by the appearance of fragment ions unique to electron transfer or electron capture dissociation. Proton transfer and electron transfer are competitive processes for any combination of anionic and cationic reactants. For reagent anions in reactions with protonated peptides, proton transfer is usually significantly more exothermic than electron transfer. If charge transfer occurs at relatively long distances, electron transfer should, therefore, be favored on kinetic grounds because the reactant and product channels cross at greater distances, provided conditions are favorable for electron transfer at the crossing point. The results are consistent with a model based on LandauZener theory that indicates both thermodynamic and geometric criteria apply for electron transfer involving polyatomic anions. Both the model and the data suggest that electron affinities associated with the anionic reagents greater than about 6070 kcal/mol minimize the likelihood that electron transfer will be observed. Provided the electron affinity is not too high, the FranckCondon factors associated with the anion and its corresponding neutral must not be too low. When one or the other of these criteria is not met, proton transfer tends to occur essentially exclusively. Experiments involving ion/ion attachment products also suggest that a significant barrier exists to the isomerization between chemical complexes that, if formed, lead to either proton transfer or electron transfer. PMID:16144411

  13. Using Gas-Phase Guest-Host Chemistry to Probe the Structures of b Ions of Peptides

    NASA Astrophysics Data System (ADS)

    Somogyi, Árpád; Harrison, Alex G.; Paizs, Béla

    2012-12-01

    Middle-sized b n ( n ≥ 5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen-deuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b n ( n ≤ 4) fragments do not form stable ammonia adducts. We propose that complex formation of b n ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b n ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b 4 , b 5 , and b 7 ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N+-H…O H-bonds; this stabilization is much stronger for macrocyclic b n isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest-host chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b 9 , b 9 -A, and b 9 -2A of A8YA, and b 13 of A20YVFL are observed indicating that even these large b-type ions form macrocyclic structures.

  14. 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.

  15. Gas-Phase Acidities of Cysteine-Polyalanine Peptides I: A3,4CSH and HSCA3,4

    NASA Astrophysics Data System (ADS)

    Ren, Jianhua; Tan, John P.; Harper, Robert T.

    2009-09-01

    The gas-phase acidities of four cysteine-polyalanine peptides, A3,4CSH and HSCA3,4, were determined using the extended Cooks kinetic method with full entropy analysis. A triple-quadrupole mass spectrometer with an electrospray interface was employed for the experimental study. The ion activation was achieved via collision-induced dissociation (CID) experiments. The deprotonation enthalpies (ΔacidH) of the peptides were determined to be 332.2 ± 2.0 kcal/mol (A3CSH), 325.9 ± 2.0 kcal/mol (A4CSH), 319.3 ± 3.0 kcal/mol (HSCA3), and 319.2 ± 4.0 kcal/mol (HSCA4). The deprotonation entropies (ΔacidS) of the peptides were estimated based on the entropy term (Δ(ΔS)) and the deprotonation entropies of the reference acids. By using the deprotonation enthalpies and entropies, the gas-phase acidities (ΔacidG) of the peptides were derived: 325.0 ± 2.0 kcal/mol (A3CSH), 320.2 ± 2.0 kcal/mol (A4CSH), 316.3 ± 3.0 kcal/mol (HSCA3), and 315.4 ± 4.0 kcal/mol (HSCA4). Conformations and energetic information of the peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single-point energy calculations (B3LYP/6-31+G(d)), respectively. The calculated theoretical deprotonation enthalpies (ΔacidH) of 334.2 kcal/mol (A3CSH), 327.7 kcal/mol (A4CSH), 320.6 kcal/mol (HSCA3), and 318.6 kcal/mol (HSCA4) are in good agreement with the experimentally determined values. Both the experimental and computational studies suggest that the two N-terminal cysteine peptides, HSCA3,4, are significantly more acidic than the corresponding C-terminal ones, A3,4CSH. The high acidities of the former are likely due to the helical conformational effects for which the thiolate anion may be strongly stabilized by the interaction with the helix macrodipole.

  16. High-sensitivity gas phase sequence analysis of proteins and peptides on PVDF membranes using short cycle times.

    PubMed

    Reim, D F; Speicher, D W

    1993-10-01

    An optimized sequencer program with a cycle time of 38 min which is specifically tailored for analysis using polyvinylidene difluoride (PVDF) membranes has been developed. The program was developed using a pulsed liquid-phase instrument which was converted to gas-phase acid delivery. Gas-phase acid delivery minimized sample extraction from PVDF membranes and improved tryptophan yields in at least some cases. Other modifications which contributed to reliable high sensitivity sequencer performance included use of a Blott cartridge, substitution of ethyl acetate:heptane (1:1, v/v) instead of butyl chloride as the extraction solvent, use of a modified 100-microliters injection loop with an internal restrictor to reliably inject nearly 90% of the sample, and an HPLC gradient which resolved tryptophan from diphenylurea. These shortened cycle times were achieved at the conventional gas-phase reaction temperature. A slight increase in lag or carryover at prolines was compensated by reduced background from nonspecific acid cleavage which facilitated extended and/or high sensitivity sequencing of large proteins. Reproducible high initial and repetitive cycle yields were obtained with a wide range of experimental peptides which were electroblotted from either 1D or 2D polyacrylamide gels onto high retention PVDF membranes. Initial yields of the majority of the experimental samples analyzed with this program were less than 5 pmol. In addition, most samples with initial yields below 1-2 pmol yielded sufficient sequence information to identify the protein by comparison to protein sequence data-bases or to design oligonucleotide probes. PMID:8250259

  17. 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.

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

    PubMed

    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 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. PMID:25338898

  19. Liquid hot NAGMA cooled to 0.4 K: benchmark thermochemistry of a gas-phase peptide.

    PubMed

    Leavitt, Christopher M; Moore, Kevin B; Raston, Paul L; Agarwal, Jay; Moody, Grant H; Shirley, Caitlyne C; Schaefer, Henry F; Douberly, Gary E

    2014-10-16

    Vibrational spectroscopy and helium nanodroplet isolation are used to determine the gas-phase thermochemistry for isomerization between conformations of the model dipeptide, N-acetylglycine methylamide (NAGMA). A two-stage oven source is implemented to produce a gas-phase equilibrium distribution of NAGMA conformers, which is preserved when individual molecules are captured and cooled to 0.4 K by He nanodroplets. With polarization spectroscopy, the IR spectrum in the NH stretch region is assigned to a mixture of two conformers having intramolecular hydrogen bonds composed of either five- or seven-membered rings, C5 and C7, respectively. The C5 to C7 interconversion enthalpy and entropy, obtained from a van't Hoff analysis, are -4.52 ± 0.12 kJ/mol and -12.4 ± 0.2 J/(mol · K), respectively. The experimental thermochemistry is compared to high-level electronic structure theory computations. PMID:25244309

  20. 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.

  1. 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 ?-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.

  2. 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

  3. METHODS FOR SIMULATING GAS PHASE SO2 OXIDATION IN ATMOSPHERIC MODELS

    EPA Science Inventory

    Two different approaches are presented for simulating gas phase sulfur dioxide oxidation in atmospheric models. The first approach was to develop an empirical relationship based on rate data collected at four coal-fired power plants during 11 separate studies. Cosine functions we...

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

    SciTech Connect

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

    2010-11-17

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

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

    SciTech Connect

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

    1992-06-01

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

  6. Gas-Phase Reactivity of Peptide Thiyl (RS•), Perthiyl (RSS•), and Sulfinyl (RSO•) Radical Ions Formed from Atmospheric Pressure Ion/Radical Reactions

    NASA Astrophysics Data System (ADS)

    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.

  7. Liquid-gas phase transition in strange hadronic matter with relativistic models

    NASA Astrophysics Data System (ADS)

    Torres, James R.; Gulminelli, F.; Menezes, Débora P.

    2016-02-01

    Background: The advent of new dedicated experimental programs on hyperon physics is rapidly boosting the field, and the possibility of synthesizing multiple strange hypernuclei requires the addition of the strangeness degree of freedom to the models dedicated to nuclear structure and nuclear matter studies at low energy. Purpose: We want to settle the influence of strangeness on the nuclear liquid-gas phase transition. Because of the large uncertainties concerning the hyperon sector, we do not aim at a quantitative estimation of the phase diagram but rather at a qualitative description of the phenomenology, as model independent as possible. Method: We analyze the phase diagram of low-density matter composed of neutrons, protons, and Λ hyperons using a relativistic mean field (RMF) model. We largely explore the parameter space to pin down generic features of the phase transition, and compare the results to ab initio quantum Monte Carlo calculations. Results: We show that the liquid-gas phase transition is only slightly quenched by the addition of hyperons. Strangeness is seen to be an order parameter of the phase transition, meaning that dilute strange matter is expected to be unstable with respect to the formation of hyperclusters. Conclusions: More quantitative results within the RMF model need improved functionals at low density, possibly fitted to ab initio calculations of nuclear and Λ matter.

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

    SciTech Connect

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

    1993-02-01

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

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

    NASA Technical Reports Server (NTRS)

    Kuhn, David K.; Shanabarger, Mickey R.

    1989-01-01

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

  10. 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.

  11. Peptide Bond Formation through Gas-phase Reactions in the Interstellar Medium: Formamide and Acetamide as Prototypes

    NASA Astrophysics Data System (ADS)

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

    2014-09-01

    A theoretical study of the reactions of NH_4+ with formaldehyde and CH_5+ 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. 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.

  13. 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.

  14. A hybrid formalism of aerosol gas phase interaction for 3-D global models

    NASA Astrophysics Data System (ADS)

    Benduhn, F.

    2009-04-01

    Aerosol chemical composition is a relevant factor to the global climate system with respect to both atmospheric chemistry and the aerosol direct and indirect effects. Aerosol chemical composition determines the capacity of aerosol particles to act as cloud condensation nuclei both explicitly via particle size and implicitly via the aerosol hygroscopic property. Due to the primary role of clouds in the climate system and the sensitivity of cloud formation and radiative properties to the cloud droplet number it is necessary to determine with accuracy the chemical composition of the aerosol. Dissolution, although a formally fairly well known process, may be subject to numerically prohibitive properties that result from the chemical interaction of the species engaged. So-far approaches to model the dissolution of inorganics into the aerosol liquid phase in the framework of a 3-D global model were based on an equilibrium, transient or hybrid equilibrium-transient approach. All of these methods present the disadvantage of a priori assumptions with respect to the mechanism and/or are numerically not manageable in the context of a global climate system model. In this paper a new hybrid formalism to aerosol gas phase interaction is presented within the framework of the H2SO4/HNO3/HCl/NH3 system and a modal approach of aerosol size discretisation. The formalism is distinct from prior hybrid approaches in as much as no a priori assumption on the nature of the regime a particular aerosol mode is in is made. Whether a particular mode is set to be in the equilibrium or the transitory regime is continuously determined during each time increment against relevant criteria considering the estimated equilibration time interval and the interdependence of the aerosol modes relative to the partitioning of the dissolving species. Doing this the aerosol composition range of numerical stiffness due to species interaction during transient dissolution is effectively eluded, and the numerical expense of dissolution in the transient regime is reduced through the minimisation of the number of modes in this regime and a larger time step. Containment of the numerical expense of the modes in the equilibrium regime is ensured through the usage of either an analytical equilibrium solver that requires iteration among the equilibrium modes, or a simple numerical solver based on a differential approach that requires iteration among the chemical species. Both equilibrium solvers require iteration over the water content and the activity coefficients. Decision for using either one or the other solver is made upon the consideration of the actual equilibrating mechanism, either chemical interaction or gas phase partial pressure variation, respectively. The formalism should thus ally appropriate process simplification resulting in reasonable computation time to a high degree of real process conformity as it is ensured by a transitory representation of dissolution. The resulting effectiveness and limits of the formalism are illustrated with numerical examples.

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

    EPA Science Inventory

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

  16. 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

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

    PubMed

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

    2015-08-01

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

  18. Enantioselective supramolecular devices in the gas phase. Resorcin[4]arene as a model system

    PubMed Central

    Letzel, Matthias C; Filippi, Antonello; Speranza, Maurizio; Mattay, Jochen

    2012-01-01

    Summary This review describes the state-of-art in the field of the gas-phase reactivity of diastereomeric complexes formed between a chiral artificial receptor and a biologically active molecule. The presented experimental approach is a ligand-displacement reaction carried out in a nano ESI-FT-ICR instrument, supported by a thermodynamic MS-study and molecular-mechanics and molecular-dynamics (MM/MD) computational techniques. The noncovalent ion–molecule complexes are ideal for the study of chiral recognition in the absence of complicating solvent and counterion effects. PMID:22563353

  19. 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.

  20. 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.

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

    SciTech Connect

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

    1993-02-01

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

  2. 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.

  3. Gas-phase study of new organozinc reagents by IRMPD-spectroscopy, computational modelling and tandem-MS.

    PubMed

    Massah, Ahmad R; Dreiocker, Frank; Jackson, Richard F W; Pickup, Barry T; Oomens, Jos; Meijer, Anthony J H M; Schäfer, Mathias

    2011-08-01

    An extensive set of organozinc iodides, useful for Negishi-type cross-coupling reactions, are investigated as respective cations after formal loss of iodide in the gas phase. Firstly, two new alkylzinc compounds derived from Tyrosine (Tyr) and Tryptophan (Trp) are closely examined. Secondly, the influence of specific protecting groups on the subtle balance between intra- and intermolecular coordination of zinc in these reagents is probed through trifluoroacetyl (TFA)-derivatized alkylzinc compounds. Finally, the influence of the strongly coordinating bidentate ligand N,N,N',N'-tetramethylethylenediamine (TMEDA) on the structure of alkylzinc cations is further explored in order to better understand the stability of the respective complexes towards water. A combination of electrospray (ESI)-MS/MS, accurate ion mass measurements, infrared multiple-photon dissociation (IRMPD) spectroscopy and computational modelling allowed the full characterisation of all dimethylformamide (DMF)-solvated and TMEDA-coordinated alkylzinc cations in the gas phase. The calculations indicate that the zinc cation in gas-phase alkylzinc-DMF or TMEDA-complex ions preferentially adopts a tetrahedral coordination sphere with four ligands. Additionally, conformers with only three binding partners bound to zinc but with effectively combined hydrogen-bond interactions are also found. Collision induced dissociation (CID) patterns demonstrate that the zinc-DMF interaction in tetrahedral four-coordinate mono-DMF-zinc complex ions as well as the interaction between TMEDA and zinc in the corresponding complex ions is even stronger than typical covalent bonds. In most cases, all major features of the IRMPD spectra are consistent with only a single major isomer, allowing secured identification and assignment. PMID:21698303

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

    PubMed

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

    1994-06-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  6. 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.

  7. 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.

  8. 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.

  9. Gas phase kinetics during normal combustion

    NASA Technical Reports Server (NTRS)

    Price, C. F.; Boggs, T. L.; Eisel, J. L.; Atwood, A. I.; Zurn, D. E.

    1980-01-01

    The role of gas phase kinetics during combustion was explored in the steady state modeling efforts and in the analysis of ignition phenomena. In both cases it was shown that the combustion characteristics of some high energy ingredients and propellants are strongly affected, if not dictated, by the gas phase reactions which take place.

  10. Effects of inert species in the gas phase in a model for the catalytic oxidation of CO

    NASA Astrophysics Data System (ADS)

    Buendía, G. M.; Rikvold, P. A.

    2012-03-01

    We study by kinetic Monte Carlo simulations the catalytic oxidation of carbon monoxide on a surface in the presence of contaminants in the gas phase. The process is simulated by a Ziff-Gulari-Barshad (ZGB) model that has been modified to include the effect of the contaminants and to eliminate an unphysical oxygen poisoned phase at very low CO partial pressures. The impurities can adsorb and desorb on the surface but otherwise remain inert. We find that if the impurities cannot desorb, no matter how small their proportion in the gas mixture, the reactive window and discontinuous transition to a CO poisoned phase at high CO pressures that characterize the original ZGB model disappear. The coverages become continuous, and once the surface has reached a steady state there is no production of CO2. This is quite different from the behavior of systems in which the surface presents a fixed percentage of impurities. When the contaminants are allowed to desorb, the reactive phase appears again for CO pressures below a value that depends on the proportion of contaminants in the gas and on their desorption rate.

  11. 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).

  12. 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

  13. 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.

  14. Gas-phase heterogeneous photocatalytic oxidation of ethanol: Pathways and kinetic modeling

    SciTech Connect

    Nimlos, M.R.; Wolfrum, E.J.; Brewer, M.L.; Fennell, J.A.; Bintner, G.

    1996-10-01

    The kinetics of photocatalytic oxidation of ethanol has been studied, and the formation and destruction rates of products have been measured. The important intermediates were identified as acetaldehyde, acetic acid, formaldehyde, and formic acid. Minor reaction channels resulted in the formation of methyl formate, ethyl formate, and methyl acetate. Kinetic and `dark` adsorption parameters were measured for ethanol and all of the important intermediates. We have modeled the complete oxidation process using a sequential chemical reaction mechanism. This mechanism is based primarily upon known homogeneous chemistry. However, the formation of acids from aldehydes in photocatalytic oxidation is different from known homogeneous chemistry and demonstrates the ability of the solid surface to stabilize energized transient species. We have measured the adsorption isotherms for ethanol and the oxidized intermediates and have concluded that there are two adsorption sites for some of the chemical species. We think it is possible that the adsorption properties of the compounds will change when the solid is illuminated. 42 refs., 11 figs., 3 tabs.

  15. 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

  16. 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. PMID:22224369

  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. The simulation with updated glyoxal yields gives a factor of 2 higher mixing ratio of glyoxal. The uncertainties in the model treatments as well as future work will also be discussed.

  18. 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

  19. 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.

  20. Di-Tyrosine Cross-Link Decreases the Collisional Cross-Section of Aβ Peptide Dimers and Trimers in the Gas Phase: An Ion Mobility Study

    PubMed Central

    Sitkiewicz, Ewa; Olędzki, Jacek; Poznański, Jarosław; Dadlez, Michał

    2014-01-01

    Oligomeric forms of Aβ peptide are most likely the main synaptotoxic and neurotoxic agent in Alzheimer’s disease. Toxicity of various Aβ oligomeric forms has been confirmed in vivo and also in vitro. However, in vitro preparations were found to be orders of magnitude less toxic than oligomers obtained from in vivo sources. This difference can be explained by the presence of a covalent cross-link, which would stabilize the oligomer. In the present work, we have characterized the structural properties of Aβ dimers and trimers stabilized by di- and tri-tyrosine cross-links. Using ion mobility mass spectrometry we have compared the collisional cross-section of non-cross-linked and cross-linked species. We have found that the presence of cross-links does not generate new unique forms but rather shifts the equilibrium towards more compact oligomer types that can also be detected for non-cross-linked peptide. In consequence, more extended forms, probable precursors of off-pathway oligomeric species, become relatively destabilized in cross-linked oligomers and the pathway of oligomer evolution becomes redirected towards fibrillar structures. PMID:24945725

  1. 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.

  2. 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.

  3. Modeling of the process of formation of the gas-phase component of TiO2 in the working zone of a plasma-chemical reactor

    NASA Astrophysics Data System (ADS)

    Aul'Chenko, S. M.

    2011-05-01

    Based on the quasi-gas-dynamical system of equations, an algorithm for solving the problem of modeling the formation of the gas-phase component of titanium dioxide in the working zone of a plasma-chemical reactor has been developed. Parametric calculations of the process of formation of titanium dioxide depending on the magnitude of the flow rate and on the place of injection of titanium tetrachloride were carried out. The gasdynamical aspects of the process of injection and mixing of the mixture components were investigated. The qualitative and quantitative characteristics of the process have been obtained.

  4. On the crystallographic accuracy of structure prediction by implicit water models: Tests for cyclic peptides

    NASA Astrophysics Data System (ADS)

    Goldtzvik, Yonathan; Goldstein, Moshe; Benny Gerber, R.

    2013-03-01

    Five small cyclic peptides and four implicit water models, were selected for this study. DEEPSAM, a structure prediction algorithm built upon TINKER, was used. Structures predicted using implicit water models were compared with experimental data, and with predictions calculated in the gas phase. The existence of very accurate X-ray crystallographic data allowed firm and conclusive comparisons between predictions and experiment. The introduction of implicit water models into the calculations improved the RMSD from experiment by about 13% compared with computations neglecting the presence of water. GBSA is shown to be consistently the best implicit water model.

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

    PubMed

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

    2007-06-01

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

  6. 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.

  7. Simulation of aromatic SOA formation using the lumping model integrated with explicit gas-phase kinetic mechanisms and aerosol-phase reactions

    NASA Astrophysics Data System (ADS)

    Im, Y.; Jang, M.; Beardsley, R. L.

    2014-04-01

    The Unified Partitioning-Aerosol phase Reaction (UNIPAR) model has been developed to predict the secondary organic aerosol (SOA) formation through multiphase reactions. The model was evaluated with aromatic SOA data produced from the photooxidation of toluene and 1,3,5-trimethylbenzene (135-TMB) under various concentrations of NOx and SO2 using an outdoor reactor (University of Florida Atmospheric PHotochemical Outdoor Reactor (UF-APHOR) chamber). When inorganic species (sulfate, ammonium and water) are present in aerosol, the prediction of both toluene SOA and 135-TMB SOA, in which the oxygen-to-carbon (O : C) ratio is lower than 0.62, are approached under the assumption of a complete organic/electrolyte-phase separation below a certain relative humidity. An explicit gas-kinetic model was employed to express gas-phase oxidation of aromatic hydrocarbons. Gas-phase products are grouped based on their volatility (6 levels) and reactivity (5 levels) and exploited to construct the stoichiometric coefficient (αi,j) matrix, the set of parameters used to describe the concentrations of organic compounds in multiphase. Weighting of the αi,j matrix as a function of NOx improved the evaluation of NOx effects on aromatic SOA. The total amount of organic matter (OMT) is predicted by two modules in the UNIPAR model: OMP by a partitioning process and OMAR by aerosol-phase reactions. The OMAR module predicts multiphase reactions of organic compounds, such as oligomerization, acid-catalyzed reactions, and organosulfate (OS) formation. The model reasonably simulates SOA formation under various aerosol acidities, NOx concentrations, humidities and temperatures. Furthermore, the OS fractions in the SOA predicted by the model were in good agreement with the experimentally measured OS fractions.

  8. Receptors useful for gas phase chemical sensing

    DOEpatents

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

    2015-02-17

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

  9. 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...

  10. 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...

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

  13. Effect of quantum tunneling on single strand breaks in a modeled gas phase cytidine nucleotide induced by low energy electron: A theoretical approach

    NASA Astrophysics Data System (ADS)

    Bhaskaran, Renjith; Sarma, Manabendra

    2013-07-01

    Effect of quantum mechanical tunneling on single strand breaks induced by low energy electron (LEE) has been investigated in a modeled gas phase system, 2'-deoxycytidine-3'-monophosphate (3'-dCMPH). The potential energy curves for the sugar-phosphate C-O (3' C-O) bond cleavage have been generated using second order Møller-Plesset perturbation theory at the 6-31+G(d) accuracy level. Results from the electronic structure theory calculations in conjunction with our time dependent calculations for the 3' C-O bond rupture in 3'-dCMPH using local complex potential based time dependent wave packet approach show significant quantum tunneling of the 3' C-O bond from the bound vibrational states above 1 eV of the anionic potential energy curve. A comparison of the fragmentation profile with that of our earlier gas phase investigations based on Hartree-Fock and density functional theory - Becke, 3-parameter, Lee-Yang-Parr methods with 6-31+G(d) basis set is also provided. Further, inspection of the singly occupied molecular orbitals generated at different 3' C-O bond lengths clearly indicates the electron transfer from the low lying base-π* shape resonance state to the phosphate P = O π* orbital of the DNA backbone during the strand breaks. The decisive step during LEE induced strand breaks follows via "charge induced dissociation" (CID) for the metastable anion formed below 1 eV, whereas quantum mechanical tunnel-ing is out-weighted the CID mechanism for the LEE above 1 eV.

  14. 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.

  15. 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 the fine sediment layer to function as a barrier and the 'leakage' rate required for the gas phase to breach the barrier.

  16. Competing gas-phase substitution and elimination reactions of gemini surfactants with anionic counterions by mass spectrometry. Density functional theory correlations with their bolaform halide salt models.

    PubMed

    Aimé, Carole; Plet, Benoit; Manet, Sabine; Schmitter, Jean-Marie; Huc, Ivan; Oda, Reiko; Sauers, Ronald R; Romsted, Laurence S

    2008-11-20

    Understanding ion specific effects on the solution properties of association colloids is a major unsolved problem, and we are studying the chemistry of gemini surfactants in the gas-phase by mass spectrometry and density functional theory (DFT) to probe ion specific effects in the absence of water. Products from gas-phase fragmentation chemistry of dication-monoanion pairs, M2+X(-), of C16H33(CH3)2N+-(CH2)(n-) +N(CH3)2C16H33.2X(-) gemini surfactants were determined by using sequential collision induced dissociation mass spectrometry. The spacer length "n" was systematically varied (n = 2, 3, 4, and 6) for each counterion investigated (X(-) = F(-), Br(-), Cl(-), I(-), NO3(-), CF3CO2(-), and PF6(-)). The M2+X(-) pairs fragment into monocationic products from competing E2 and S N2 pathways that are readily quantified by tandem MS. The dominant reaction pathway depends on dication and anion structure because it switches from E2 to S N2 with decreasing anion basicity and increasing spacer length. For spacer lengths n = 4 and 6, the major S N2 product shifts from attack at methylene to methyl on the quaternary ammonium group. DFT calculations of gemini headgroup model bolaform salts, CH3(CH3)2N+-(CH2)(n-)+N(CH3)2CH3.2X(-) (X(-) = F(-), Cl(-), Br(-), and I(-), n = 2-4), primarily of activation enthalpies, DeltaH, but also of free energies and entropies for the dication-monoanion pairs, M2+X(-), provide qualitative explanations for the MS structure-reactivity patterns. DeltaH values for S N2 reactions are independent of X(-) type and spacer length, while E2 reactions show a significant increase in DeltaH with decreasing anion basicity and a modest increase with spacer length. Comparisons with the DeltaH values of model CH3CH2(CH3)3N+X(-) halides show that the second charge on the dicationic ion pairs does not significantly affect DeltaH and that the change in distance between the nucleophile and leaving group in the ground and transition states structures in S N2 reactions is approximately constant indicating that DeltaH is governed primarily by electrostatic interactions. PMID:19012368

  17. 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.

  18. 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

  19. Concentrations of a water soluble, gas-phase mercury species in ambient air: Results from measurements and modeling

    SciTech Connect

    Lindberg, S.E.; Stratton, W.J.; Pai, P.; Allan, M.A.

    1997-12-31

    There are few reliable data on the speciation of Hg in ambient air, although this information is critical to understanding the fate of Hg once released from point sources. The water soluble species of Hg that are thought to exist in flue gases would be subject to far greater local removal rates than is elemental Hg vapor, but methods are lacing to quantify this species. The authors developed a method using refluxing mist chambers to measure the airborne concentrations of reactive gaseous mercury (RGM) in short-term samples under ambient conditions. The method exhibits an effective detection limit of 0.02 ng/m{sup 3} and a precision for ambient concentration levels of {+-}20--30%. Using a model that simulates atmospheric transport and fate of anthropogenic mercury emissions over the contiguous United States, the authors generated 24-hr RGM concentrations to compare to the measurement data. The average RGM concentrations measured with their mist chambers at sites in Tennessee (TN) and Indiana (IN) were 0.065 ng/m{sup 3} and 0.100 ng/m{sup 3}, respectively. These averages represent about 3% of total gaseous mercury (TGM), and RGM generally exceeds regional particulate Hg. The 24-hr model-simulated RGM concentration averages in the modeling grid cells representing TN and IN are 0.051 ng/m{sup 3} and 0.098 ng/m{sup 3} respectively, in good agreement with the data. The measured concentrations at the two sites exhibit weak positive correlations with temperature, solar radiation, O{sub 3}, SO{sub 2}, and TGM. These concentrations are high enough to suggest that RGM can play an important role in both wet and dry deposition on a regional scale.

  20. Controlling the Effluent Chemistry of a CAP jet for Biomedical Applications: FTIR Diagnostics and Gas Phase Modeling

    NASA Astrophysics Data System (ADS)

    Schmidt-Bleker, Ansgar; Winter, Joern; Iseni, Sylvain; Duennbier, Mario; Barton, Annemarie; Bundscherer, Lena; Wende, Kristian; Masur, Kai; Weltmann, Klaus-Dieter; Reuter, Stephan

    2013-09-01

    The use of cold atmospheric pressure plasma (CAP) jets with shielding gas devices has proven to be a valuable tool for biomedical applications of plasmas. In order to understand which active components generated by the plasma source trigger desired biological effects, a deeper insight into the species output of CAP jets is necessary. In this work we investigate the effect of different shielding gas compositions using a CAP jet (kinpen) operated with argon. As shielding gas various mixtures of N2 and O2 are used with relative humidity ranging from 0 to 100%. For all conditions the densities of O3, NO2, HNO3, N2O5 and N2O in the far-field of the jet are determined using Fourier-Transformed Infrared Spectroscopy (FTIR). A kinetic model for the neutral species humid air chemistry is fitted to the experimental data. The model yields insight into the processes in the CAP jets effluent. It is used to extrapolate the measured data to 2D density maps for each species depending on the O2/(O2 + N2) ratio and the relative humidity. The 2D maps serve as a basis for the design of further biological and physical experiments. The authors gratefully acknowledge the funding by the German Ministry of Education and Research (BMBF, grant number 03Z2DN11/12).

  1. 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.

  2. 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 performance in terms of controllable and predicable radical chemistry.

  3. 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

  4. 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.

  5. Gas-phase hydrogen/deuterium exchange in a travelling wave ion guide for the examination of protein conformations

    PubMed Central

    Rand, Kasper D.; Pringle, Steven D.; Murphy, James P.; Fadgen, Keith E.; Brown, Jeff; Engen, John R.

    2009-01-01

    Accumulating evidence suggests that solution-phase conformations of small globular proteins and large molecular protein assemblies can be preserved for milliseconds after electrospray ionization. Thus, the study of proteins in the gas-phase on this time-scale is highly desirable. Here we demonstrate that a travelling wave ion guide (TWIG) of a Synapt mass spectrometer offers a highly suitable environment for rapid and efficient gas-phase hydrogen/deuterium exchange (HDX). Gaseous ND3 was introduced into either the source TWIG or the TWIG located just after the ion mobility cell, such that ions underwent HDX as they passed through the ND3 on the way to the time-of-flight analyzer. The extent of deuterium labeling could be controlled by varying the quantity of ND3 or the speed of the travelling wave. The gas-phase HDX of model peptides corresponded to labeling of primarily fast exchanging sites due to the short labeling times (ranging from 0.1 to 10 ms). In addition to peptides, gas-phase HDX of ubiquitin, cytochrome c, lysozyme and apomyoglobin were examined. We conclude that HDX of protein ions in a TWIG is highly sensitive to protein conformation, enables the detection of conformers present on sub-milliseconds timescales and can readily be combined with ion mobility spectrometry. PMID:19921790

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

    EPA Science Inventory

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

  7. In Silico Models for Designing and Discovering Novel Anticancer Peptides

    NASA Astrophysics Data System (ADS)

    Tyagi, Atul; Kapoor, Pallavi; Kumar, Rahul; Chaudhary, Kumardeep; Gautam, Ankur; Raghava, G. P. S.

    2013-10-01

    Use of therapeutic peptides in cancer therapy has been receiving considerable attention in the recent years. Present study describes the development of computational models for predicting and discovering novel anticancer peptides. Preliminary analysis revealed that Cys, Gly, Ile, Lys, and Trp are dominated at various positions in anticancer peptides. Support vector machine models were developed using amino acid composition and binary profiles as input features on main dataset that contains experimentally validated anticancer peptides and random peptides derived from SwissProt database. In addition, models were developed on alternate dataset that contains antimicrobial peptides instead of random peptides. Binary profiles-based model achieved maximum accuracy 91.44% with MCC 0.83. We have developed a webserver, which would be helpful in: (i) predicting minimum mutations required for improving anticancer potency; (ii) virtual screening of peptides for discovering novel anticancer peptides, and (iii) scanning natural proteins for identification of anticancer peptides (http://crdd.osdd.net/raghava/anticp/).

  8. 3-D agricultural air quality modeling: Impacts of NH3/H2S gas-phase reactions and bi-directional exchange of NH3

    NASA Astrophysics Data System (ADS)

    Wang, Kai; Zhang, Yang

    2014-12-01

    Accurately simulating the transport and fate of reduced nitrogen (NHx = ammonia (NH3) + ammonium (NH4+))- and sulfur-containing compounds emitted from agricultural activities represents a major challenge in agricultural air quality modeling. In this study, the Community Multiscale Air Quality (CMAQ) modeling system is further developed and improved by implementing 22 ammonia (NH3)/hydrogen sulfide (H2S) related gas-phase reactions and adjusting a few key parameters (e.g., emission potential) for bi-directional exchange of NH3 fluxes. Several simulations are conducted over the eastern U.S. domain at a 12-km horizontal resolution for January and July 2002 to examine the impacts of those improved treatments on air quality. The 5th generation mesoscale model (MM5) and CMAQ predict an overall satisfactory and consistent performance with previous modeling studies, especially for 2-m temperature, 2-m relative humidity, ozone (O3), and fine particulate matter (PM2.5). High model biases exist for precipitation in July and also dry/wet depositions. The updated model treatments contribute to O3, NHx, and PM2.5 by up to 0.4 ppb, 1.0 μg m-3, and 1.0 μg m-3 in January, respectively, and reduce O3 by up to 0.8 ppb and contribute to NHx and PM2.5 by up to 1.2 and 1.1 μg m-3 in July, respectively. The spatial distributions of O3 in both months and sulfur dioxide (SO2) in January are mainly affected by inline dry deposition velocity calculation. The spatial distributions of SO2 and sulfate (SO42-) in July are affected by both inline dry deposition velocity and NH3/H2S reactions. The variation trends of NH3, NHx, ammonium nitrate (NH4NO3), PM2.5 and total nitrogen (TN) are predominated by bi-directional exchange of NH3 fluxes. Uncertainties of NH3 emission potentials and empirical constants used in the bi-directional exchange scheme may significantly affect the concentrations of NHx and PM2.5, indicating that a more accurate and explicit treatment for those parameters should be considered in the future work.

  9. 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.

  10. 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.

  11. Infrared and electronic spectroscopy of a model system for the nucleophilic substitution intermediate in the gas phase: the C-N valence bond formation in the benzene-ammonia cluster cation.

    PubMed

    Mizuse, Kenta; Fujii, Asuka; Mikami, Naohiko

    2006-05-25

    Infrared and electronic spectroscopy was applied to the benzene-ammonia cluster cation in the gas phase, and the observed spectra revealed the formation of a new C-N valence bond between the benzene and ammonia moieties, which has been predicted by the quantum chemical calculations (Tachikawa, H. Phys. Chem. Chem.Phys. 2002, 4, 6018). This cluster cation is regarded as a model for the cyclohexadienyl type intermediate in nucleophilic substitution reactions. PMID:16706391

  12. 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 .

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

    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.

  14. Gas-phase reactivity of carboxylic acid functional groups with carbodiimides.

    PubMed

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

    2013-01-01

    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

  15. 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.

  16. An adaptive classification model for peptide identification

    PubMed Central

    2015-01-01

    Background Peptide sequence assignment is the central task in protein identification with MS/MS-based strategies. Although a number of post-database search algorithms for filtering target peptide spectrum matches (PSMs) have been developed, the discrepancy among the output PSMs is usually significant, remaining a few disputable PSMs. Current studies show that a number of target PSMs which are close to decoy PSMs can hardly be separated from those decoys by only using the discrimination function. Results In this paper, we assign each target PSM a weight showing its possibility of being correct. We employ a SVM-based learning model to search the optimal weight for each target PSM and develop a new score system, CRanker, to rank all target PSMs. Due to the large PSM datasets generated in routine database searches, we use the Cholesky factorization technique for storing a kernel matrix to reduce the memory requirement. Conclusions Compared with PeptideProphet and Percolator, CRanker has identified more PSMs under similar false discover rates over different datasets. CRanker has shown consistent performance on different test sets, validated the reasonability the proposed model. PMID:26578406

  17. Peptide folding and aggregation studied using a simplified atomic model

    NASA Astrophysics Data System (ADS)

    Irbäck, Anders

    2005-05-01

    Using an atomic model with a simplified sequence-based potential, the folding properties of several different peptides are studied. Both α-helical (Trp cage, Fs) and β-sheet (GB1p, GB1m2, GB1m3, Betanova, LLM) peptides are considered. The model is able to fold these different peptides for one and the same choice of parameters, and the melting behaviour of the peptides (folded population against temperature) is in very good agreement with experimental data. Furthermore, using the same model with unchanged parameters, the aggregation behaviour of a fibril-forming fragment of the Alzheimer's A β peptide is studied, with very promising results.

  18. Establishing Effective Simulation Protocols for β- and α/β-Mixed Peptides. I. QM and QM/MM Models.

    PubMed

    Zhu, Xiao; Yethiraj, Arun; Cui, Qiang

    2007-07-01

    A quantum mechanical (QM) model for non-natural β- and α/β-mixed peptides is investigated using an approximate density functional method (called SCC-DFTB). In the gas phase the predictions of the model for cyclic and acyclic dipeptides and several acyclic heptapeptides are compared to ab initio B3LYP and LMP2 calculations. The SCC-DFTB reproduces the global minimum of the configurations with the root-mean-square (rms) error in the key dihedral angles of less than 14 degrees. The relative energies of different conformers are also well described in general, with the typical rms error of 2-3 kcal/mol relative to LMP2 energies at either B3LYP or LMP2 optimized structures. The dipole moments are reproduced with a systematic underestimate of less than 15%. The QM model is also used with a molecular mechanical (MM) model of the solvent. For a tetrameric α/β-peptide in water, the SCC-DFTB/MM energies are well correlated with B3LYP/6-31+G**/MM single point energies for a wide range of structures sampled in 2 ns of SCC-DFTB/MM molecular dynamics. For an octameric α/β-peptide in methanol the predicted structures are in qualitative agreement with experimental NOE data. These results suggest that the SCC-DFTB model provides a fairly accurate representation of the structure and thermodynamics of these peptides. PMID:26633224

  19. 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.

  20. Transport of model peptides across Ascaris suum cuticle.

    PubMed

    Sheehy, B A; Ho, N F; Burton, P S; Day, J S; Geary, T G; Thompson, D P

    2000-01-01

    Several FMRFamide-related peptides (FaRPs) found in nematodes exert potent excitatory or inhibitory effects on the somatic musculature of Ascaris suum and other nematode species when injected into the pseudocoelom or applied directly to isolated neuromuscular preparations. These peptides, however, generally fail to induce detectable effects on the neuromusculature when applied externally to intact nematodes. The apparent lack of activity for these peptides when administered externally in whole-organism assays is likely a function of both absorption and metabolism. To delineate the factors that govern transport of peptides across the cuticle/hypodermis complex of nematodes, we measured the rates of absorption of a series of structurally related model peptides using isolated cuticle/hypodermis segments from A. suum and two-chamber diffusion cells. [14C]-Labeled peptides were prepared from D-phenylalanine, with the amide nitrogens sequentially methylated to give AcfNH2, Acf3NH2, Acf(NMef)2NH2, and Ac(NMef)3NHMe. These model peptides were designed to allow systematic analysis of the influence of peptide size, hydrogen bonding and lipophilicity on transport. Results of these studies show that, within this series, permeability across the cuticle increases with addition of each methyl group. The permeability coefficient of Ac(NMef)3NHMe, with four methyl groups, was 10-fold greater than that of the smaller peptide, AcfNH2, even though both peptides contain five hydrogen bonds. When compared with vertebrate membranes, transport of the model peptides across A. suum cuticle was about 10-fold slower. A biophysical model for transcuticular transport of peptides predicted that nematode FaRPs, which are larger, less methylated and less lipophilic than the model peptides tested, would not be absorbed across the cuticle of nematodes. This prediction was confirmed for the excitatory FaRP, AF2 (KHEYLRFamide), which did not diffuse across the cuticle/hypodermis complex, but diffused rapidly across lipid-extracted cuticle preparations. PMID:10613697

  1. Analysis of the gas phase reactivity of chlorosilanes.

    PubMed

    Ravasio, Stefano; Masi, Maurizio; Cavallotti, Carlo

    2013-06-27

    Trichlorosilane is the most used precursor to deposit silicon for photovoltaic applications. Despite of this, its gas phase and surface kinetics have not yet been completely understood. In the present work, it is reported a systematic investigation aimed at determining what is the dominant gas phase chemistry active during the chemical vapor deposition of Si from trichlorosilane. The gas phase mechanism was developed calculating the rate constant of each reaction using conventional transition state theory in the rigid rotor-harmonic oscillator approximation. Torsional vibrations were described using a hindered rotor model. Structures and vibrational frequencies of reactants and transition states were determined at the B3LYP/6-31+G(d,p) level, while potential energy surfaces and activation energies were computed at the CCSD(T) level using aug-cc-pVDZ and aug-cc-pVTZ basis sets extrapolating to the complete basis set limit. As gas phase and surface reactivities are mutually interlinked, simulations were performed using a microkinetic surface mechanism. It was found that the gas phase reactivity follows two different routes. The disilane mechanism, in which the formation of disilanes as reaction intermediates favors the conversion between the most stable monosilane species, and the radical pathway, initiated by the decomposition of Si2HCl5 and followed by a series of fast propagation reactions. Though both mechanisms are active during deposition, the simulations revealed that above a certain temperature and conversion threshold the radical mechanism provides a faster route for the conversion of SiHCl3 into SiCl4, a reaction that favors the overall Si deposition process as it is associated with the consumption of HCl, a fast etchant of Si. Also, this study shows that the formation of disilanes as reactant intermediates promotes significantly the gas phase reactivity, as they contribute both to the initiation of radical chain mechanisms and provide a catalytic route for the conversion between the most stable monosilanes. PMID:23731215

  2. Peptides

    SciTech Connect

    Blackburn, S.

    1986-01-01

    This text includes tables on the following topics: gas chromatography; liquid chromatography; paper chromatography; thin layer chromatography. The techniques of high performance liquid chromatography; gel permeation chromatography; peptide mapping; prediction of peptide retention times in HPLC; fluorescence techniques for the detection of peptides; electrochemical detection. Also included are techniques for the detection of peptides; electrochemical detection and detection reagents, method of sample preparation, products and sources of chromatographic materials, chromatography book directory reviews of chromatographic methods and equipment.

  3. Effect of structural parameters on the electron capture dissociation and collision-induced dissociation pathways of copper(II)-peptide complexes.

    PubMed

    Chen, Xiangfeng; Wang, Ze; Li, Wan; Wong, Y L Elaine; Chan, T-W Dominic

    2015-01-01

    The gas-phase dissociation pathways of proteins/peptides are usually affected by the nature of the charge carrier and the sequence of amino acid residues. The effects of peptide structural parameters, including peptide composition, chain length and amide hydrogen, on the gas-phase dissociation of Cu(II)-model peptide complexes were explored in this study. Polyglycine peptides with flexible frames were used as probes to reduce the complexity of the system and illustrate the mechanism. Results revealed that the types of fragment ions generated in the electron capture dissociation (ECD) of Cu(II)-adducted peptides changed according to the basic amino acid residue composition. Charged or neutral tryptophan side-chain losses were observed in the collision-induced dissociation (CID) of Cu(II)-peptide complexes. Internal electron transfer between tryptophan and metal ion within the complex occurred during the CID reaction, leaving the charge-reduced Cu(+) as a closed d-shell stable electron configuration. The choice of the reaction channel was then determined by the gas-phase basicity of the peptide. Amide hydrogen was critical in the formation of metalated b-/y-ions in the ECD process as determined through mutation of the backbone amide group. Increasing the chain length suppressed the ECD of Cu-metalated peptide species. Our results indicate that the structural parameters of peptides play important roles in the gas-phase dissociation processes of Cu-peptide complexes. PMID:26353987

  4. Modelling water molecules inside cyclic peptide nanotubes

    NASA Astrophysics Data System (ADS)

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2016-03-01

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

  5. Novel kinetic scheme for the ammonium perchlorate gas phase

    SciTech Connect

    Sahu, H.; Sheshadri, T.S.; Jain, V.K. )

    1990-01-11

    A novel gas-phase kinetic scheme for ammonium perchlorate (AP) deflagration involving 22 reactions among 18 species is developed. The kinetic scheme is based on a study of the effect of initial conditions on the solution of the differential equations of adiabatic constant-pressure combustion kinetics. The existence of condensed-phase reaction products provides alternate pathways for the consumption of NH{sub 3} and HClO{sub 4} produced by gas-phase dissociation of AP. Theoretically obtained temperature-time profiles of the novel scheme do not change when the conventional reaction pathways are included, indicating that the novel scheme is a substantially faster rate process. The new scheme does not involve the species ClO, which has long been considered a critical component of the AP gas phase and which is included in the conventional reaction pathways. The new scheme develops faster overall reaction rates, steeper temperature-time profiles, and in a deflagration model will result in higher heat-transfer rates from gas phase to the condensed phase.

  6. Defying entropy: forming large head-to-tail macrocycles in the gas phase.

    PubMed

    Tirado, Marcus; Polfer, Nicolas C

    2012-06-25

    Spectral fingerprints: Collision-induced dissociation (CID) of protonated peptides in the gas phase results in linear fragment ions with a five-membered oxazolone ring on their C-terminal side. Infrared spectroscopy confirms that smaller fragments adopt oxazolone structures. Conversely, in mid-sized and larger fragments an isomerization to "head-to-tail" macrocycles is observed (see picture). PMID:22615257

  7. 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. PMID:20421139

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

    SciTech Connect

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

    2004-11-01

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

  9. Liquid-gas phase transition of strange hadronic matter

    SciTech Connect

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

    2004-11-01

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

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

    PubMed

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

    2015-10-21

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

  11. 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 radical species derived from amino acids, peptides and proteins described in the literature are made.

  12. 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.

  13. 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.

  14. Gas phase dynamics of triplet formation in benzophenone.

    PubMed

    Spighi, Gloria; Gaveau, Marc-André; Mestdagh, Jean-Michel; Poisson, Lionel; Soep, Benoît

    2014-05-28

    Benzophenone is a prototype molecule for photochemistry in the triplet state through its high triplet yield and reactivity. We have investigated its dynamics of triplet formation under the isolated gas phase conditions via femtosecond and nanosecond time resolved photoelectron spectroscopy. This represents the complete evolution from the excitation in S2 to the final decay of T1 to the ground state S0. We have found that the triplet formation can be described almost as a direct process in preparing T1, the lowest reacting triplet state, from the S1 state after S2 → S1 internal conversion. The molecule was also deposited by a pick-up technique on cold argon clusters providing a soft relaxation medium without evaporation of the molecule and the mechanism was identical. This cluster technique is a model for medium influenced electronic relaxation and provides a continuous transition from the isolated gas phase to the relaxation dynamics in solution. PMID:24728443

  15. Peptide fragmentation as an approach in modeling of an active peptide and designing a competitive inhibitory peptide for HMG-CoA reductase.

    PubMed

    Pak, Valeriy V; Koo, Minseon; Kwon, Dae Young; Shakhidoyatov, Khusnutdin M; Yun, Lyubov

    2010-06-15

    This study presents a simple method to design an active peptide based on a description of the structural preferences of peptide via its peptide fragments. In a previous design, while searching for lead peptide candidates, the efficacy of a design approach that was based on the use of a cyclic peptide as a model of linear analog was demonstrated. Analysis of the conformational behavior of the peptide models showed that an analogical approach could be applied in order to assess the conformational space that was occupied by a peptide by using peptide fragments. In order to assess the proposed method, a design of a competitive inhibitor for HMG-CoA reductase (HMGR) was performed. Two starting points were used in the design: (1) determined recognized residues and (2) the structural preference of a peptide, such as a beta-turn conformation in the present design. Two sets of peptides were developed based on the different location of a beta-turn structure relative to a recognized residue. Set 1 contains peptides in which a recognized residue is included in turn conformation. In Set 2, the turn structure is located distantly from the recognized residues. The design parameter 'V' that was applied in previous studies was slightly modified for the purpose of the current research. The 17 previously and 8 newly designed peptides were estimated by this parameter. In each set, one sequence was selected as a lead peptide candidate for each set: GF(4-fluoro)PEGG for Set 1 and DFGYVAE for Set 2. The inhibitory activities improved in each set. The IC(50) for the GF(4-fluoro)PEGG peptide was found to be 0.75 microM, while the linear DFGYVAE peptide (IC(50)=0.16 microM) showed a 3000-fold increase in inhibitory activity compared to the first isolated LPYP peptide (IC(50)=484 microM) from soybeans. The comparison of the structure-activity relationship (SAR) data between Set 1 and 2 provided an opportunity to design the peptides in terms of peptide selectivity. A structural analysis of the modeled peptides confirmed the appropriateness of the proposed method for the design of active peptides. PMID:20494585

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

    PubMed

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

    2013-09-21

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  19. Gas-Phase Photoionization Of A Protein

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  1. PeptideBuilder: A simple Python library to generate model peptides

    PubMed Central

    Tien, Matthew Z.; Sydykova, Dariya K.; Meyer, Austin G.

    2013-01-01

    We present a simple Python library to construct models of polypeptides from scratch. The intended use case is the generation of peptide models with pre-specified backbone angles. For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code. We do not provide any tools for energy minimization or rotamer packing, since powerful tools are available for these purposes. Instead, we provide a simple Python interface that enables one to add residues to a peptide chain in any desired conformation. Bond angles and bond lengths can be manipulated if so desired, and reasonable values are used by default. PMID:23717802

  2. 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.

  3. 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.

  4. Combining Laser Spectroscopy and Mass Spectrometry for Conformation-Specific Studies of Gas-Phase Biomolecules

    NASA Astrophysics Data System (ADS)

    Rizzo, Thomas R.; Boyarkin, Oleg V.; Stearns, Jaime A.; Guidi, Monia; Seaiby, Caroline; Nagornova, Natalia; Svendsen, Annette

    2010-06-01

    Developments over the last few years at the interface between laser spectroscopy and mass spectrometry have opened up new horizons for the spectroscopic study of biological molecules. The combination of electrospray ionization for producing large biological molecules in the gas phase with cooled ion traps and multiple-resonance laser schemes are allowing spectroscopic investigation of individual conformers of peptides of increasing size. Highly resolved infrared spectra of single conformations of such species provide important benchmarks for testing the accuracy of theoretical calculations. This talk will give an overview of techniques employed in our laboratory for measuring conformer-selected vibrational spectroscopy of cold, gas-phase peptides of increasing size and complexity. I will show examples that demonstrate the power of these techniques and evaluate the challenges to extending them to still larger biological molecules.

  5. 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.

  6. Ion gradient-induced membrane translocation of model peptides.

    PubMed Central

    de Kroon, A I; Vogt, B; van't Hof, R; de Kruijff, B; de Gier, J

    1991-01-01

    The K+ diffusion potential-induced association of synthetic model peptides carrying a single positive charge originating from the NH2-terminal amino function with large unilamellar vesicles (LUV) consisting of phosphatidylcholine (PC) has been reported previously (de Kroon, A. I. P. M., J. de Gier, and B. de Kruijff. 1989. Biochim. Biophys. Acta. 981:371-373). To determine the vesicle localization of the associated peptides, fluorescence measurements utilizing the peptides' tryptophan residue as intrinsic fluorescent probe were performed. The application in these measurements, of vesicles that exhibit an asymmetric transbilayer distribution of brominated PC which is a quencher of tryptophan fluorescence, unequivocally demonstrated that the peptide H3N(+)-AIMLWA-Ome (AIXme+) is accumulated in the interface of the inner leaflet of the vesicle membrane in response to the valinomycin-induced K+ diffusion potential (negative inside). The relative contributions of the membrane potential (delta psi) and the pH gradient (delta pH, acidic inside) induced by the K+ diffusion potential, to the process have been assessed. An analysis of the pH and delta pH dependencies of the process demonstrated that the K+ diffusion potential-induced peptide accumulation is largely determined by a redistribution of peptide according to the transbilayer pH gradient, in agreement with a translocation across the vesicle membrane of the neutral, deprotonated form of the peptide. The general validity of the mechanism proposed for the vesicle-uptake of AIXme+ has been examined by extending the experiments to peptide analogues with a single negative charge and to peptides with two positive charges, and by investigating the effect of incorporating the acidic phospholipid cardiolipin (CL) into the LUV. The incorporation of CL appeared not to affect the K+ diffusion, potential-induced vesicle uptake of AIXme+. The peptide H3N(+)-RMLWA-Ome (RXme2+) showed a small delta pH independent fluorescence response to the delta psi upon raising the CL content of the vesicles to 25%. PMID:1932545

  7. 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.

  8. Evolutionary sequence modeling for discovery of peptide hormones.

    PubMed

    Sonmez, Kemal; Zaveri, Naunihal T; Kerman, Ilan A; Burke, Sharon; Neal, Charles R; Xie, Xinmin; Watson, Stanley J; Toll, Lawrence

    2009-01-01

    There are currently a large number of "orphan" G-protein-coupled receptors (GPCRs) whose endogenous ligands (peptide hormones) are unknown. Identification of these peptide hormones is a difficult and important problem. We describe a computational framework that models spatial structure along the genomic sequence simultaneously with the temporal evolutionary path structure across species and show how such models can be used to discover new functional molecules, in particular peptide hormones, via cross-genomic sequence comparisons. The computational framework incorporates a priori high-level knowledge of structural and evolutionary constraints into a hierarchical grammar of evolutionary probabilistic models. This computational method was used for identifying novel prohormones and the processed peptide sites by producing sequence alignments across many species at the functional-element level. Experimental results with an initial implementation of the algorithm were used to identify potential prohormones by comparing the human and non-human proteins in the Swiss-Prot database of known annotated proteins. In this proof of concept, we identified 45 out of 54 prohormones with only 44 false positives. The comparison of known and hypothetical human and mouse proteins resulted in the identification of a novel putative prohormone with at least four potential neuropeptides. Finally, in order to validate the computational methodology, we present the basic molecular biological characterization of the novel putative peptide hormone, including its identification and regional localization in the brain. This species comparison, HMM-based computational approach succeeded in identifying a previously undiscovered neuropeptide from whole genome protein sequences. This novel putative peptide hormone is found in discreet brain regions as well as other organs. The success of this approach will have a great impact on our understanding of GPCRs and associated pathways and help to identify new targets for drug development. PMID:19132080

  9. Multinuclear NMR spectroscopy in the gas phase

    NASA Astrophysics Data System (ADS)

    Jackowski, K.

    2006-04-01

    Nuclear magnetic resonance (NMR) of some nuclei (e.g. 1H, 13C, 19F, 29Si or 31P, I=1/2) gives strong signals which allow analytical studies of gaseous compounds. The other magnetic nuclei have low natural abundance or/and contain an electric quadrupole moment and their NMR signals are rather weak. In our laboratory we have developed new experimental techniques, which permit us to monitor several micrograms of chemical compounds in gaseous matrices. Applying this approach we have observed magnetic shielding of various nuclei, including 17O and 33S at the natural abundance, in the gas phase as a function of density. Density-dependent spin-spin couplings were also found for many chemical compounds. It has been shown that NMR gas-phase studies can easily be extended on molecules, which exhibit strong intermolecular interactions and are liquids at room temperature. All the latter NMR experimental results obtained for gaseous matrices are reviewed in this paper.

  10. 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.

  11. Improved short peptide identification using HILIC-MS/MS: retention time prediction model based on the impact of amino acid position in the peptide sequence.

    PubMed

    Le Maux, Solène; Nongonierma, Alice B; FitzGerald, Richard J

    2015-04-15

    Short peptides can have interesting beneficial effects but they are difficult to identify in complex mixtures. We developed a method to improve short peptide identification based on HILIC-MS/MS. The apparent hydrophilicity of peptides was determined as a function of amino acid position in the sequence. This allowed the differentiation of peptides with the same amino acid composition but with a different sequence (homologous peptides). A retention time prediction model was established using the hydrophilicity and peptide length of 153 di- to tetrapeptides. This model was proven to be reliable (R(2)=0.992), it was validated using statistical methods and a mixture of 14 synthetic peptides. A whey protein hydrolysate was analysed to assess the ability of the model to identify unknown peptides. In parallel to milk protein database and de novo searches, the retention time prediction model permitted reduction and ranking of potential short peptides, including homologous peptides, present in the hydrolysate. PMID:25466098

  12. Peptide immunotherapies in Type 1 diabetes: lessons from animal models.

    PubMed

    Fierabracci, A

    2011-01-01

    Insulin dependent diabetes mellitus (Type 1 diabetes, T1D) is a chronic autoimmune disorder characterized by the destruction of insulin-producing pancreatic beta cells by proinflammatory autoreactive T cells. In the past, several therapeutic approaches have been exploited by immunologists aiming to regulate the autoimmune response; this can occur by deleting lymphocyte subsets and/or re-establishing immune tolerance via activation of regulatory T cells. The use of broad immunosuppressive drugs was the first approach to be explored. Subsequently, antibody-based immunotherapies failed to discriminate between autoreactive versus non-autoimmune effectors. Antigen-based immunotherapy is a third approach developed to manipulate beta cell autoimmunity. This approach allows the selective targeting of disease-relevant T cells, while leaving the remainder of the immune system intact. Animal models have been successfully employed to prevent or treat T1D by injection of either the self proteins or peptides derived from them. Peptide immunotherapies have been mainly experimented in the NOD mouse spontaneous model of disease. In this review we therefore report the main approaches that rely on the use of peptides obtained from relevant autoantigens such as glutamic acid decarboxylase, isoform 65 (GAD65), insulin, proinsulin and islet-specific glucose 6 phosphatase catalytic subunit-related protein (IGRP). Protective peptides have proven to be effective in treating or delaying the diabetic process. We also highlight the main difficulties encountered in extrapolating data to guide clinical translational investigations in humans. PMID:21143110

  13. Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry

    PubMed Central

    Halloran, John T.; Bilmes, Jeff A.; Noble, William S.

    2014-01-01

    We present a peptide-spectrum alignment strategy that employs a dynamic Bayesian network (DBN) for the identification of spectra produced by tandem mass spectrometry (MS/MS). Our method is fundamentally generative in that it models peptide fragmentation in MS/MS as a physical process. The model traverses an observed MS/MS spectrum and a peptide-based theoretical spectrum to calculate the best alignment between the two spectra. Unlike all existing state-of-the-art methods for spectrum identification that we are aware of, our method can learn alignment probabilities given a dataset of high-quality peptide-spectrum pairs. The method, moreover, accounts for noise peaks and absent theoretical peaks in the observed spectrum. We demonstrate that our method outperforms, on a majority of datasets, several widely used, state-of-the-art database search tools for spectrum identification. Furthermore, the proposed approach provides an extensible framework for MS/MS analysis and provides useful information that is not produced by other methods, thanks to its generative structure. PMID:25298752

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

    NASA Astrophysics Data System (ADS)

    Balucani, Nadia; Ceccarelli, Cecilia; Taquet, Vianney

    2015-04-01

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

  15. 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.

  16. Gas phase equilibrium structure of histamine.

    PubMed

    Tikhonov, Denis S; Rykov, Anatolii N; Grikina, Olga E; Khaikin, Leonid S

    2016-02-17

    The first gas electron diffraction (GED) experiment for histamine was carried out. The equilibrium structure of histamine in the gas phase was determined on the basis of the data obtained. The refinement was also supported by the rotational constants obtained in previous studies [B. Vogelsanger, et al., J. Am. Chem. Soc., 1991, 113, 7864-7869; P. Godfrey, et al., J. Am. Chem. Soc., 1998, 120, 10724-10732] and quantum chemical calculations. The proposed mechanism of tautomerization by simultaneous intermolecular transfer of hydrogens in a histamine dimer helps to explain the distribution of tautomers in different experiments. The estimations of the conformational interconversion times provided the explanation for the absence of some conformers in the rotational spectroscopy experiments. PMID:26845147

  17. Gas-phase protonation thermochemistry of adenosine.

    PubMed

    Touboul, David; Bouchoux, Guy; Zenobi, Renato

    2008-09-18

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

  18. Theoretical and experimental investigation of the energetics of cis-trans proline isomerization in peptide models.

    PubMed

    Schroeder, Olivia E; Carper, Emily; Wind, Joshua J; Poutsma, Jennifer L; Etzkorn, Felicia A; Poutsma, John C

    2006-05-25

    The energetics of cis-trans proline isomerization in small peptide models have been investigated using the hybrid density functional theory method B3LYP with a 6-31+G* basis set. The molecules studied are models for the phospho-Ser/Thr-Pro substrate for Pin-1, a peptidyl-prolyl isomerase (PPIase) involved in cell division. Pin-1 requires phosphorylation of a Ser or Thr residue adjacent to a Pro residue in the substrate and catalyzes cis-trans isomerization about the proline amide bond. The dihedral angle that would correspond to the reaction coordinate for isomerization of the omega peptide bond was investigated for several small models. Relaxed potential energy scans for this dihedral angle in N-methylacetamide, 1, N,N-dimethylacetamide, 2, acetylpyrrolidine, 3 and acetylproline, 4, were carried out in 20 degrees steps using the B3LYP/6-31+G* level of theory. In addition, similar scans were carried out for 1-4 protonated on the acetylamide carbonyl oxygen. Optimized structures for 1-4 protonated on the amide nitrogen were also obtained at B3LYP/6-31+G*. Relative proton affinities were determined for each site at various angles along the reaction coordinate for isomerization. The relative proton affinities were anchored to experimental gas phase proton affinities, which were taken from the literature for 1 and 2, or determined in an electrospray ionization-quadrupole ion trap instrument using the extended kinetic method for 3 and 4. Proton affinities of 925 +/- 10 and 911 +/- 12 kJ/mol were determined for 3 and 4, respectively. These studies suggest that the nitrogen atom in these amides becomes the most basic site in the molecule at a dihedral angle of ca. 130 degrees . In addition, the nitrogen atoms in 2-4 are predicted to attain basicities in the range 920-950 kJ/mol, making them basic enough to be the preferred site for hydrogen bonding in the Pin-1 active site, in support of the proposed mechanism for PPIases. PMID:16706410

  19. CHAOS II. Gas-phase Abundances in NGC 5194

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    We have observed NGC 5194 (M51a) as part of the CHemical Abundances of Spirals project. Using the Multi Object Double Spectrographs on the Large Binocular Telescope we are able to measure one or more of the temperature-sensitive auroral lines ([O iii] ?4363, [N ii] ?5755, [S iii] ?6312) and thus measure direct gas-phase abundances in 29 individual H ii regions. [O iii] ?4363 is only detected in two H ii regions, both of which show indications of excitation by shocks. We compare our data to previous direct abundances measured in NGC 5194 and find excellent agreement ({{? }}[{log}({{O}}/{{H}})]? 0.05) for all but one region. We find no evidence of trends in Ar/O, Ne/O, or S/O within NGC 5194 or compared to other galaxies. We find modest negative gradients in both O/H and N/O with very little scatter (? ? 0.08 dex), most of which can be attributed to random error and not to intrinsic dispersion. The gas-phase abundance gradient is consistent with the gradients observed in other interacting galaxies, which tend to be shallower than gradients measured in isolated galaxies. The N/O ratio (< {log}({{N}}/{{O}})> =-0.62) suggests secondary nitrogen production is responsible for a significantly larger fraction of nitrogen (e.g., factor of 8-10), relative to primary production mechanisms than predicted by theoretical models.

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Dennis, Jacob Daniel

    Traditional hypergolic propellant combinations, such as those used on the space shuttle orbital maneuvering system first flown in 1981, feature hydrazine based fuels and nitrogen tetroxide (NTO) based oxidizers. Despite the long history of hypergolic propellant implementation, the processes that govern hypergolic ignition are not well understood. In order to achieve ignition, condensed phase fuel and oxidizer must undergo simultaneous physical mixing and chemical reaction. This process generates heat, intermediate condensed phase species, and gas phase species, which then may continue to react and generate more heat until ignition is achieved. The process is not well understood because condensed and gas phase reactions occur rapidly, typically in less than 200 μs, on much faster timescales than traditional diagnostic methods can observe. A detailed understanding of even the gas phase chemistry is lacking, but is critical for model development. Initial research has provided confidence that a study of condensed phase hypergolic reactions is useful and possible. Results obtained using an impinging jet apparatus have shown a critical residence time of 0.3 ms is required for the reaction between monomethylhydrazine (MMH) and red fuming nitric acid (RFNA, ~85% HNO3 + 15% N2O4) to achieve conditions favorable for ignition. This critical residence time spans the time required for liquid phase reactions to occur at the fuel/oxidizer interface and can give some insight into the reaction rates for this propellant combination. Experiments performed in a forced mixing constant volume reactor have demonstrated that the chamber pressurization rate for MMH/RFNA can be significantly reduced by diluting the MMH with deionized water. This result indicates that propellant dilution can slow the chemical reaction rates to occur over observable time scales. The research described in this document consists of two efforts that contribute knowledge to the propulsion community regarding the hypergolic liquid propellant combination of MMH and RFNA or pure nitric acid. The first and most important effort focuses on furthering the understanding of condensed phase reactions between MMH and nitric acid. To accomplish this goal diluted MMH and nitric acid were studied in a Fourier transform infrared spectrometer. By tracking the generation or destruction of specific chemical species in the reacting fluid we can measure the reaction progress as a function of reactant concentration and temperature. This work provides the propulsion community with a quantitative global condensed phase reaction rate equation for MMH/nitric acid. The second effort focuses on improving understanding the recently proposed gas phase hypergolic reaction mechanisms using a streak camera based ultraviolet and visible spectrometer. The time resolution on the streak camera system allows for detailed investigation of the pre-ignition and early stage gas phase species present during the reaction between MMH and RFNA.

  3. Instabilities in Lean Gas-Phase Combustion

    NASA Astrophysics Data System (ADS)

    Schneider, K.; Bockhorn, H.; Eigenbrod, Ch.; Emerson, D.; Haldenwang, P.; Hoffmann, F.; Roekaerts, D.; Ronney, P.; Triebel, W.; Tummers, M.

    2005-06-01

    Lean burning is the burning of fuel-air mixtures with less than the chemically- balanced (stoichiometric) mixture. It produces a significant increase in fuel efficiency and reduction in pollution. However, the limits and control of lean burning are still not well understood.This is the motivation behind the study of instabilities in lean gas-phase combustion under microgravity conditions via direct numerical simulations and comparison of the results with experimental data.The goal is to gain fundamental insights in order to identify and understand the intrinsic chemical and fluid dynamical mechanisms responsible for these instabilities.The potential of this microgravity combustion research includes the development of technology that would reduce pollution and fire and explosion hazards, improve hazardous waste incineration and increase efficiency of the conversion of chemical energy to electric power or motive force.The results from this fundamental research will thus benefit chemical engineering and power generation. Its wide range of applications in industry includes lean-burning car engines.

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

    PubMed

    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. PMID:26723675

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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.

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

    DOE PAGESBeta

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

    2015-12-29

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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Gas-phase interaction of protonated lysine with water

    NASA Astrophysics Data System (ADS)

    Rozman, Marko; Srzic, Dunja; Klasinc, Leo

    2006-07-01

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

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

    PubMed Central

    2015-01-01

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

  14. Gas-phase protonation thermochemistry of arginine.

    PubMed

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

    2008-03-20

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

  15. Gas-phase nitronium ion affinities.

    PubMed Central

    Cacace, F; de Petris, G; Pepi, F; Angelelli, F

    1995-01-01

    Evaluation of nitronium ion-transfer equilibria, L1NO2+ + L2 = L2NO2+ + L1 (where L1 and L2 are ligands 1 and 2, respectively) by Fourier-transform ion cyclotron resonance mass spectrometry and application of the kinetic method, based on the metastable fragmentation of L1(NO2+)L2 nitronium ion-bound dimers led to a scale of relative gas-phase nitronium ion affinities. This scale, calibrated to a recent literature value for the NO2+ affinity of water, led for 18 ligands, including methanol, ammonia, representative ketones, nitriles, and nitroalkanes, to absolute NO2+ affinities, that fit a reasonably linear general correlation when plotted vs. the corresponding proton affinities (PAs). The slope of the plot depends to a certain extent on the specific nature of the ligands and, hence, the correlations between the NO2+ affinities, and the PAs of a given class of compounds display a better linearity than the general correlation and may afford a useful tool for predicting the NO2+ affinity of a molecule based on its PA. The NO2+ binding energies are considerably lower than the corresponding PAs and well below the binding energies of related polyatomic cations, such as NO+, a trend consistent with the available theoretical results on the structure and the stability of simple NO2+ complexes. The present study reports an example of extension of the kinetic method to dimers, such as L1(NO2+)L2, bound by polyatomic ions, which may considerably widen its scope. Finally, measurement of the NO2+ affinity of ammonia allowed evaluation of the otherwise inaccessible PA of the amino group of nitramide and, hence, direct experimental verification of previous theoretical estimates. PMID:11607578

  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. Numerical simulation of unsteady planar ammonium perchlorate flames including detailed gas phase chemistry and fluid-structure interaction

    NASA Astrophysics Data System (ADS)

    Giovangigli, Vincent; Rahman, Shihab

    2013-01-01

    A one-dimensional unsteady combustion model is presented for ammonium perchlorate flames taking into account a detailed gas phase chemistry with 36 species and 216 reactions, a fully-coupled fluid-structure interaction and allowing for acoustic and elastic waves propagation. The model is used to calculate a wave propagating from the gas phase into the solid phase and reflected by the interface. The interface temporal response shows a linear behavior for the test case of interest in this article.

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

    NASA Astrophysics Data System (ADS)

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

    1995-03-01

    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 103/cc to 105/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.

  19. 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

  20. Single-conformation spectroscopy and population analysis of model γ-peptides: new tests of amide stacking.

    PubMed

    Buchanan, Evan G; James, William H; Gutberlet, Anna; Dean, Jacob C; Guo, Li; Gellman, Samuel H; Zwier, Timothy S

    2011-01-01

    Single-conformation ultraviolet and infrared spectra of a series of model gamma-peptides are reported, with the goal of providing new tests of amide stacking as an amide-amide binding motif. The data also serve to illustrate the power and challenges of carrying out single-conformation spectroscopy of neutral molecules of this size in the gas phase under jet-cooled conditions. Building on recent work on Ac-γ2-hPhe-NHMe (James et al., J. Am. Chem. Soc., 2009, 131, 14243), the effects of derivatization and H2O complexation on amide stacking are studied. Ac-γ2-hPhe-N(Me)2 shows only amide stacked structures, blocking the competing position for formation of an amide-amide H-bond. The Ac-γ2-hPhe-NHMe-H2O complex includes structures in which the H2O molecule forms a bridge between the two stacked amide planes, retaining and enhancing amide stacking. IR population transfer methods are also employed to study the dynamics of photodissociation of the amide stacked-H2O complex. Finally, IR ion-gain spectroscopy is introduced as a means of recording infrared spectra containing contributions from all conformers present, based on IR-induced broadening of the UV absorptions. Its role in estimating fractional abundances is tested on Ac-γ2-hPhe-NHMe. PMID:22457950

  1. 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

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

    PubMed

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

    2016-04-01

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

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

    PubMed Central

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

    2013-01-01

    Data mining was performed on 28,330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pair-wise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly-charged Arg- and Lys- ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially-mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton(s) and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton(s). 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 and/or y ions depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially-mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion intensities. PMID:16159109

  4. 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

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

    SciTech Connect

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

    1994-08-01

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

  6. Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions.

    PubMed

    London, Nir; Raveh, Barak; Cohen, Eyal; Fathi, Guy; Schueler-Furman, Ora

    2011-07-01

    Peptide-protein interactions are among the most prevalent and important interactions in the cell, but a large fraction of those interactions lack detailed structural characterization. The Rosetta FlexPepDock web server (http://flexpepdock.furmanlab.cs.huji.ac.il/) provides an interface to a high-resolution peptide docking (refinement) protocol for the modeling of peptide-protein complexes, implemented within the Rosetta framework. Given a protein receptor structure and an approximate, possibly inaccurate model of the peptide within the receptor binding site, the FlexPepDock server refines the peptide to high resolution, allowing full flexibility to the peptide backbone and to all side chains. This protocol was extensively tested and benchmarked on a wide array of non-redundant peptide-protein complexes, and was proven effective when applied to peptide starting conformations within 5.5 Å backbone root mean square deviation from the native conformation. FlexPepDock has been applied to several systems that are mediated and regulated by peptide-protein interactions. This easy to use and general web server interface allows non-expert users to accurately model their specific peptide-protein interaction of interest. PMID:21622962

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

    PubMed

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

    2005-11-30

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

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

    PubMed

    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. PMID:26828575

  9. 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.

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

    PubMed

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

    2013-11-15

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

  11. 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)

  12. 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.

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

    PubMed

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

    2014-05-01

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

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

    PubMed Central

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

    2014-01-01

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

  15. Optimal grade transitions in a gas phase polyethylene reactor

    SciTech Connect

    McAuley, K.B.; MacGregor, J.F. . Dept. of Chemical Engineering)

    1992-10-01

    This paper reports that using gas-phase technology many grades of polyethylene can be produced in a single reactor. For a series of three polyethylene products, model-based dynamic optimization is used to determine optimal grade changeover policies. Optimal manipulated variable profiles are determined for hydrogen and butene feed rates, reactor temperature setpoint, gas bleed flow, catalyst feed rate, and bed level setpoint. It is shown that large transitions in melt index are hampered by slow hydrogen dynamics, and that the time required for such a transition can be reduced by manipulating the temperature setpoint and the bleed stream flow. Reduction of the bed level and catalyst feed rates during changeovers can significantly reduce the quantity of off-specification polymer produced. it is demonstrated that melt index and density are not sufficient to characterize the properties of polymer produced during grade transitions, and that the shape of the cumulative copolymer composition distribution is very sensitive to the grade changeover policy used.

  16. Modeling the QSAR of ACE-Inhibitory Peptides with ANN and Its Applied Illustration

    PubMed Central

    He, Ronghai; Ma, Haile; Zhao, Weirui; Qu, Wenjuan; Zhao, Jiewen; Luo, Lin; Zhu, Wenxue

    2012-01-01

    A quantitative structure-activity relationship (QSAR) model of angiotensin-converting enzyme- (ACE-) inhibitory peptides was built with an artificial neural network (ANN) approach based on structural or activity data of 58 dipeptides (including peptide activity, hydrophilic amino acids content, three-dimensional shape, size, and electrical parameters), the overall correlation coefficient of the predicted versus actual data points is R = 0.928, and the model was applied in ACE-inhibitory peptides preparation from defatted wheat germ protein (DWGP). According to the QSAR model, the C-terminal of the peptide was found to have principal importance on ACE-inhibitory activity, that is, if the C-terminal is hydrophobic amino acid, the peptide's ACE-inhibitory activity will be high, and proteins which contain abundant hydrophobic amino acids are suitable to produce ACE-inhibitory peptides. According to the model, DWGP is a good protein material to produce ACE-inhibitory peptides because it contains 42.84% of hydrophobic amino acids, and structural information analysis from the QSAR model showed that proteases of Alcalase and Neutrase were suitable candidates for ACE-inhibitory peptides preparation from DWGP. Considering higher DH and similar ACE-inhibitory activity of hydrolysate compared with Neutrase, Alcalase was finally selected through experimental study. PMID:21822439

  17. The SMART model: Soft Membranes Adapt and Respond, also Transiently, in the presence of antimicrobial peptides.

    PubMed

    Bechinger, Burkhard

    2015-05-01

    Biophysical and structural studies of peptide-lipid interactions, peptide topology and dynamics have changed our view on how antimicrobial peptides insert and interact with membranes. Clearly, both the peptides and the lipids are highly dynamic, change and mutually adapt their conformation, membrane penetration and detailed morphology on a local and a global level. As a consequence, the peptides and lipids can form a wide variety of supramolecular assemblies in which the more hydrophobic sequences preferentially, but not exclusively, adopt transmembrane alignments and have the potential to form oligomeric structures similar to those suggested by the transmembrane helical bundle model. In contrast, charged amphipathic sequences tend to stay intercalated at the membrane interface where they cause pronounced disruptions of the phospholipid fatty acyl packing. At increasing local or global concentrations, the peptides result in transient membrane openings, rupture and ultimately lysis. Depending on peptide-to-lipid ratio, lipid composition and environmental factors (temperature, buffer composition, ionic strength, etc.), the same peptide sequence can result in a variety of those responses. Therefore, the SMART model has been introduced to cover the full range of possibilities. With such a view in mind, novel antimicrobial compounds have been designed from amphipathic polymers, peptide mimetics, combinations of ultra-short polypeptides with hydrophobic anchors or small designer molecules. PMID:25522713

  18. Gas-phase production of complex hydrocarbons, cyanopolyynes, and related compounds in dense interstellar clouds

    SciTech Connect

    Herbst, E.; Leung, C.M.

    1989-02-01

    The pseudo-time-dependent gas-phase model of Herbst and Leung (1986) for the chemistry of dense interstellar clouds is extended to include hydrocarbons as complex as C9H2 and CH3C6H, and organonitrogen compounds as complex as HC9N and CH3C7N. About 600 reactions are added to the model. Most of the reaction rate coefficients and product branching ratios are estimated based on analogous reactions involving smaller species or on theoretical considerations. Calculated abundances are compared with observations in TMC-1, showing generally good agreement. It is found that the observed C(n)H abundances in TMC-1 can be understood in terms of gas-phase production schemes, although the model contains predictions at early time that are too large. The calculated peak abundances for cyanopolyynes show a small but increasing tendency to be low compared with observation as molecular size increases. 72 references.

  19. 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

    Proteins are dynamic molecules that exhibit conformational flexibility to function properly. Well-known examples of this are allosteric regulation of protein activity and ligand-induced conformational changes in protein receptors. Detailed knowledge of the conformational properties of proteins is therefore pertinent to both basic and applied research, including drug development, since the majority of drugs target protein receptors and a growing number of drugs introduced to the market are therapeutic peptides or proteins. X-ray crystallography provides a static picture at atomic resolution of the lowest-energy structure of the native ensemble. There is a growing need for sensitive analytical tools to explore all of the significant molecular structures in the conformational landscape of proteins. Hydrogen/deuterium exchange monitored by mass spectrometry (HDX-MS) has recently emerged as a powerful method for characterizing protein conformational dynamics. The basis of this method is the fact that backbone amides in stable hydrogen-bonded structures (e.g., α-helices and β-sheets) are protected against exchange with the aqueous solvent. All protein structures are dynamic, however, and eventually all of the protecting hydrogen bonds will transiently break as the protein--according to thermodynamic principles--cycles through partially unfolded states that correspond to excited free energy levels. As a result, all of the backbone amides will eventually become temporarily solvent-exposed and exchange-competent over time. Consequently, a folded protein in D2O will gradually incorporate deuterium into its backbone amides, and the kinetics of the process can be readily monitored by mass spectrometry. The deuterium uptake kinetics for the intact protein (global exchange kinetics) represents the sum of the exchange kinetics for the individual backbone amides. Local exchange kinetics is typically achieved by using pepsin digestion under quench conditions (i.e., under cold acidic conditions where the amide hydrogen exchange rate is slowed by many orders of magnitude). The ability to localize the individual deuterated residues (the spatial resolution) is determined by the size (typically ∼7-15 residues) and the number of peptic peptides. These peptides provide a relatively coarse-grained picture of the protein dynamics. A fundamental understanding of the relationship between protein function/dysfunction and conformational dynamics requires in many cases higher resolution and ultimately single-residue resolution. In this Account, we summarize our efforts to achieve single-residue deuterium levels in proteins by electron-based or laser-induced gas-phase fragmentation methods. A crucial analytical requirement for this approach is that the pattern of deuterium labeling from solution is retained in the gas-phase fragment ions. It is therefore essential to control and minimize any occurrence of gas-phase randomization of the solution deuterium label (H/D scrambling) during the MS experiment. For this purpose, we have developed model peptide probes to accurately measure the onset and extent of H/D scrambling. Our analytical procedures to control the occurrence of H/D scrambling are detailed along with the physical parameters that induce it during MS analysis. In light of the growing use of gas-phase dissociation experiments to measure the HDX of proteins in order to obtain a detailed characterization and understanding of the dynamic conformations and interactions of proteins at the molecular level, we discuss the perspectives and challenges of future high-resolution HDX-MS methodology. PMID:25171396

  20. Modeling of ion-pairing effect in peptide reversed-phase chromatography.

    PubMed

    Gétaz, David; Hariharan, Subrahmaniam B; Butté, Alessandro; Morbidelli, Massimo

    2012-08-01

    The modeling of counterion and organic modifier concentration effects in peptide APIs reversed-phase preparative chromatography is discussed in this manuscript. A stoichiometric retention model based on the counterion binding to the charged functional groups of the peptide is proposed. The model parameters were evaluated using a rather large set of retention data measured in mobile phases with various counterions and acetonitrile concentrations. The model parameters were experimentally validated by a new counterion binding measurement technique. The n(max) model parameter value was found to be equal to the peptide net charge, whereas the K model parameter value was found to be specific to the counterion type (i.e. AcO(-)peptide saturation capacity was also investigated. It was shown that, at low acetonitrile concentration, the peptide saturation capacity was constant for all investigated counterion types and concentrations. On the other hand, at intermediate acetonitrile concentration, the peptide saturation capacity was significantly lower and with a tendency to increase with the counterion concentration. On the whole, the developed model provides a reliable a reliable tool for the design and development of peptide purification processes at the preparative and industrial scale. PMID:22748374

  1. Gas phase acetaldehyde production in a continuous bioreactor

    SciTech Connect

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

    1993-08-20

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

  2. 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.

  3. 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.

  4. 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).

  5. 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).

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

    PubMed

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

    2016-05-01

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

  7. Selected Examples of Gas-Phase Ion Chemistry Studies

    PubMed Central

    Nibbering, Nico M. M.

    2013-01-01

    Gas-phase ion chemistry is an area in mass spectrometry that has received much research interest since the mid fifties of the last century. Although the focus of mass spectrometric research has shifted the last twenty years largely to life science studies, including proteomics, genomics and metabolomics, there are still several groups in the world active in gas-phase ion chemistry of both positive and negative ions, either unimolecularly and/or bimolecularly. In this tutorial lecture the formation and determination of tautomeric ion structures and intra-ionic catalyzed tautomerization in the gas phase will be discussed. In addition, an example of formation of different tautomeric structures in protic and aprotic solvents under electrospray ionization conditions will be given, as established by gas-phase infrared multiphoton dissociation spectroscopy. This will be followed by presenting an example of time-resolved MS/MS which enables to identify the structure of an ion, generated at a particular molecular ion lifetime. At the end of the lecture the power of ion mobility will be shown in elucidating the mechanism of epimerization of bis-Tröger bases having chiral nitrogen centers. PMID:24349921

  8. 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...

  9. 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)

  10. The Dipeptide Ala-Gly in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Bermúdez, Celina; Varela, Marcelino; Cabezas, Carlos; Peña, Isabel; Alonso, José L.

    2014-06-01

    The dipeptide Ala-Gly has been examined in gas phase by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy in the frequency region 3-12 GHz. Three rotamers have been detected in the supersonic expansion. The quadrupole hyperfine structure of two 14N (I=1) nuclei has been totally resolved allowing the conclusive identification of one conformer.

  11. Gas-Phase Theoretical Kinetics for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Klippenstein, Stephen

    2013-05-01

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

  12. Gas Phase Theoretical Kinetics for Astrochemistry

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  13. 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.

  14. 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. PMID:24399766

  15. Two-Dimensional Gas-Phase Separations Coupled to Mass Spectrometry for Analysis of Complex Mixtures

    SciTech Connect

    Tang, Keqi; Li, Fumin; Shvartsburg, Alexandre A.; Strittmatter, Eric F.; Smith, Richard D.

    2005-10-01

    Ion mobility spectrometry (IMS) has been explored for decades, and its versatility in separation and identification of gas-phase ions, including in isomeric mixtures, is well established. Recently, field asymmetric waveform IMS (FAIMS) has been gaining acceptance in similar applications. Coupled to mass spectrometry (MS), both IMS and FAIMS have shown the potential for broad utility in proteomics and other biological analyses. A major attraction of these separations is extremely high speed, exceeding that of condensed-phase alternatives by orders of magnitude. However, modest separation peak capacities have limited the utility of FAIMS and IMS for analyses of complex mixtures. We report 2-D gas-phase separations that join FAIMS to IMS, in conjunction with high-resolution and accuracy time-of-flight MS. Evaluation of FAIMS/IMS/TOF performance using a protein mixture tryptic digest reveals high orthogonality between FAIMS and IMS dimensions, and hence the benefit of FAIMS filtering prior to IMS/MS. The effective overall peak capacities are ~500 for FAIMS/IMS separations, and ~106 for 3-D FAIMS/IMS/MS analyses of tryptic peptides. Implementation of FAIMS/IMS and IMS/MS interfaces using electrodynamic ion funnels greatly improves sensitivity, making FAIMS/IMS/MS a potential platform for ultrahigh-throughput analyses of complex mixtures.

  16. The Gas-Phase Deuterium Fractionation of Formaldehyde

    NASA Astrophysics Data System (ADS)

    Osamura, Yoshihiro; Roberts, Helen; Herbst, Eric

    2005-03-01

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

  17. 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.

  18. Flavin adenine dinucleotide structural motifs: from solution to gas phase.

    PubMed

    Molano-Arevalo, Juan Camilo; Hernandez, Diana R; Gonzalez, Walter G; Miksovska, Jaroslava; Ridgeway, Mark E; Park, Melvin A; Fernandez-Lima, Francisco

    2014-10-21

    Flavin adenine dinucleotide (FAD) is involved in important metabolic reactions where the biological function is intrinsically related to changes in conformation. In the present work, FAD conformational changes were studied in solution and in gas phase by measuring the fluorescence decay time and ion-neutral collision cross sections (CCS, in a trapped ion mobility spectrometer, TIMS) as a function of the solvent conditions (i.e., organic content) and gas-phase collisional partner (i.e., N2 doped with organic molecules). Changes in the fluorescence decay suggest that FAD can exist in four conformations in solution, where the abundance of the extended conformations increases with the organic content. TIMS-MS experiments showed that FAD can exist in the gas phase as deprotonated (M = C27H31N9O15P2) and protonated forms (M = C27H33N9O15P2) and that multiple conformations (up to 12) can be observed as a function of the starting solution for the [M + H](+) and [M + Na](+)molecular ions. In addition, changes in the relative abundances of the gas-phase structures were observed from a "stack" to a "close" conformation when organic molecules were introduced in the TIMS cell as collision partners. Candidate structures optimized at the DFT/B3LYP/6-31G(d,p) were proposed for each IMS band, and results showed that the most abundant IMS band corresponds to the most stable candidate structure. Solution and gas-phase experiments suggest that the driving force that stabilizes the different conformations is based on the interaction of the adenine and isoalloxazine rings that can be tailored by the "solvation" effect created with the organic molecules. PMID:25222439

  19. Synthetic model peptides phosphorylated in vitro by NII kinase and cation-mediated interactions with DNA.

    PubMed

    Gianfranceschi, G L; Cardellini, E; Piccinini, G; Bramucci, M; Miano, A; Maccari, E; Amici, D; Durban, E

    1989-01-01

    Minimum substrate requirements for nuclear NII kinase (casein II kinase) were analyzed with synthetic peptides modeled according to amino acid composition of phosphopeptides isolated from chromatin. Uncharged blocked peptide termini decreased the requirement for acidic clusters neighboring the phosphate acceptor amino acid (serine) such that only one group immediately N-terminal to serine was sufficient for kinase activity. Studies on peptide interaction with DNA showed that the model phosphopeptides bound to DNA only in the phosphorylated form suggesting involvement of phosphorylation in protein-DNA interactions yet to be identified. PMID:2535125

  20. Conformer-selective photoelectron spectroscopy of α-lactalbumin derived multianions in the gas phase.

    PubMed

    Vonderach, Matthias; Winghart, Marc-Oliver; MacAleese, Luke; Chirot, Fabien; Antoine, Rodolphe; Dugourd, Philippe; Weis, Patrick; Hampe, Oliver; Kappes, Manfred M

    2014-02-21

    We have recorded conformer-selective, gas-phase photoelectron spectra of α-lactalbumin derived multianions generated by electrospraying solutions of both the native protein and its denatured form (as prepared by breaking the sulfur-sulfur bonds by chemical reduction). Three different groups of gas-phase multianion conformers have been observed and characterized. Highly-folded and partially-unfolded structures are obtained from solutions of the native protein. Only highly-elongated conformers are observed upon electrospraying the denatured protein. Adiabatic detachment energies were determined at several negative charge states for each conformer group. In comparison to highly-elongated conformations, highly-folded structures show a steeper decrease of electron binding energy with increasing negative charge. By comparing experimental detachment energies for highly-elongated structures with the predictions of a simple electrostatic model calculation, we have determined the effective dielectric shielding constant. PMID:24394607

  1. 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.

  2. Gas phase glyoxal and methylglyoxal yields from the oxidation of isoprene and first generation products

    NASA Astrophysics Data System (ADS)

    Galloway, Melissa; Loza, Christine; Yee, Lindsay; Chan, Arthur; Crounse, John; Wennberg, Paul; Seinfeld, John; Keutsch, Frank

    2010-05-01

    α-dicarbonyls such as glyoxal and methylglyoxal are of increasing interest due to their importance in atmospheric processes and their ability to partition from the gas to aerosol phase. Isoprene oxidation is a major source of glyoxal and methylglyoxal in the atmosphere. However, the reaction pathways for these compounds are not well known, nor are the yields. Incorporation of the formation rates and yields of these compounds determined from our studies will allow us to improve chemical models that include isoprene oxidation. To achieve this, we performed experiments at the Caltech environmental chambers to determine the gas phase yields of glyoxal, methylglyoxal, and formaldehyde from isoprene and its primary reaction products, methyl vinyl ketone and methacrolein, under varied oxidation conditions. Gas phase glyoxal, methylglyoxal, and formaldehyde yields from the oxidation of these precursors will be presented as well as analysis of first generation glyoxal formation from isoprene oxidation.

  3. 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.

  4. 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 (?-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. PMID:22048904

  5. Ion Yields for Some Salts in MALDI: Mechanism for the Gas-Phase Ion Formation from Preformed Ions

    NASA Astrophysics Data System (ADS)

    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 (?-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.

  6. Gas phase laser synthesis and processing of calcium phosphate nanoparticles for biomedical applications

    NASA Astrophysics Data System (ADS)

    Bapat, Parimal V.

    Biochemical processes make pervasive use of calcium and phosphate ions. Calcium phosphate salts that are naturally nontoxic and bioactive have been used for several medical applications in form of coatings and micropowders. Nanoparticle-based calcium phosphates have been shown to be internalized by living cells and be effective in DNA transfection, drug delivery, and transport of fluorophores for imaging of intracellular processes. They are also expected to interact strongly with cell adhesive proteins and are therefore promising elements in approaches to mimic the complex environment of the extra cellular matrix of bone. Harnessing this biomedical potential requires the ability to control the numerous characteristics of nanophase calcium phosphates that affect biological response, including nanoparticle chemical composition, crystal phase, crystallinity, crystallographic orientation of exposed faces, size, shape, surface area, number concentration, and degree of aggregation. This dissertation focuses on the use of laser-induced gas-phase synthesis for creation of calcium phosphate nanoparticles, and corresponding nanoparticle-based substrates that could offer new opportunities for guiding biological responses through well-controlled biochemical and topological cues. Gas-phase synthesis of nanoparticles has several characteristics that could enhance control over particle morphology, crystallinity, and surface area, compared to liquid-phase techniques. Synthesis from gas-phase precursors can be carried out at high temperatures and in high-purity inert or reactive gas backgrounds, enabling good control of chemistry, crystal structure, and purity. Moreover, the particle mean free path and number concentration can be controlled independently. This allows regulation of interparticle collision rates, which can be adjusted to limit aggregation. High-temperature synthesis of well-separated particles is therefore possible. In this work high power lasers are employed to vaporize microcrystalline calcium phosphate materials to generate an aerosol of nanoparticles which is further processed and deposited using principles of aerosol mechanics. Particles and resulting particle-based systems are analyzed by transmission electron microscopy, atomic force microscopy, X-ray diffraction, and optical absorption. Obtained substrates are functionalized with cell adhesive peptides. Findings show that laser-induced gas-phase synthesis provides attractive new dimensions in the controlled fabrication of calcium phosphate nanoparticles, including manipulation not only of size and chemical composition, but also crystal phase make-up, fractal structure, and nanotopography of derived substrates.

  7. Interaction between ion channel-inactivating peptides and anionic phospholipid vesicles as model targets.

    PubMed Central

    Encinar, J A; Fernandez, A M; Gavilanes, F; Albar, J P; Ferragut, J A; Gonzalez-Ros, J M

    1996-01-01

    Studies of rapid (N-type) inactivation induced by different synthetic inactivating peptides in several voltage-dependent cation channels have concluded that the channel inactivation "entrance" (or "receptor" site for the inactivating peptide) consists of a hydrophobic vestibule within the internal mouth of the channel, separated from the cytoplasm by a region with a negative surface potential. These protein domains are conformed from alternative sequences in the different channels and thus are relatively unrestricted in terms of primary structure. We are reporting here on the interaction between the inactivating peptide of the Shaker B K+ channel (ShB peptide) or the noninactivating ShB-L7E mutant with anionic phospholipid vesicles, a model target that, as the channel's inactivation "entrance," contains a hydrophobic domain (the vesicle bilayer) separated from the aqueous media by a negatively charged vesicle surface. When challenged by the anionic phospholipid vesicles, the inactivating ShB peptide 1) binds to the vesicle surface with a relatively high affinity, 2) readily adopts a strongly hydrogen-bonded beta-structure, likely an intramolecular beta "hairpin," and 3) becomes inserted into the hydrophobic bilayer by its folded N-terminal portion, leaving its positively charged C-terminal end exposed to the extravesicular aqueous medium. Similar experiments carried out with the noninactivating, L7E-ShB mutant peptide show that this peptide 1) binds also to the anionic vesicles, although with a lower affinity than does the ShB peptide, 2) adopts only occasionally the characteristic beta-structure, and 3) has completely lost the ability to traverse the anionic interphase at the vesicle surface and to insert into the hydrophobic vesicle bilayer. Because the negatively charged surface and the hydrophobic domains in the model target may partly imitate those conformed at the inactivation "entrance" of the channel proteins, we propose that channel inactivation likely includes molecular events similar to those observed in the interaction of the ShB peptide with the phospholipid vesicles, i.e., binding of the peptide to the region of negative surface potential, folding of the bound peptide as a beta-structure, and its insertion into the channel's hydrophobic vestibule. Likewise, we relate the lack of channel inactivation seen with the mutant ShB-L7E peptide to the lack of ability shown by this peptide to cross through the anionic interphase and insert into the hydrophobic domains of the model vesicle target. PMID:8874005

  8. 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.

  9. Evidence of Microporous Carbon Nanosheets Showing Fast Kinetics in both Gas Phase and Liquid Phase Environments.

    PubMed

    Jin, Zhen-Yu; Xu, Yuan-Yuan; Sun, Qiang; Lu, An-Hui

    2015-10-01

    Despite the great advantages of microporous carbons for applications in gas phase separation, liquid phase enrichment, and energy storage devices, direct experiment data and theoretical calculations on the relevance of properties and structures are quite limited. Herein, two model carbon materials are designed and synthesized, i.e., microporous carbon nanosheets (MCN) and microporous carbon spheres (MCS). They both have nearly same composition, surface chemistry, and specific surface area, known morphology, but distinguishable diffusion paths. Based on these two types of materials, a reliable relationship between the morphology with different diffusion paths and adsorption kinetics in both gas phase and liquid phase environments is established. When used for CO2 capture, MCN shows a high saturated CO2 capacity of 8.52 ?mol m(-2) and 18.4 mmol cm(-3) at 273 K and ambient pressure, and its calculated first-order rate constant is ?7.4 times higher than that of MCS. Moreover, MCN shows a quick and high uptake of Cr (VI) and a higher-rate performance for supercapacitors than MCS does. These results strongly confirm that MCN exhibits improved kinetics in gas phase separation, liquid phase enrichment, and energy storage devices due to its shorter diffusion paths and larger exposed geometrical area resulting from the nanosheet structure. PMID:26192395

  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. 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

  12. In vitro selection and analysis of RNA aptamer recognize arginine-rich motif (ARM) model peptide on a QCM.

    PubMed

    Fukusho, S; Furusawa, H; Okahata, Y

    2000-01-01

    To study RNA-peptide interactions, we performed an in vitro selection of RNA on a 27 MHz quartz-crystal microbalance (QCM) on which a simple R5 helix peptide was immobilized as a model of N peptide from bacteriophade lambda. The consensus sequences including a GNRA tetraloop were obtained from a random RNA pool after the 7th cycle selection. PMID:12903331

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

    EPA Science Inventory

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

  14. Development of Monopole Interaction Models for Ionic Compounds. Part I: Estimation of Aqueous Henrys 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 Henrys Law Constant (HLC) for charged species by incorporating ionic electrostatic interaction models. Combinations of absolute aq...

  15. 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.

  16. 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

  17. Hydration of Gas-Phase Ions Formed by Electrospray Ionization

    PubMed Central

    Rodriguez-Cruz, Sandra E.; Klassen, John S.; Williams, Evan R.

    2005-01-01

    The hydration of gas-phase ions produced by electrospray ionization was investigated. Evidence that the hydrated ions are formed by two mechanisms is presented. First, solvent condensation during the expansion inside the electrospray source clearly occurs. Second, some solvent evaporation from more extensively solvated ions or droplets is apparent. To the extent that these highly solvated ions have solution-phase structures, then the final isolated gas-phase structure of the ion will be determined by the solvent evaporation process. This process was investigated for hydrated gramicidin S in a Fourier-transform mass spectrometer. Unimolecular dissociation rate constants of isolated gramicidin S ions with between 2 and 14 associated water molecules were measured. These rate constants increased from 16 to 230 s−1 with increasing hydration, with smaller values corresponding to magic numbers. PMID:10497808

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

    SciTech Connect

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

    1989-12-20

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

  19. FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

    PubMed Central

    Hamelryck, Thomas; Jensen, Jan H.

    2014-01-01

    We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license. PMID:24688855

  20. 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.

  1. Gas-phase terpene oxidation products: a review

    NASA Astrophysics Data System (ADS)

    Calogirou, A.; Larsen, B. R.; Kotzias, D.

    Terpenes are emitted in large quantities from vegetation into the troposphere, where they react readily with ozone, OH and NO 3 radicals leading to a number of oxidation products. The current knowledge about gas-phase terpene oxidation products is reviewed. Their formation and decomposition pathways, their products and their relevance for the troposphere, and their chemical analysis are discussed. Data on oxidation kinetics, and product yields is presented for 23 terpenes and 65 oxidation products. A total of 84 references are quoted.

  2. 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.

  3. Simulation Approach for Microscale Noncontinuum Gas-Phase Heat Transfer

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

    In microscale thermal actuators, gas-phase heat transfer from the heated beams to the adjacent unheated substrate is often the main energy-loss mechanism. Since the beam-substrate gap is comparable to the molecular mean free path, noncontinuum gas effects are important. A simulation approach is presented in which gas-phase heat transfer is described by Fourier's law in the bulk gas and by a wall boundary condition that equates the normal heat flux to the product of the gas-solid temperature difference and a heat transfer coefficient. The dimensionless parameters in this heat transfer coefficient are determined by comparison to Direct Simulation Monte Carlo (DSMC) results for heat transfer from beams of rectangular cross section to the substrate at free-molecular to near-continuum gas pressures. This simulation approach produces reasonably accurate gas-phase heat-transfer results for wide ranges of beam geometries and gas pressures. 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.

  4. Exploration of Peptide Inhibitors of Human Squalene Synthase through Molecular Modeling and Phage Display Technique.

    PubMed

    Shiuan, David; Lin, Hwan-Kang; Chen, Yue-Hao; Chang, Ding-Kwo; Huang, Kao-Jean; Farh, Lynn

    2016-01-01

    Many studies have demonstrated the role of elevated levels of serum cholesterol in the pathogenesis of atherosclerosis and coronary heart disease. Various drugs targeting the key enzymes involved in the cholesterol biosynthesis pathway have been investigated for the treatment of hypercholesterolemia. Human squalene synthase has been one of the most important targets for therapeutic intervention. In the present study, we used the recombinant human squalene synthase as the lure for screening the peptide inhibitors from phage-displayed random peptide library. The tightly bound phages and their derived peptides were further evaluated based on their potential binding capabilities, molecular modeling characteristics and predicted absorption, distribution, metabolism, excretion, toxicity (ADMET) properties. Several hexa-peptides and tetra-peptides were finally synthesized to assay their inhibitory effects toward the recombinant human squalene synthase. The results demonstrated that the hexa-peptide FTACNW and tetra-peptide VACL can inhibit human squalene synthase effectively (with IC50 values near 100 μM) and may have potential to develop further as future hypocholesterolemia agents. PMID:26438313

  5. A model for the controlled assembly of semiconductor peptides

    NASA Astrophysics Data System (ADS)

    Kim, Se Hye; Parquette, Jon R.

    2012-10-01

    The self-assembly of small molecules provides a potentially powerful method to create functional nanomaterials for many applications ranging from optoelectronics to oncology. However, the design of well-defined nanostructures via molecular assembly is a highly empirical process, which severely hampers efforts to create functional nanostructures using this method. In this review, we describe a simple strategy to control the assembly of functionalized peptides by balancing attractive hydrophobic effects that drive assembly with opposing electrostatic repulsions. Extended π-π contacts are created in the nanostructures when assembly is driven by π-stacking interactions among chromophores that are appended to the peptide. The formation of insoluble β-sheet aggregates are mitigated by incorporating charged side-chains capable of attenuating the assembly process. Although the application of this approach to the assembly of organic semiconductors is described, we expect this strategy to be effective for many other functional organic materials.

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  7. ESEEM Studies of Peptide Nitrogen Hyperfine Coupling in Tyrosyl Radicals and Model Peptides

    PubMed Central

    Vassiliev, Ilya R.; Yang, En-Che; Range, Kevin

    2008-01-01

    Tyrosyl radicals are important in long-range electron transfer in several enzymes, but the protein environmental factors that control midpoint potential and electron transfer rate are not well understood. To develop a more detailed understanding of the effect of protein sequence, we have performed 14N and 15N electron spin echo envelope modulation (ESEEM) measurements on tyrosyl radical, generated either in polycrystalline tyrosinate or in its 15N labeled isotopomer, by UV photolysis. 14N ESEEM was also performed on tyrosyl radical generated in tyrosine-containing pentapeptide samples. Simulation of the 14N and 15N tyrosyl radical ESEEM measurements yielded no significant isotropic hyperfine splitting to the amine or amide nitrogen; the amplitude of the anisotropic, nitrogen hyperfine coupling (0.21 MHz) was consistent with a dipole-dipole distance of 3.0 . Density functional theory was used to calculate the isotropic and anisotropic hyperfine couplings to the amino nitrogen in four different tyrosyl radical conformers. Comparison with the simulated data suggested that the lowest energy radical conformer, generated in tyrosine at pH 11, has a 76 C?-C?-C1?-C2? ring and a ?73 C-C?-C?-C1? backbone dihedral angle. In addition, the magnitude, orientation, and asymmetry of the nuclear quadrupole coupling tensor were derived from analysis of the tyrosyl radical 14N ESEEM. The simulations showed differences in the coupling and orientation of the nuclear quadrupole tensor, when the tyrosinate and pentapeptide samples were compared. These results suggest sequence- or conformation-induced changes in the ionic character of the NH bond in different tyrosine-containing peptides. PMID:17518496

  8. 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.

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

    PubMed

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

    2016-01-01

    The aim of this review is to critically analyze recent literature on charged supramolecular assemblies formed by surfactant molecules in gas phase. Apart our specific interest on this research area, the stimuli to undertake the task arise from the widespread theoretical and applicative benefits emerging from a comprehensive view of this topic. In fact, the study of the formation, stability, and physicochemical peculiarities of non-covalent assemblies of surfactant molecules in gas phase allows to unveil interesting aspects such as the role of attractive, repulsive, and steric intermolecular interactions as driving force of supramolecular organization in absence of interactions with surrounding medium and the size and charge state dependence of aggregate structural and dynamical properties. Other interesting aspects worth to be investigated are joined to the ability of these assemblies to incorporate selected solubilizates molecules as well as to give rise to chemical reactions within a single organized structure. In particular, the incorporation of large molecules such as proteins has been of recent interest with the objective to protect their structure and functionality during the transition from solution to gas phase. Exciting fall-out of the study of gas phase surfactant aggregates includes mass and energy transport in the atmosphere, origin of life and simulation of supramolecular aggregation in the interstellar space. Moreover, supramolecular assemblies of amphiphilic molecules in gas phase could find remarkable applications as atmospheric cleaning agents, nanosolvents and nanoreactors for specialized chemical processes in confined space. Mass spectrometry techniques have proven to be particularly suitable to generate these assemblies and to furnish useful information on their size, size polydispersity, stability, and structural organization. On the other hand molecular dynamics simulations have been very useful to rationalize many experimental findings and to furnish a vivid picture of the structural and dynamic features of these aggregates. Thus, in this review, we will focus on the most important achievements gained in recent years by both these investigative tools. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35: 170-187, 2016. PMID:26113001

  10. On Utilizing Optimal and Information Theoretic Syntactic Modeling for Peptide Classification

    NASA Astrophysics Data System (ADS)

    Aygün, Eser; Oommen, B. John; Cataltepe, Zehra

    Syntactic methods in pattern recognition have been used extensively in bioinformatics, and in particular, in the analysis of gene and protein expressions, and in the recognition and classification of bio-sequences. These methods are almost universally distance-based. This paper concerns the use of an Optimal and Information Theoretic (OIT) probabilistic model [11] to achieve peptide classification using the information residing in their syntactic representations. The latter has traditionally been achieved using the edit distances required in the respective peptide comparisons. We advocate that one can model the differences between compared strings as a mutation model consisting of random Substitutions, Insertions and Deletions (SID) obeying the OIT model. Thus, in this paper, we show that the probability measure obtained from the OIT model can be perceived as a sequence similarity metric, using which a Support Vector Machine (SVM)-based peptide classifier, referred to as OIT_SVM, can be devised.

  11. 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 temperature or below. For many spectroscopic measurements, low temperatures have been achieved by co-condensing the actinide vapor in rare gas or inert molecule host matrices. Spectra recorded in matrices are usually considered to be minimally perturbed. Trapping the products from gas-phase reactions that occur when trace quantities of reactants are added to the inert host gas has resulted in the discovery of many new actinide species. Selected aspects of the matrix isolation data were discussed in chapter 17. In the present chapter we review the spectroscopic matrix data in terms of its relationship to gas-phase measurements, and update the description of the new reaction products found in matrices to reflect the developments that have occurred during the past two years. Spectra recorded in matrix environments are usually considered to be minimally perturbed, and this expectation is borne out for many closed shell actinide molecules. However, there is growing evidence that significant perturbations can occur for open shell molecules, resulting in geometric distortions and/or electronic state reordering. Studies of actinide reactions in the gas phase provide an opportunity to probe the relationship between electronic structure and reactivity. Much of this work has focused on the reactions of ionic species, as these may be selected and controlled using various forms of mass spectrometry. As an example of the type of insight derived from reaction studies, it has been established that the reaction barriers for An+ ions are determined by the promotion energies required to achieve the 5fn6d7s configuration. Gas-phase reaction studies also provide fundamental thermodynamic properties such as bond dissociation and ionization energies. In recent years, an increased number of gas-phase ion chemistry studies of bare (atomic) and ligated (molecular) actinide ions have appeared, in which relevant contributions to fundamental actinide chemistry have been made. These studies were initiated in the 1970's and carried out in an uninterrupted way over the course of the past three decades. Initial studies unsurprisingly focused on naturally occurring U (and Th) and were later extended (starting ten years ago) to Pa and several of the more abundant members of the transuranium series, Np through Es. The main purpose of the reaction dynamics section of this chapter is to summarize (up to late 2008) the work done in the gas phase involving ionic species, with an emphasis on the key accomplishments. This topic was recently reviewed in a comprehensive way (Gibson 2002a; Gibson and Marcalo 2006). The small number of studies reported for gas-phase reactions of neutral actinide species are also briefly summarized.

  12. 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

  13. Single channel conductance modeling of the peptide alamethicin in synthetically formed bilayers

    NASA Astrophysics Data System (ADS)

    Creasy, M. Austin; Leo, Donald J.

    2011-04-01

    Bilayers are synthetically made cell membranes that are used to study cell membrane properties and make functional devices that incorporate inherent properties of the cell membranes. Lipids and proteins are two of the main components of a cell membrane. Lipids provide the structure of the membrane in the form of two leaflets or layers that are held together by the amphiphilic interaction between the lipids and water. Proteins are made from a combination of amino acids and the properties of these proteins are dependent on the amino acid sequence. Some proteins are antibiotics and can easily self insert into the membrane of a cell or into a synthetically formed bilayer. The peptide alamethicin is one such antibiotic that easily inserts into a bilayer and changes the conductance properties of the bilayer. Analytical models of the conductance change with respect to the potential and other variables across the bilayer follows the nonlinear conductance changes seen with the incorporation of the peptide in a bilayer. The individual channels formed by the peptide have been studied and the peptide has several discrete conductance levels. These discrete levels have been shown to be dependent on the potential across the bilayer and several other variables including the lipid variety. The conductance level for a single channel can change with time in a probabilistic fashion. This paper will model these discrete conductance levels of the peptide alamethicin and the model of the single channel conductance will be used to model the cumulative effect of multiple channels within a bilayer.

  14. Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models

    PubMed Central

    Larsson, Per; Kasson, Peter M.

    2013-01-01

    Fusion peptides from influenza hemagglutinin act on membranes to promote membrane fusion, but the mechanism by which they do so remains unknown. Recent theoretical work has suggested that contact of protruding lipid tails may be an important feature of the transition state for membrane fusion. If this is so, then influenza fusion peptides would be expected to promote tail protrusion in proportion to the ability of the corresponding full-length hemagglutinin to drive lipid mixing in fusion assays. We have performed molecular dynamics simulations of influenza fusion peptides in lipid bilayers, comparing the X-31 influenza strain against a series of N-terminal mutants. As hypothesized, the probability of lipid tail protrusion correlates well with the lipid mixing rate induced by each mutant. This supports the conclusion that tail protrusion is important to the transition state for fusion. Furthermore, it suggests that tail protrusion can be used to examine how fusion peptides might interact with membranes to promote fusion. Previous models for native influenza fusion peptide structure in membranes include a kinked helix, a straight helix, and a helical hairpin. Our simulations visit each of these conformations. Thus, the free energy differences between each are likely low enough that specifics of the membrane environment and peptide construct may be sufficient to modulate the equilibrium between them. However, the kinked helix promotes lipid tail protrusion in our simulations much more strongly than the other two structures. We therefore predict that the kinked helix is the most fusogenic of these three conformations. PMID:23505359

  15. Contribution of Electrostatics in the Fibril Stability of a Model Ionic-Complementary Peptide.

    PubMed

    Owczarz, Marta; Casalini, Tommaso; Motta, Anna C; Morbidelli, Massimo; Arosio, Paolo

    2015-12-14

    In this work we quantified the role of electrostatic interactions in the self-assembly of a model amphiphilic peptide (RADA 16-I) into fibrillar structures by a combination of size exclusion chromatography and molecular simulations. For the peptide under investigation, it is found that a net charge of +0.75 represents the ideal condition to promote the formation of regular amyloid fibrils. Lower net charges favor the formation of amorphous precipitates, while larger net charges destabilize the fibrillar aggregates and promote a reversible dissociation of monomers from the ends of the fibrils. By quantifying the dependence of the equilibrium constant of this reversible reaction on the pH value and the peptide net charge, we show that electrostatic interactions contribute largely to the free energy of fibril formation. The addition of both salt and a charged destabilizer (guanidinium hydrochloride) at moderate concentration (0.3-1 M) shifts the monomer-fibril equilibrium toward the fibrillar state. Whereas the first effect can be explained by charge screening of electrostatic repulsion only, the promotion of fibril formation in the presence of guanidinium hydrochloride is also attributed to modifications of the peptide conformation. The results of this work indicate that the global peptide net charge is a key property that correlates well with the fibril stability, although the peptide conformation and the surface charge distribution also contribute to the aggregation propensity. PMID:26594824

  16. Estimation of prehepatic insulin secretion: comparison between standardized C-peptide and insulin kinetic models.

    PubMed

    Tura, Andrea; Pacini, Giovanni; Kautzky-Willer, Alexandra; Gastaldelli, Amalia; DeFronzo, Ralph A; Ferrannini, Ele; Mari, Andrea

    2012-03-01

    Our aim was to compare traditional C-peptide-based method and insulin-based method with standardized kinetic parameters in the estimation of prehepatic insulin secretion rate (ISR). One-hundred thirty-four subjects with varying degrees of glucose tolerance received an insulin-modified intravenous glucose tolerance test and a standard oral glucose tolerance test with measurement of plasma insulin and C-peptide. From the intravenous glucose tolerance test, we determined insulin kinetics parameters and selected standardized kinetic parameters based on mean values in a selected subgroup. We computed ISR from insulin concentration during the oral glucose tolerance test using these parameters and compared ISR with the standard C-peptide deconvolution approach. We then performed the same comparison in an independent data set (231 subjects). In the first data set, total ISRs from insulin and C-peptide were highly correlated (R(2) = 0.75, P < .0001), although on average different (103 ± 6 vs 108 ± 3 nmol, P < .001). Good correlation was also found in the second data set (R(2) = 0.54, P < .0001). The insulin method somewhat overestimated total ISR (85 ± 5 vs 67 ± 3 nmol, P = .002), in part because of differences in insulin assay. Similar results were obtained for fasting ISR. Despite the modest bias, the insulin and C-peptide methods were consistent in predicting differences between groups (eg, obese vs nonobese) and relationships with other physiological variables (eg, body mass index, insulin resistance). The insulin method estimated first-phase ISR peak similarly to the C-peptide method and better than the simple use of insulin concentration. The insulin-based ISR method compares favorably with the C-peptide approach. The method will be particularly useful in data sets lacking C-peptide to assess β-cell function through models requiring prehepatic secretion. PMID:21944265

  17. 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

  18. Revision of the thermodynamics of the proton in gas phase.

    PubMed

    Fifen, Jean Jules; Dhaouadi, Zoubeida; Nsangou, Mama

    2014-11-20

    Proton transfer is ubiquitous in various physical/chemical processes, and the accurate determination of the thermodynamic parameters of the proton in the gas phase is useful for understanding and describing such reactions. However, the thermodynamic parameters of such a proton are usually determined by assuming the proton as a classical particle whatever the temperature. The reason for such an assumption is that the entropy of the quantum proton is not always soluble analytically at all temperatures. Thereby, we addressed this matter using a robust and reliable self-consistent iterative procedure based on the Fermi-Dirac formalism. As a result, the free proton gas can be assumed to be classical for temperatures higher than 200 K. However, it is worth mentioning that quantum effects on the gas phase proton motion are really significant at low temperatures (T ≤ 120 K). Although the proton behaves as a classical particle at high temperatures, we strongly recommend the use of quantum results at all temperatures, for the integrated heat capacity and the Gibbs free energy change. Therefore, on the basis of the thermochemical convention that ignores the proton spin, we recommend the following revised values for the integrated heat capacity and the Gibbs free energy change of the proton in gas phase and, at the standard pressure (1 bar): ΔH0→T = 6.1398 kJ mol(-1) and ΔG0→T = -26.3424 kJ mol(-1). Finally, it is important noting that the little change of the pressure from 1 bar to 1 atm affects notably the entropy and the Gibbs free energy change of the proton. PMID:25338234

  19. 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.

  20. Gas-phase energetics of thorium fluorides and their ions.

    PubMed

    Irikura, Karl K

    2013-02-14

    Gas-phase thermochemistry for neutral ThF(n) and cations ThF(n)(+) (n = 1-4) is obtained from large-basis CCSD(T) calculations, with a small-core pseudopotential on thorium. Electronic partition functions are computed with the help of relativistic MRCI calculations. Geometries, vibrational spectra, electronic fine structure, and ion appearance energies are tabulated. These results support the experimental results by Lau, Brittain, and Hildenbrand for the neutral species, except for ThF. The ion thermochemistry is presented here for the first time. PMID:23137388

  1. 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.

  2. Gas-phase synthesis of zinc oxide nanorods

    NASA Astrophysics Data System (ADS)

    Bagamadova, A. M.; Omaev, A. K.

    2015-09-01

    Gas-phase synthesis of zinc oxide (ZnO) nanorods on silicon and glass substrates has been studied. Using the proposed method, arrays of ZnO nanorods can be grown on these substrates without preliminary deposition of a thin ZnO sublayer and/or metal catalyst. The influence of the temperature regime, substrate arrangement, and growth time on the synthesis is considered. The shape, dimensions, and orientation of nanorods have been studied by electron microscopy and X-ray diffraction. Luminescence spectra and X-ray diffraction patterns of oriented arrays of nanorods have been investigated.

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

    NASA Technical Reports Server (NTRS)

    Lutz, Barry L.

    1987-01-01

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

  4. Formation and dissociation of phosphorylated peptide radical cations.

    PubMed

    Kong, Ricky P W; Quan, Quan; Hao, Qiang; Lai, Cheuk-Kuen; Siu, Chi-Kit; Chu, Ivan K

    2012-12-01

    In this study, we generated phosphoserine- and phosphothreonine-containing peptide radical cations through low-energy collision-induced dissociation (CID) of the ternary metal-ligand phosphorylated peptide complexes [Cu(II)(terpy)(p)M](·2+) and [Co(III)(salen)(p)M](·+) [(p)M: phosphorylated angiotensin III derivative; terpy: 2,2':6',2''-terpyridine; salen: N,N'-ethylenebis(salicylideneiminato)]. Subsequent CID of the phosphorylated peptide radical cations ((p)M(·+)) revealed fascinating gas-phase radical chemistry, yielding (1) charge-directed b- and y-type product ions, (2) radical-driven product ions through cleavages of peptide backbones and side chains, and (3) different degrees of formation of [M - H(3)PO(4)](·+) species through phosphate ester bond cleavage. The CID spectra of the (p)M(·+) species and their non-phosphorylated analogues featured fragment ions of similar sequence, suggesting that the phosphoryl group did not play a significant role in the fragmentation of the peptide backbone or side chain. The extent of neutral H(3)PO(4) loss was influenced by the peptide sequence and the initial sites of the charge and radical. A preliminary density functional theory study, at the B3LYP 6-311++G(d,p) level of theory, of the neutral loss of H(3)PO(4) from a prototypical model--N-acetylphosphorylserine methylamide--revealed several factors governing the elimination of neutral phosphoryl groups through charge- and radical-induced mechanisms. PMID:22968907

  5. 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.

  6. 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.

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

    PubMed

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

    2016-04-01

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

  8. 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. PMID:18443779

  9. 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.

    2016-01-01

    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.

  10. Influence of end-capping on the self-assembly of model amyloid peptide fragments.

    PubMed

    Castelletto, Valeria; Hamley, Ian W; Cenker, Çelen; Olsson, Ulf; Adamcik, Jozef; Mezzenga, Raffaele; Miravet, Juan F; Escuder, Beatriu; Rodríguez-Llansola, Francisco

    2011-03-10

    The influence of charge and aromatic stacking interactions on the self-assembly of a series of four model amyloid peptides has been examined. The four model peptides are based on the KLVFF motif from the amyloid β peptide, Aβ(16-20) extended at the N terminus with two β-alanine residues. We have studied NH(2)-βAβAKLVFF-COOH (FF), NH(2)-βAβAKLVF-COOH (F), CH(3)CONH-βAβAKLVFF-CONH(2) (CapF), and CH(3)CONH-βAβAKLVFF-CONH(2) (CapFF). The former two are uncapped (net charge +2) and differ by one hydrophobic phenylalanine residue; the latter two are the analogous capped peptides (net charge +1). The self-assembly characteristics of these peptides are remarkably different and strongly dependent on concentration. NMR shows a shift from carboxylate to carboxylic acid forms upon increasing concentration. Saturation transfer measurements of solvent molecules indicate selective involvement of phenylalanine residues in driving the self-assembly process of CapFF due presumably to the effect of aromatic stacking interactions. FTIR spectroscopy reveals β-sheet features for the two peptides containing two phenylalanine residues but not the single phenylalanine residue, pointing again to the driving force for self-assembly. Circular dichroism (CD) in dilute solution reveals the polyproline II conformation, except for F which is disordered. We discuss the relationship of this observation to the significant pH shift observed for this peptide when compared the calculated value. Atomic force microscopy and cryogenic-TEM reveals the formation of twisted fibrils for CapFF, as previously also observed for FF. The influence of salt on the self-assembly of the model β-sheet forming capped peptide CapFF was investigated by FTIR. Cryo-TEM reveals that the extent of twisting decreases with increased salt concentration, leading to the formation of flat ribbon structures. These results highlight the important role of aggregation-induced pK(a) shifts in the self-assembly of model β-sheet peptides. PMID:21309578

  11. Strategies for Generating Peptide Radical Cations via Ion/Ion Reactions

    PubMed Central

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

    2014-01-01

    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. PMID:25800024

  12. 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. PMID:25800024

  13. 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.

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

    PubMed

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

    2016-04-21

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

  15. 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.

  16. Gas phase contributions to topochemical hydride reduction reactions

    SciTech Connect

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

    2013-11-15

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

  17. 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.

  18. Gas-Phase Acidities of Phosphorylated Amino Acids.

    PubMed

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

    2015-11-19

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

  19. 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.

  20. Ultrafast non-radiative decay of gas-phase nucleosides.

    PubMed

    De Camillis, Simone; Miles, Jordan; Alexander, Grace; Ghafur, Omair; Williams, Ian D; Townsend, Dave; Greenwood, Jason B

    2015-09-28

    The ultrafast photo-physical properties of DNA are crucial in providing a stable basis for life. Although the DNA bases efficiently absorb ultraviolet (UV) radiation, this energy can be dissipated to the surrounding environment by the rapid conversion of electronic energy to vibrational energy within about a picosecond. The intrinsic nature of this internal conversion process has previously been demonstrated through gas phase experiments on the bases, supported by theoretical calculations. De-excitation rates appear to be accelerated when individual bases are hydrogen bonded to solvent molecules or their complementary Watson-Crick pair. In this paper, the first gas-phase measurements of electronic relaxation in DNA nucleosides following UV excitation are reported. Using a pump-probe ionization scheme, the lifetimes for internal conversion to the ground state following excitation at 267 nm are found to be reduced by around a factor of two for adenosine, cytidine and thymidine compared with the isolated bases. These results are discussed in terms of a recent proposition that a charge transfer state provides an additional internal conversion pathway mediated by proton transfer through a sugar to base hydrogen bond. PMID:26299204

  1. 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.

  2. Charge transfer and charge localization in extended radical cations: Investigation of model molecules for peptides

    NASA Astrophysics Data System (ADS)

    Weinkauf, Rainer; Lehrer, Florian

    1998-12-01

    Molecules consisting of a flexible tail and an aromatic chromophore are used as model systems to understand the situation of a single chromophore in a small peptide. Their S0-S1 resonant multiphoton ionization (REMPI) spectra show, that in neutral molecules the tail-chromophore interaction is weak and electronic excitation is localized at the chromophore. For molecules, where the ionization energy of the tail is considerable higher than that of the chromophore, by high resolution REMPI photoelectron spectroscopy we find the charge to be localized on the aromatic chromophore. This scheme also in suitable peptides allows local ionization at the aromatic chromophore. An estimate for various charge positions in peptide chains, however, shows, that for most of the amino acids electron hole positions in the nitrogen and oxygen "lone pair" orbitals of the peptide bond are nearly degenerate. REMPI photoelectron spectra of phenylethylamine, which as a model system contains such two degenerate charge positions, show small energetic shift of the ionization energy but strong geometry changes upon electron removal. This result is interpreted as direct ionization into a mixed charge delocalized state. Consequences for the charge transfer mechanism in peptides are discussed.

  3. Characterization of Model Peptide Adducts with Reactive Metabolites of Naphthalene by Mass Spectrometry

    PubMed Central

    Pham, Nathalie T.; Jewell, William T.; Morin, Dexter; Jones, A. Daniel; Buckpitt, Alan R.

    2012-01-01

    Naphthalene is a volatile polycyclic aromatic hydrocarbon generated during combustion and is a ubiquitous chemical in the environment. Short term exposures of rodents to air concentrations less than the current OSHA standard yielded necrotic lesions in the airways and nasal epithelium of the mouse, and in the nasal epithelium of the rat. The cytotoxic effects of naphthalene have been correlated with the formation of covalent protein adducts after the generation of reactive metabolites, but there is little information about the specific sites of adduction or on the amino acid targets of these metabolites. To better understand the chemical species produced when naphthalene metabolites react with proteins and peptides, we studied the formation and structure of the resulting adducts from the incubation of model peptides with naphthalene epoxide, naphthalene diol epoxide, 1,2-naphthoquinone, and 1,4-naphthoquinone using high resolution mass spectrometry. Identification of the binding sites, relative rates of depletion of the unadducted peptide, and selectivity of binding to amino acid residues were determined. Adduction occurred on the cysteine, lysine, and histidine residues, and on the N-terminus. Monoadduct formation occurred in 39 of the 48 reactions. In reactions with the naphthoquinones, diadducts were observed, and in one case, a triadduct was detected. The results from this model peptide study will assist in data interpretation from ongoing work to detect peptide adducts in vivo as markers of biologic effect. PMID:22870282

  4. Using string kernel to predict signal peptide cleavage site based on subsite coupling model.

    PubMed

    Wang, M; Yang, J; Chou, K-C

    2005-06-01

    Owing to the importance of signal peptides for studying the molecular mechanisms of genetic diseases, reprogramming cells for gene therapy, and finding new drugs for healing a specific defect, it is in great demand to develop a fast and accurate method to identify the signal peptides. Introduction of the so-called {-3,-1, +1} coupling model (Chou, K. C.: Protein Engineering, 2001, 14-2, 75-79) has made it possible to take into account the coupling effect among some key subsites and hence can significantly enhance the prediction quality of peptide cleavage site. Based on the subsite coupling model, a kind of string kernels for protein sequence is introduced. Integrating the biologically relevant prior knowledge, the constructed string kernels can thus be used by any kernel-based method. A Support vector machines (SVM) is thus built to predict the cleavage site of signal peptides from the protein sequences. The current approach is compared with the classical weight matrix method. At small false positive ratios, our method outperforms the classical weight matrix method, indicating the current approach may at least serve as a powerful complemental tool to other existing methods for predicting the signal peptide cleavage site. The software that generated the results reported in this paper is available upon requirement, and will appear at http://www.pami.sjtu.edu.cn/wm. PMID:15838592

  5. Interaction of VP3(110-121) Peptide with Hepatocyte and Erythrocyte Membrane Models.

    PubMed

    Sospedra; Alsina; Haro; Mestres; Busquets

    1999-03-01

    The use of synthetic peptides in the goal of developing a new, inexpensive vaccine against hepatitis A virus is one of the encouraging approaches followed by many laboratories. These peptides have to be well characterized, being their physicochemical properties one of the most relevant points to control. In that sense, one can consider the study of the peptide interaction with lipid monolayers by means of the Wilhelmy plate method, to gain insight into the possible mechanism of action at the membrane level. The peptide chosen corresponds to the lineal epitope of hepatitis A virus VP3(110-121). As far as the lipids used are concerned, they were selected according to the composition of hepatocytes and erythrocytes because these structures seem to play an important role in hepatitis proliferation and infection. The peptide was able to accommodate into lipid monolayers. Interaction was slightly lower in the hepatocyte model than in the erythrocyte model, probably due to the presence of cholesterol in the hepatocyte membrane. Copyright 1999 Academic Press. PMID:9929444

  6. 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.

  7. Formation of Peptide Bound Pyrraline in the Maillard Model Systems with Different Lys-Containing Dipeptides and Tripeptides.

    PubMed

    Liang, Zhili; Li, Lin; Qi, Haiping; Wan, Liting; Cai, Panfu; Xu, Zhenbo; Li, Bing

    2016-01-01

    Peptide-bound advanced glycation end-products (peptide-bound AGEs) can be formed when peptides are heated with reducing saccharides. Pyrraline is the one of most commonly studied AGEs in foods, but the relative importance of the precursor peptide structure is uncertain. In the present study, model systems were prepared by heating peptides with glucose from 60 °C to 220 °C for up to 65 min, and the amounts of peptide-bound pyrraline formed were monitored to evaluate the effect of the neighboring amino acids on the peptide-bound pyrraline formation. The physico-chemical properties were introduced to explore the quantitative structure-reactivity relationships between physicochemical properties and peptide bound formation. 3-DG content in dipeptide-glucose model system was higher than that in the corresponding tripeptide-glucose model systems. Dipeptides produced higher amounts of peptide-bound pyrraline than the corresponding tripeptides. The peptide-bound pyrraline and 3-DG production were influenced by the physico-chemical properties of the side chain of amino acids adjacent to Lys in the following order: Lys-Leu/glucose > Lys-Ile/glucose > Lys-Val/ glucose > Lys-Thr/glucose > Lys-Ser/glucose > Lys-Ala/ glucose > Lys-Gly/glucose; Lys-Leu-Gly/glucose > Lys-Ile-Gly/glucose > Lys-Val-Gly/glucose > Lys-Thr-Gly/glucose > Lys-Ser-Gly/glucose > Lys-Ala-Gly/glucose > Lys-Gly-Gly/glucose. For the side chain of amino acids adjacent to Lys in dipeptides, residue volume, polarizability, molecular volume and localized electrical effect were positively related to the yield of peptide bound pyrraline, while hydrophobicity and pKb were negatively related to the yield of peptide bound pyrraline. In terms of side chain of amino acid adjacent to Lys in tripeptides, a similar result was observed, except hydrophobicity was positively related to the yield of peptide bound pyrraline. PMID:27070556

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

    SciTech Connect

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

    1995-08-01

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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Peptide neuroregulators: the opioid system as a model.

    PubMed

    Barchas, J D; Evans, C; Elliott, G R; Berger, P A

    1985-01-01

    Aaron Lerner's work provides a stunning set of examples of substances that help to transmit information in the brain and body. His characterization of alpha-MSH and melatonin and his sparking of interest in the further discovery of previously unknown substances have been of inestimable value for the field of neurobiology. Efforts such as those that Lerner undertook so successfully in the field of investigative dermatology now constitute a major research thrust in the field of behavioral neurochemistry and are directly related to advances in psychiatry and neurology. This review considers aspects of research on the neuropeptides, with particular attention to the endogenous opioid (morphine-like) peptides that are active on neural tissue. Neuropeptide research can be categorized broadly as efforts to discover and characterize new families and classes of active agents, investigations of their genetic and molecular processing, and studies of their relationships to behavior in animals and human beings. This review selectively considers some key research questions and strategies that arise from such research. PMID:2938344

  14. The Role of Cross-Chain Ionic Interactions for the Stability of Collagen Model Peptides

    PubMed Central

    Keshwani, Neelam; Banerjee, Shounak; Brodsky, Barbara; Makhatadze, George I.

    2013-01-01

    The contribution of ionic interactions to the stability of the collagen triple helix was studied using molecular dynamics (MD) simulations and biophysical methods. To this end, we examined the stability of a host-guest collagen model peptide, Ac-GPOGPOGPYGXOGPOGPO-NH2, substituting KGE, KGD, EGK, and DGK for the YGX sequence. All-atom, implicit solvent MD simulations show that the fraction of cross-chain ionic interactions formed is different, with the most pronounced in the KGE and KGD sequences, and the least in the DGK sequence. To test whether the fraction of cross-chain ionic interactions correlates with the stability, experimental measurements of thermostability were done using differential scanning calorimetry and circular dichroism spectroscopy. It was found that the melting temperature is very similar for KGE and KGD peptides, whereas the EGK peptide has lower thermostability and the DGK peptide is the least thermostable. A novel, to our knowledge, computational protocol termed temperature-scan MD was applied to estimate the relative stabilities of the peptides from MD simulations. We found an excellent correlation between transition temperatures obtained from temperature-scan MD and those measured experimentally. These results suggest the importance of cross-chain ionic interactions for the stability of collagen triple helix and confirm the utility of MD simulations in predicting interactions and stability in this system. PMID:24094409

  15. Amyloidβ Peptides in interaction with raft-mime model membranes: a neutron reflectivity insight

    PubMed Central

    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

  16. What determines the activity of antimicrobial and cytolytic peptides in model membranes.

    PubMed

    Clark, Kim S; Svetlovics, James; McKeown, Alesia N; Huskins, Laura; Almeida, Paulo F

    2011-09-20

    We previously proposed three hypotheses relating the mechanism of antimicrobial and cytolytic peptides in model membranes to the Gibbs free energies of binding and insertion into the membrane [Almeida, P. F., and Pokorny, A. (2009) Biochemistry 48, 8083-8093]. Two sets of peptides were designed to test those hypotheses, by mutating of the sequences of δ-lysin, cecropin A, and magainin 2. Peptide binding and activity were measured on phosphatidylcholine membranes. In the first set, the peptide charge was changed by mutating basic to acidic residues or vice versa, but the amino acid sequence was not altered much otherwise. The type of dye release changed from graded to all-or-none according to prediction. However, location of charged residues in the sequence with the correct spacing to form salt bridges failed to improve binding. In the second set, the charged and other key residues were kept in the same positions, whereas most of the sequence was significantly but conservatively simplified, maintaining the same hydrophobicity and amphipathicity. This set behaved completely different from predicted. The type of release, which was expected to be maintained, changed dramatically from all-or-none to graded in the mutants of cecropin and magainin. Finally, contrary to the hypotheses, the results indicate that the Gibbs energy of binding to the membrane, not the Gibbs energy of insertion, is the primary determinant of peptide activity. PMID:21870782

  17. Amyloidβ 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

  18. 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) instrument have been completed. Thermochromatography is a technique that can be used to study the volatility and {Delta}H{sub a} of longer-lived isotopes off-line, Future work will include a comparison between the two techniques and the use of thermochromatography to study isotopes in a wider range of half-lives and molecular structures.

  19. The peptide-catalyzed stereospecific synthesis of tetroses: a possible model for prebiotic molecular evolution.

    PubMed

    Weber, Arthur L; Pizzarello, Sandra

    2006-08-22

    Using a water-based prebiotic model of sugar synthesis involving glycolaldehyde self-condensation, we demonstrate that homochiral L-dipeptide catalysts lead to the stereospecific syntheses of tetroses. The asymmetric effect is largest for erythrose, which may reach a D-enantiomeric excess of >80% with L-Val-L-Val catalyst. Based on results obtained with various peptides, we propose a possible catalytic-reaction intermediate, consisting of an imidazolidinone ring formed between the two nitrogen atoms of the peptide catalyst and the C1 of one glycolaldehyde molecule. The study was motivated by the premise that exogenous material, such as the nonracemic amino acids found in meteorites, could have participated in the terrestrial evolution of molecular asymmetry by stereospecific catalysis. Because peptides might have formed readily on the early Earth, it is possible that their catalytic contribution was relevant in the prebiotic processes that preceded the onset of life. PMID:16905650

  20. Action spectroscopy of a protonated peptide in the ultraviolet range.

    PubMed

    Canon, Francis; Milosavljević, Aleksandar R; Nahon, Laurent; Giuliani, Alexandre

    2015-10-21

    Action spectroscopy of protonated substance P, a model undecapeptide, has been probed from 5.2 eV to 20 eV. For photon energy above the ionization threshold measured at 10.3 ± 0.1 eV, the radical dication is observed along with side chain losses and abundant formation of all kinds of sequence ions. Below the photoionization threshold, the photoproducts involve side chain cleavages and backbone cleavages into a-, b-/y-, and c-sequence ions. Different electronic excited states appear to produce different fragment ions. Norrish type I and II reactions are proposed to account for some photoproducts. This study bridges the gap between laser activation and electron-induced dissociation of peptides. Moreover, our results report for the first time a comprehensive picture of the photochemical fragmentation of a gas phase peptide in a wide photon energy range. PMID:25586594

  1. Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification.

    PubMed

    Fu, Yan; Gao, Wen; He, Simin; Sun, Ruixiang; Zhou, Hu; Zeng, Rong

    2007-01-01

    The assumption on the mass error distribution of fragment ions plays a crucial role in peptide identification by tandem mass spectra. Previous mass error models are the simplistic uniform or normal distribution with empirically set parameter values. In this paper, we propose a more accurate mass error model, namely conditional normal model, and an iterative parameter learning algorithm. The new model is based on two important observations on the mass error distribution, i.e. the linearity between the mean of mass error and the ion mass, and the log-log linearity between the standard deviation of mass error and the peak intensity. To our knowledge, the latter quantitative relationship has never been reported before. Experimental results demonstrate the effectiveness of our approach in accurately quantifying the mass error distribution and the ability of the new model to improve the accuracy of peptide identification. PMID:17990507

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. The gas phase acidities of substituted silanoic acids

    NASA Astrophysics Data System (ADS)

    Remko, Milan

    Ab initio molecular orbital methods at the CBS-Q level of theory have been used to study the structure, gas phase acidities and vibrational spectra of silanoic acid, HSiO2H, and several of its derivatives RSiO2H (R = F, Cl, NH2, OH and CH3). Geometry optimizations were performed at the MP2(FC)/6-31G(†) level of theory. The syn forms always are more stable than the anti. The silanoic acid derivatives are more acidic than their parent oxygen acid analogues. The fundamental vibrational frequencies have been computed using the MP2(Full)/6-31G(d) method. The ν(Si=O) = 1261 cm-1 value agrees with the experimentally determined normal mode (1249 cm-1) in silanoic acid.

  7. Gas-phase syntheses for interstellar carboxylic and amino acids

    NASA Astrophysics Data System (ADS)

    Blagojevic, Voislav; Petrie, Simon; Bohme, Diethard K.

    2003-02-01

    We report experimental results that demonstrate gas-phase, ionic syntheses of glycine and β-alanine, as well as acetic and propanoic acid, from smaller molecules found in space; in doing so, we infer the formation of these acids in the interstellar environment. We show that ionized glycine and β-alanine are produced in the reactions of hydroxylamine ions, NH2OH+, with acetic and propanoic acid respectively. Even more promising in the context of interstellar synthesis are our results that demonstrate the corresponding production of the protonated amino acids from analogous reactions with protonated hydroxylamine. The striking specificity of these syntheses for the β-isomer of alanine suggests that the amino acids of CI (Carbonaceous Ivona) chondrite meteorites are products of interstellar chemistry and supports the hypothesis that these meteorites are of cometary origin.

  8. 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

  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. Ceramic microreactors for heterogeneously catalysed gas-phase reactions.

    PubMed

    Knitter, Regina; Liauw, Marcel A

    2004-08-01

    The high surface to volume ratio of microchannel components offers many advantages in micro chemical engineering. It is obvious, however, that the reactor material and corrosion phenomena play an important role when applying these components. For chemical reactions at very high temperatures or/and with corrosive reactants involved, microchannel components made of metals or polymers are not suited. Hence, a modular microreactor system made of alumina was developed and fabricated using a rapid prototyping process chain. With exchangeable inserts the system can be adapted to the requirements of various reactions. Two heterogeneously catalysed gas-phase reactions (oxidative coupling of methane, isoprene selective oxidation to citraconic anhydride) were investigated to check the suitability of the system at temperatures of up to 1000 degrees C. Apart from the high thermal and chemical resistance, the lack of any blind activity was found to be another advantage of ceramic components. PMID:15269808

  12. Excited-state tautomerization of gas-phase cytosine.

    PubMed

    Triandafillou, Catherine G; Matsika, Spiridoula

    2013-11-21

    In order to investigate experimentally observed phototautomerization of gas-phase cytosine, several excited-state tautomerization mechanisms were characterized at the EOM-CCSD and TDDFT levels. All pathways that took place exclusively on the S1 surface were found to have significant barriers that were much higher than the barriers involved in radiationless decay of cytosine tautomers through conical intersections back to the ground state; tautomerization in this fashion cannot compete with radiationless relaxation. However, an alternative possibility is that the conical intersections that facilitate radiationless decay could also facilitate tautomerization. Barrierless pathways indicate that it is energetically possible that bifurcation at the conical intersections can lead to a subset of the population reaching different tautomers. This could be an explanation for the observed tautomerization of keto cytosine after exposure to low-energy UV light. PMID:24094271

  13. 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.

  14. Reduced-background gas-phase absorption spectroscopy.

    PubMed

    Sweetser, J N; Trebino, R

    1998-08-15

    We propose and demonstrate a new method for single-shot multiplex absorption spectroscopy that permits enhanced sensitivity in the simultaneous measurement of multiple spectral lines in rapidly changing gas-phase media, such as turbulent flames. It uses an ultrashort laser pulse that propagates through the absorbing medium, for which the relevant absorption information resides in the free-induction decay that is trailing behind the transmitted pulse. Time gating out most of the transmitted pulse, but not the free-induction decay, enhances the relative fraction of light that contains absorption information when the spectrum is measured. This procedure reduces the background associated with the input light, thus enhancing detection sensitivity. PMID:18087501

  15. Low-energy electron collisions with gas-phase uracil.

    PubMed

    Winstead, Carl; McKoy, Vincent

    2006-11-01

    We have studied gas-phase collisions between slow electrons and uracil molecules with a view to understanding the resonance structure of the scattering cross section. Our symmetry-resolved results for elastic scattering, computed in the fixed-nuclei, static-exchange and static-exchange-plus-polarization approximations, provide locations for the expected pi* shape resonances and indicate the possible presence of a low-energy sigma* resonance as well. Electron-impact excitation calculations were carried out for low-lying triplet and singlet excitation channels and yield a very large singlet cross section. We discuss the connection between the resonances found in our elastic cross section and features observed in dissociative attachment. PMID:17100436

  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. PMID:23382211

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

    PubMed

    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

  18. Investigating site-specific effects of the -X glutamate in a parvalbumin CD site model peptide.

    PubMed

    Franchini, P L; Reid, R E

    1999-12-01

    The -X glutamate in a 33-residue model peptide comprising the CD site of carp parvalbumin 4.25 (ParvCD) was replaced with aspartate (ParvCD-XD) and the effect on calcium-dependent dimerization and calcium affinity assessed. The peptide ParvCD demonstrates a 10(5)-fold lower calcium affinity than the same site in the native protein. Both the ParvCD and ParvCD-XD model peptides fail to bind magnesium. The low calcium affinity and failure of the model ParvCD site to bind magnesium may be due to higher enthalpic costs of chelation by the -X glutamate. Replacement of the -X glutamate with an aspartate resulted in a twofold increase in the calcium affinity of both the monomer and dimer forms and a twofold increase in the calcium dependent dimerization of the peptide. A -X glutamate to aspartate replacement in 33-residue model peptides corresponding to bovine brain calmodulin site 3 (R. M. Procyshyn and R. E. Reid, Arch. Biochem. Biophys. 311, 425-429, 1994) and in Escherichia coli d-galactose-binding protein (S. K. Drake, K. L. Lee, and J. J. Falke, Biochemistry 35, 6697-6705, 1996) agree with results in the ParvCD site. However, in rat oncomodulin a -X glutamate to aspartate replacement increases calcium affinity (R. C. Hapak, P. J. Lammers, W. A. Palmisano, E. R. Birnbaum, and M. T. Henzl, J. Biol. Chem. 264, 18751-18760, 1989). The different effect of a -X glutamate to aspartate substitution in the different sites suggests site-specific factors dictating the thermodynamic contribution of the -X glutamate to calcium affinity. PMID:10562419

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

    Feketeov, Linda; Chan, Bun; Khairallah, George N; Steinmetz, Vincent; Matre, 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 ionmolecule 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

  3. Neutral-Neutral Gas-Phase Reactions In Extraterrestrial Environments: Laboratory Investigations By Crossed Molecular Beams

    NASA Astrophysics Data System (ADS)

    Balucani, Nadia; Casavecchia, Piergiorgio

    2006-09-01

    In this contribution we report experimental results obtained by the crossed molecular beam technique with mass spectrometric detection on several neutral-neutral gas-phase reactions of relevance in astrochemistry. More specifically, we provide experimental evidence that the reactions of electronically excited state nitrogen atoms, N(2D), with several hydrocarbons observed in the atmosphere of Titan can generate molecular products containing a novel CN bond, thus suggesting possible routes towards the production of gas-phase nitriles in that environment. We also report on the reaction between C(3P) and acetylene, an important neutral-neutral reaction in the chemistry of interstellar clouds. The branching ratio between the cyclic and linear C3H isomers has been derived for a collision energy of 3.5 kJ mol-1. Further evidence of the occurrence of the C3 formation channel is given. Finally we report on recent studies of reactions involving two open shell species, namely O+CH3 and O+C3H5. Products other than those already considered in the modeling of planetary atmospheres and interstellar medium have been identified.

  4. First Detection of Gas-phase Methanol in a Protoplanetary Disk

    NASA Astrophysics Data System (ADS)

    Walsh, Catherine; Loomis, Ryan A.; Öberg, Karin I.; Kama, Mihkel; van ’t Hoff, Merel L. R.; Millar, Tom J.; Aikawa, Yuri; Herbst, Eric; Widicus Weaver, Susanna L.; Nomura, Hideko

    2016-05-01

    The first detection of gas-phase methanol in a protoplanetary disk (TW Hya) is presented. In addition to being one of the largest molecules detected in disks to date, methanol is also the first disk organic molecule with an unambiguous ice chemistry origin. The stacked methanol emission, as observed with the Atacama Large Millimeter/submillimeter Array, is spectrally resolved and detected across six velocity channels (\\gt 3σ ), reaching a peak signal-to-noise of 5.5σ , with the kinematic pattern expected for TW Hya. Using an appropriate disk model, a fractional abundance of 3× {10}-12{--}4× {10}-11 (with respect to H2) reproduces the stacked line profile and channel maps, with the favored abundance dependent upon the assumed vertical location (midplane versus molecular layer). The peak emission is offset from the source position, suggesting that the methanol emission has a ring-like morphology: the analysis here suggests it peaks at ≈ 30 {{au}}, reaching a column density ≈ 3{--}6× {10}12 cm‑2. In the case of TW Hya, the larger (up to millimeter-sized) grains, residing in the inner 50 au, may thus host the bulk of the disk ice reservoir. The successful detection of cold gas-phase methanol in a protoplanetary disk implies that the products of ice chemistry can be explored in disks, opening a window into studying complex organic chemistry during planetary system formation.

  5. Algorithmically designed peptides ameliorate behavioral defects in animal model of ADHD by an allosteric mechanism.

    PubMed

    Kinkead, Becky; Selz, Karen A; Owens, Michael J; Mandell, Arnold J

    2006-02-15

    This study exemplifies the use of three ADHD-relevant methodological innovations. (1) The use of novel, patented, computational peptide design techniques to generate peptides targeting the extra-cellular and para-transmembrane amino acid loops of the putatively ADHD-involved, D(2) dopamine receptor, D(2)DAR; (2) experimental evidence that these peptides in L-amino acid/ortho ordered or D-amino acid/reverse ordered (retro-inverso), D(2)DAR, hydrophobic eigenmode matched forms, evoked positive allosteric and indirect agonist influences on in vitro stably receptor transfected CHO and LtK cells and on in vivo, brain mediated activity; (3) a representative 15 residue all-D-amino acid, D(2) mode matched peptide, given parenterally, was found to "repair" a key aberrant ADHD behavioral characteristic in a standard animal model of ADHD, the Spontaneously Hypertensive Rat, SHR, relative to its progenitor species control, the Wistar-Kyoto rat, WKY. The representative, retro-inverso peptide, all-D-LLYKNKPRYPKRNRE, reversed SHR's relative deficiency in sensory motor gating (pre-pulse inhibition, PPI) while leaving SHR's nonselective attention (rearings), impulsive behavior (time in center), and activity level (timed total motor behavior) unchanged. Amphetamine also reversed SHRs sensory gating defect, but with significant increases in nonselective attention, impulsivity and hyperactivity. These preliminary results suggest the possibility of a new, "softer" pharmacological approach to ADHD: hydrophobic mode matched peptide allosteric augmentation of the activity of indigenous dopamine with respect to D(2)DAR mediated function, in place of stimulant drug-induced presynaptic dopamine release or impairment of dopamine uptake. PMID:16423408

  6. 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

  7. Gas-phase Mechanisms of Sulfur Isotope Mass-independent Fractionation

    NASA Astrophysics Data System (ADS)

    Lyons, J. R.

    2006-12-01

    Mass-independent fractionation (MIF) in sulfur isotopes in ancient sulfur-bearing rocks (Farquhar et al. 2000a) is interpreted as evidence for gas-phase MIF processes in the early Earth atmosphere. This interpretation is made by analogy with oxygen isotope MIF in the modern atmosphere (produced during ozone formation), and by laboratory photolysis experiments on SO2 (Farquhar et al. 2001; Wing et al. 2004) that yield both elemental sulfur and sulfate with S MIF signatures at wavelengths above and below the SO2 dissociation limit. What is lacking is a quantitative understanding of the mechanisms of gas-phase S MIF. Quantification is essential in order to extract the full implications of sulfur MIF throughout Earth history, including for bacterial sulfate reduction processes which largely conserve D33S and D36S. Several sulfur MIF mechanisms are possible. The most obvious is the gas-phase thiozone reaction, which is isovalent to the ozone formation reaction. Ozone formation produces a well-known MIF signature in oxygen isotopes (Thiemens and Heidenreich 1983), and a symmetry-dependent non-RRKM mechanism has been proposed as the origin of O MIF (Gao and Marcus 2001). It is possible and perhaps likely that S3 formation also proceeds by a non-RRKM process. Data are lacking on isotopic (an even non-isotopic) rates of S3 formation, so it is not possible to make definitive statements about MIF in S3 at this time. However modeling results suggest that the vapor pressure of S2 is too low for gas-phase S3 formation to be significant. Two additional species that may exhibit a non-RRKM MIF signature are S2O2 and S4. Again, there is a lack of isotopomer-specific kinetic data for these reactions, and gas-phase formation of S4 is likely inconsequential. Perhaps the most obvious mechanism is simply the primary act of SO2 photolysis. The SO2 absorption spectrum is highly structured, with strong vibronic bands above and below the dissociation limit. In contrast H2S, with its mostly unstructured absorption spectrum, yields a small MIF signature (Farquhar et al. 2000b; Wing pers. comm.). The modeling work of Pavlov and Kasting (2002) assigned MIF to SO2 and SO photodissociation, but without specifying a mechanism. I have preformed radiative transfer modeling of a column of SO2 gas with all sulfur isotopologues included, and observe a large mass-dependent fractionation associated with small frequency shifts. Larger frequency shifts, as would be expected for high vibrational quantum numbers in the upper state, yield MIF signatures; anharmonic effects may be evident in these MIF signatures. Additionally, some vibronic bands are rotationally resolved, and line-type self-shielding also leads to a MIF signature. The significance of these results for the ancient atmosphere will be discussed. References Farquhar, J. et al. (2000a) Science 289, 756-758. Farquhar, J. et al. (2000b) Nature 404, 50-52. Farquhar, J. et al. (2001) J. Geophys. Res. 106, 32829-32839. Gao, Y. and R. Marcus (2001) Science 293, 259-263. Pavlov, A. A. and J. F. Kasting, (2002) Astrobiology 2, 27-41. Savarino, J. et al. (2003) Geophys. Res. Lett. 30, 11-1, 11-4. Thiemens, M. H. and H. Heindenreich, Science 219, 1073-1075. Wing, B. et al. (2004) 228th ACS meeting, Aug. 22-26, Philadelphia.

  8. 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.

  9. Model-based description of peptide retention on doped reversed-phase media.

    PubMed

    Khalaf, Rushd; Forrer, Nicola; Buffolino, Gianluca; Butté, Alessandro; Morbidelli, Massimo

    2015-08-14

    Reversed-phase (RP) chromatography is one of the main tools for the preparative purification of therapeutic peptides. In previous works [1,2], a new type of RP chromatography, doped reversed-phase chromatography (DRP) was presented. By adding small amounts (up to 15% of the surface ligands) of repulsive ion exchange ligands to a traditional RP material, significant improvements in peptide purification performance were observed, at the same or in similar operating conditions. These improvements included increases in selectivity in diluted conditions (up to twice as high), increases in yield in preparative conditions (up to 20% higher) and in productivity in preparative conditions (up to twice as high), when compared to RP materials [2]. A proper physical model is developed in this work to quantitatively explain and rationalize this behavior. The developed model is then used to correctly fit the retention data of several peptides in different buffering conditions. The increase in selectivity is related to a controlled decrease in free surface area available for adsorption due to the ionic ligands creating a repulsive sphere the analytes cannot enter. This decrease in adsorption surface is calculated using Debye-Hückel theory, and in combination with linear solvent strength theory, allows for the quantitative description of peptide retention on DRP media. PMID:26150253

  10. 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.

  11. Platinum-mediated coupling of methane and small nucleophiles (H{sub 2}O, PH{sub 3}, H{sub 2}S, CH{sub 3}NH{sub 2}) as a model for C-N, C-O, C-P, and C-S bond formation in the gas phase

    SciTech Connect

    Broenstrup, M.; Schroeder, D.; Schwarz, H.

    1999-05-10

    The reactions of Pt{sup +} and PtCH{sub 2}{sup +} with the nucleophiles H{sub 2}O, PH{sub 3}, H{sub 2}S, HCl, CH{sub 3}NH{sub 2}, and CH{sub 3}OH are studied by Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry. In the reactions of PtCH{sub 2}{sup +}, carbon-heteroatom bond formation can be accomplished for all substrates except CH{sub 3}OH and HCl. The reaction of PtCH{sub 2}{sup +} with two molecules of water yields Pt(CO)(H{sub 2}O){sup +} and constitutes a gas-phase model for the platinum-mediated generation of water gas according to CH{sub 4} + H{sub 2}O {r_arrow} CO + 3H{sub 2}. In the reactions with PH{sub 3} and H{sub 2}S, carbon-phosphorus and carbon-sulfur bond formation to PtCPH{sup +} and PtCS{sup +} competes with demethanation and dehydrogenation of the substrates to yield PtS{sub n}{sup +} (n = 1--4) and PtP{sub n}H{sub m}{sup +} (n = 1--6; m = 0--3) compounds, respectively. For organic nucleophiles such as CH{sub 3}NH{sub 2} and CH{sub 3}OH, C-N and C-O coupling is much less efficient than platinum-mediated C-H bond activation of the substrates.

  12. Dissociation of Peptides by Ions and Photons

    NASA Astrophysics Data System (ADS)

    Bari, Sadia

    2015-05-01

    Little is known about biological radiation action on the molecular level. The response of isolated biomolecules upon energetic photons is of great interest i.e. for astrobiology and radiobiology. Key questions concern ion chemistry in the interstellar medium, possible transport of biomolecules from space to earth and molecular mechanisms underlying biological radiation damage. Experiments with small biomolecules in the gas phase have the advantage of studying ionization and fragmentation dynamics in finite systems but are less realistic radiation damage models. To be able to investigate more complex biomolecular systems, such as peptides and proteins, we have developed a new apparatus in which a home-made electrospray source can be interfaced with a low energy (keV) ion beamline or different photon beamlines (e.g. of synchrotrons or free electron lasers). Spectra of peptides obtained with this set-up will be presented. Dependencies on energy and polarization of the radiation as well as peptide length and structure will be thereby discussed.

  13. Urea unfolding of peptide helices as a model for interpreting protein unfolding.

    PubMed Central

    Scholtz, J M; Barrick, D; York, E J; Stewart, J M; Baldwin, R L

    1995-01-01

    To provide a model system for understanding how the unfolding of protein alpha-helices by urea contributes to protein denaturation, urea unfolding was measured for a homologous series of helical peptides with the repeating sequence Ala-Glu-Ala-Ala-Lys-Ala and chain lengths varying from 14 to 50 residues. The dependence of the helix propagation parameter of the Zimm-Bragg model for helix-coil transition theory (s) on urea molarity ([urea]) was determined at 0 degree C with data for the entire set of peptides, and a linear dependence of In s on [urea] was found. The results were fitted by the binding-site model and by the solvent-exchange model for the interaction of urea with the peptides. Each of these thermodynamic models is able to describe the data quite well and we are not able to discern any difference between the ability of each model to fit the data. Thus a linear relation, ln s = ln s0 - (m/RT).[urea], fits the data for alpha-helix unfolding, just as others have found for protein unfolding. When the m value determined here for alpha-helix unfolding is multiplied by the number of helical residues in partly helical protein molecules, the resulting values agree within a factor of 2 with observed m values for these proteins. This result indicates that the interaction between urea and peptide groups accounts for a major part of the denaturing action of urea on proteins, as predicted earlier by some model studies with small molecules. PMID:7816813

  14. Selective and sensitive chromogenic detection of cyanide and HCN in solution and in gas phase.

    PubMed

    Gotor, Raúl; Costero, Ana M; Gil, Salvador; Parra, Margarita; Martínez-Máñez, Ramón; Sancenón, Félix; Gaviña, Pablo

    2013-06-25

    Two triphenylmethane based chemodosimeters for selective and chromogenic sensing of cyanide anions in aqueous environments and of hydrogen cyanide in gas phase were prepared and studied. PMID:23680816

  15. Left-handed and ambidextrous helices in the gas phase.

    PubMed

    Sudha, Rajagopalan; Jarrold, Martin F

    2005-06-16

    We have used ion mobility mass spectrometry to study the effect of d-residues on helix formation in unsolvated alanine-based peptides. The right-handed helix of AC-A15K + H+ is significantly disrupted when five or more of the natural L-residues are randomly replaced with D-residues. On the other hand, when a block of L-residues is replaced with D-residues, an unusual ambidextrous structure with helical segments of opposite chirality is formed. A peptide with all D-residues forms a left-handed helix. PMID:16852446

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

    ERIC Educational Resources Information Center

    Mendes, Debora 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

  17. 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…

  18. Gas-phase supersaturation effects on morphology properties of ZnO nano and microstructures grown by PVT

    NASA Astrophysics Data System (ADS)

    Montenegro, D. N.; Martínez Tomas, M. C.; Muñoz Sanjosé, V.; Sallet, V.

    2016-02-01

    A systematic study of the morphology evolution of ZnO nanostructures grown by physical vapour transport was carried out. The evolution of the shape with the growth time is shown to depend on the different gas-phase supersaturation and temperature conditions encountered in the crystallization zone of the tube furnace. The observed morphology transitions are discussed, and a growth model for ZnO nanostructures is given.

  19. Novel Detox Gel Depot sequesters β-Amyloid Peptides in a mouse model of Alzheimer's Disease.

    PubMed

    Sundaram, Ranjini K; Kasinathan, Chinnaswamy; Stein, Stanley; Sundaram, Pazhani

    2012-06-01

    Alzheimer's Disease (AD), a debilitating neurodegenerative disease is caused by aggregation and accumulation of a 39-43 amino acid peptide (amyloid β or Aβ) in brain parenchyma and cerebrovasculature. The rational approach would be to use drugs that interfere with Aβ-Aβ interaction and disrupt polymerization. Peptide ligands capable of binding to the KLVFF (amino acids 16-20) region in the Aβ molecule have been investigated as possible drug candidates. Retro-inverso (RI) peptide of this pentapeptide, ffvlk, has been shown to bind artificial fibrils made from Aβ with moderate affinity. We hypothesized that a 'detox gel', which is synthesized by covalently linking a tetrameric version of RI peptide ffvlk to poly (ethylene glycol) polymer chains will act like a 'sink' to capture Aβ peptides from the surrounding environment. We previously demonstrated that this hypothesis works in an in vitro system. The present study extended this hypothesis to an in vivo mouse model of Alzheimer's Disease and determined the therapeutic effect of our detox gel. We injected detox gel subcutaneously to AD model mice and analyzed brain levels of Aβ-42 and improvement in memory parameters. The results showed a reduction of brain amyloid burden in detox gel treated mice. Memory parameters in the treated mice improved. No undesirable immune response was observed. The data strongly suggest that our detox gel can be used as an effective therapy to deplete brain Aβ levels. Considering recent abandonment of failed antibody based therapies, our detox gel appears to have the advantage of being a non-immune based therapy. PMID:22712003

  20. 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. PMID:25375223

  1. 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 ...

  2. Substrate-free gas-phase synthesis of graphene

    NASA Astrophysics Data System (ADS)

    Dato, Albert Manglallan

    Graphene is a single atomic layer of sp2-bonded carbon atoms tightly packed in a two-dimensional honeycomb lattice. The material possesses remarkable properties and has been envisioned for use in numerous applications. Contemporary graphene production techniques require substrates or graphite crystals to create graphene. Furthermore, these approaches involve multiple steps, and sometimes non-ambient conditions, to produce atomically-thin sheets. This dissertation presents the first substrate-free gas-phase graphene synthesis method. The technique can synthesize graphene in a single step at atmospheric pressure, without the use of graphite or substrates. The novel synthesis method was discovered through experiments that tested the hypothesis that graphene could be synthesized through the delivery of alcohols into argon plasmas. The experiments presented in this dissertation were conducted in an atmospheric-pressure microwave plasma reactor. Solid carbon materials were produced by delivering liquid ethanol droplets directly into argon plasmas. Numerous characterization techniques were used to unambiguously prove that the synthesized materials were clean and highly ordered graphene sheets. Additional studies investigated the effects of variable experimental parameters on the graphene synthesis process. The applied microwave power did not significantly affect the types of structures produced in the reactor. Lowering the volumetric flow rate of the plasma gas resulted in the synthesis of graphitic particles. The composition of the precursors delivered into the reactor also affected graphene synthesis. Graphene was not produced through the delivery of methanol or isopropyl alcohol droplets. However, graphene was obtained through dimethyl ether, which is an organic compound with the same atomic composition as ethanol. Thus, the flow rate and precursor composition significantly affected the nucleation, growth, and residence time of the materials created during experiments. A practical application for the synthesized graphene is also presented in this dissertation. The sheets were found to be an ideal support structure for the transmission electron microscopy characterization of nanoparticles coated with molecular layers. The substrate-free gas-phase method is capable of rapid and continuous graphene synthesis at ambient pressure. The simplicity of the approach makes it scalable for industrial graphene production. The novel technique presented in this dissertation could substantially enable graphene research and applications.

  3. Sol-gel transition of charged fibrils composed of a model amphiphilic peptide.

    PubMed

    Owczarz, Marta; Bolisetty, Sreenath; Mezzenga, Raffaele; Arosio, Paolo

    2015-01-01

    We characterized the sol-gel transition of positively charged fibrils composed of the model amphiphilic peptide RADARADARADARADA (RADA 16-I) using a combination of microscopy, light scattering, microrheology and rheology techniques, and we investigated the dependence of the hydrogel formation on fibril concentration and ionic strength. The peptide is initially present as a dispersion of short rigid fibrils with average length of about 100 nm. During incubation, the fibrils aggregate irreversibly into longer fibrils and fibrillar aggregates. At peptide concentrations in the range 3-6.5 g/L, the fibrillar aggregates form a weak gel network which can be destroyed upon dilution. Percolation occurs without the formation of a nematic phase at a critical peptide concentration which decreases with increasing ionic strength. The gel structure can be well described in the frame of the fractal gel theory considering the network as a collection of fibrillar aggregates characterized by self-similar structure with a fractal dimension of 1.34. PMID:25441357

  4. 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

  5. Simulations of Gas-Phase Chemical Reactions: Applications to SN2 Nucleophilic Substitution.

    PubMed

    Hase, W L

    1994-11-11

    Computer simulations and animations of the motion of atoms as a chemical reaction proceeds give a detailed picture of how the reaction occurs at a microscopic level. This information is particularly useful for testing the accuracy of statistical models, which are used to calculate various attributes of chemical reactions. Such simulations and animations, in concert with experimental and ab initio studies, have begun to provide a microscopic picture of the intimate details of a particular class of gas-phase ion-molecule bimolecular reactions known as S(N)2 nucleophilic substitution. In these reactions, a nucleophile is displaced from a molecule by another nucleophile. The dynamical model of S(N)2 reactions that emerges from the computer studies, and its relation to statistical theories, is discussed here. PMID:17779941

  6. 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.

  7. 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

  8. Comparative modeling of human kappa opioid receptor and docking analysis with the peptide YFa.

    PubMed

    Patra, Mahesh Chandra; Kumar, Krishan; Pasha, Santosh; Chopra, Madhu

    2012-03-01

    The kappa opioid receptor belongs to the super family of G protein - coupled receptors that are of utmost significance in the development of potent analgesic drugs for the treatment of severe pain. An accurate evaluation of the ligand binding pathways into this receptor at molecular level may play a key role in the design of new molecules with more desirable properties and reduced side effects. In this study, homology model of the human kappa opioid receptor was developed by MODELLER using the X-ray crystal structure of bovine rhodopsin as template. Initial structure of the receptor was refined computationally with energy minimization and molecular dynamics simulation at 300 K in a pre-equilibrated phospholipid bilayer by GROMACS. The Met-enkaphalin-Arg-Phe based opioid peptide YFa (YGGFMKKKFMRF) designed and characterized by our laboratory was docked into the optimized model and the critical amino acids responsible for binding were identified. A number of low energy binding poses of YFa with the receptor were assessed after the molecular docking in which the peptide was observed to interact with the receptor's extracellular amino acids through hydrogen bonds. The human kappa opioid receptor model optimized in a phospholipid bilayer should provide a good starting point for further characterization of the binding modes of other opioid ligands. Furthermore, the biologically favorable molecular interactions between YFa and human kappa opioid receptor observed by our study might be able to justify the specificity of this peptide. PMID:22172315

  9. Nephrilin peptide modulates a neuroimmune stress response in rodent models of burn trauma and sepsis

    PubMed Central

    Mascarenhas, Desmond D; ElAyadi, Amina; Singh, Baljit K; Prasai, Anesh; Hegde, Sachin D; Herndon, David N; Finnerty, Celeste C

    2013-01-01

    Sepsis occurs three times more often in burns than in other types of trauma, suggesting an overlap or synergy between underlying immune mechanisms in burn trauma and sepsis. Nephrilin peptide, a designed inhibitor of mTORC2, has previously been shown to modulate a neuroimmune stress response in rodent models of xenobiotic and metabolic stress. Here we investigate the effect of nephrilin peptide administration in different rodent models of burn trauma and sepsis. In a rat scald burn model, daily subcutaneous bolus injection of 4 mg/kg nephrilin significantly reduced the elevation of kidney tissue substance P, S100A9 gene expression, PMN infiltration and plasma inflammatory markers in the acute phase, while suppressing plasma CCL2 and insulin C-peptide, kidney p66shc-S36 phosphorylation and PKC-beta and CGRP in dorsal root ganglia at 14 days (chronic phase). In the mouse cecal ligation and puncture model of sepsis, nephrilin fully protected mice from mortality between surgery and day 7, compared to 67% mortality in saline-treated animals, while significantly reducing elevated CCL2 in plasma. mTORC2 may modulate important neuroimmune responses in both burn trauma and sepsis. PMID:24273694

  10. 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.

  11. 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. PMID:26988873

  12. Basic amphipathic model peptides: Structural investigations in solution, studied by circular dichroism, fluorescence, analytical ultracentrifugation and molecular modelling

    NASA Astrophysics Data System (ADS)

    Mangavel, C.; Sy, D.; Reynaud, J. A.

    1999-05-01

    A twenty amino acid residue long amphipathic peptide made of ten leucine and ten lysine residues and four derivatives, in which a tryptophan, as a fluorescent probe, is substituted for a leucine, are studied. The peptides in water are mainly in an unordered conformation (~90%), and undergo a two state reversible transition upon heating, leading to a partially helical conformation (cold denaturation). Time resolved fluorescence results show that fluorescence decay for the four Trp containing peptides is best described by triple fluorescence decay kinetics. In TFE/water mixture, peptides adopt a single α-helix conformation but the Leu-Trp9 substitution leads to an effective helix destabilizing effect. In salted media, the peptides are fully helical and present a great tendency to self associate by bringing the hydrophobic faces of helices into close contact. This proceeds in non-cooperative multisteps leading to the formation of α helix aggregates with various degrees of complexation. Using modelling, the relative hydrophobic surface areas accessible to water molecules in n-mer structures are calculated and discussed. Nous avons étudié un peptide amphipathique composé de dix lysine et dix leucine, ainsi que quatre dérivés comportant un résidu tryptophane pour les études par fluorescence. Dans l'eau, les peptides ne sont pas structurés (~90%), et se structurent partiellement en hélice α par chauffage (dénaturation froide). Les mesures de déclin de fluorescence font apparaître une cinétique à trois temps de vie. Dans un mélange eau/TFE, les peptides adoptent une conformation en hélice α, mais la substitution Leu-Trp9 possède un effet déstabilisant. En mileu salin, les peptides sont totalement hélicoïdaux et ont tendance à s'agréger de façon à regrouper leur face hydrophobe. Ce processus se fait en plusieurs étapes avec des agrégats de taille variable. L'existence de tels agrégats est discutée sur la base de la modélisation moléculaire complétée par des calculs d'accessibilité des surfaces hydrophobes.

  13. Solvation models and computational prediction of orientations of peptides and proteins in membranes.

    PubMed

    Lomize, Andrei L; Pogozheva, Irina D

    2013-01-01

    Membrane-associated peptides and proteins function in the highly heterogeneous environment of the lipid bilayer whose physico-chemical properties change non-monotonically along the bilayer normal. To simulate insertion of peptides and proteins into membranes and correctly reproduce the energetics of this process, an adequate solvation model and physically realistic representation of the lipid bilayer should be employed. We present a brief overview of the existing solvation models and their application for prediction of binding affinities and orientations of proteins in membranes. Particular emphasis is placed on the recently proposed PPM method, the corresponding web server, and the OPM database that were designed for positioning in membranes of integral and peripheral proteins with known three-dimensional structures. PMID:23975775

  14. Infrared spectroscopy of pyrrole-2-carboxaldehyde and its dimer: A planar β-sheet peptide model?

    NASA Astrophysics Data System (ADS)

    Rice, Corey A.; Dauster, Ingo; Suhm, Martin A.

    2007-04-01

    Intermolecular interactions relevant for antiparallel β-sheet formation between peptide strands are studied by Fourier transform infrared spectroscopy of the low temperature, vacuum-isolated model compound pyrrole-2-carboxaldehyde and its dimer in the N-H and C O stretching range. Comparison to quantum chemical predictions shows that even for some triple-zeta quality basis sets, hybrid density functionals and Møller-Plesset perturbation calculations fail to provide a consistent and fully satisfactory description of hydrogen bond induced frequency shifts and intensity ratios in the double-harmonic approximation. The latter approach even shows problems in reproducing the planar structure of the dimer and the correct sign of the C O stretching shift for standard basis sets. The effect of matrix isolation is modeled by condensing layers of Ar atoms on the isolated monomer and dimer. The dimer structure is discussed in the context of the peptide β-sheet motif.

  15. 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. PMID:26841339

  16. 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.

  17. 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

  18. Gas phase production and loss of isoprene epoxydiols.

    PubMed

    Bates, Kelvin H; Crounse, John D; St Clair, Jason M; Bennett, Nathan B; Nguyen, Tran B; Seinfeld, John H; Stoltz, Brian M; Wennberg, Paul O

    2014-02-20

    Isoprene epoxydiols (IEPOX) form in high yields from the OH-initiated oxidation of isoprene under low-NO conditions. These compounds contribute significantly to secondary organic aerosol formation. Their gas-phase chemistry has, however, remained largely unexplored. In this study, we characterize the formation of IEPOX isomers from the oxidation of isoprene by OH. We find that cis-β- and trans-β-IEPOX are the dominant isomers produced, and that they are created in an approximate ratio of 1:2 from the low-NO oxidation of isoprene. Three isomers of IEPOX, including cis-β- and trans-β, were synthesized and oxidized by OH in environmental chambers under high- and low-NO conditions. We find that IEPOX reacts with OH at 299 K with rate coefficients of (0.84 ± 0.07) × 10(-11), (1.52 ± 0.07) × 10(-11), and (0.98 ± 0.05) × 10(-11) cm(3) molecule(-1) s(-1) for the δ1, cis-β, and trans-β isomers. Finally, yields of the first-generation products of IEPOX + OH oxidation were measured, and a new mechanism of IEPOX oxidation is proposed here to account for the observed products. The substantial yield of glyoxal and methylglyoxal from IEPOX oxidation may help explain elevated levels of those compounds observed in low-NO environments with high isoprene emissions. PMID:24476509

  19. Visible and ultraviolet spectroscopy of gas phase rhodamine 575 cations.

    PubMed

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

    2015-06-01

    The visible and ultraviolet spectroscopy of gas phase rhodamine 575 cations has been studied experimentally by action-spectroscopy in a modified linear ion trap between 220 and 590 nm and by time-dependent density functional theory (TDDFT) calculations. Three bands are observed that can be assigned to the electronic transitions S0 → S1, S0 → S3, and S0 → (S8,S9) according to the theoretical prediction. While the agreement between theory and experiment is excellent for the S3 and S8/S9 transitions, a large shift in the value of the calculated S1 transition energy is observed. A theoretical analysis of thermochromism, potential vibronic effects, and-qualitatively-electron correlation revealed it is mainly the latter that is responsible for the failure of TDDFT to accurately reproduce the S1 transition energy, and that a significant thermochromic shift is also present. Finally, we investigated the nature of the excited states by analyzing the excitations and discussed their different fragmentation behavior. We hypothesize that different contributions of local versus charge transfer excitations are responsible for 1-photon versus 2-photon fragmentation observed experimentally. PMID:25961329

  20. Synthesis of Cu nanopowders by condensation from the gas phase

    NASA Astrophysics Data System (ADS)

    Chepkasov, IV; Gafner, Yu Ya; Zobov, K. V.; Batoroev, S. B.; Bardakhanov, S. P.

    2016-02-01

    In order to determine the most efficient regimes of copper nanoparticles synthesis, a series of experiments were conducted by evaporation and subsequent condensation of the raw material in an argon atmosphere. During the tests it was found that an increase of evaporation rate increases significantly the average size of the synthesized particles. However, the study of the dependence of dimensional parameters of the produced clusters on the intensity of the buffer gas flow rate has encountered significant difficulties associated because the results significantly divergent from the previously conducted experiments on the synthesis of transition metal oxides. In order to solve this contradiction the computer simulation was held of copper atoms condensation from the gas phase for the three different cooling rates and for the two final temperatures T = 373 K and T = 77 K. It was found after analysis that the rate of cooling of the gas mixture and the final temperature directly influences the number and the size of particles produced. For instance, with the 10 times of cooling rate decreases the average size of the particles obtained had increased by 2.7 times at a final temperature of 77 K and by 3.1 times at Tf = 373 K.

  1. 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.

  2. Gas-phase Chemistry of the Cyanate Ion, OCN-

    NASA Astrophysics Data System (ADS)

    Cole, Callie A.; Wang, Zhe-Chen; Snow, Theodore P.; Bierbaum, Veronica M.

    2015-10-01

    Cyanate (OCN-) is the only ion to date whose presence has been confirmed in the icy mantles that coat interstellar dust grains. Understanding the chemical behavior of cyanate at a fundamental level is therefore integral to the advancement of astrochemistry. We seek to unravel the chemistry of this intriguing anion through a combination of gas-phase experiments and theoretical explorations. Our approach is twofold: first, employing a flowing afterglow-selected ion flow tube apparatus, the reactions between OCN- and three of the most abundant atomic species in the interstellar medium, hydrogen, nitrogen, and oxygen, are examined. Hydrogen atoms readily react by associative detachment, but the remarkable stability of OCN- does not give rise to an observable reaction with either nitrogen or oxygen atoms. To explain these results, the potential energy surfaces of several reactions are investigated at the B3LYP/6-311++G(d,p) level of theory. Second, collision induced dissociation experiments involving deprotonated uracil, thymine, and cytosine in an ion trap mass spectrometer reveal an interesting connection between these pyrimidine nucleobase anions and OCN-. Theoretical calculations at the B3LYP/6-311++G(d,p) level of theory are performed to delineate the mechanisms of dissociation and explore the possible role of OCN- as a biomolecule precursor.

  3. 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. PMID:26213024

  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. 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

  6. Gas phase synthesis of two ensembles of silicon nanoparticles

    NASA Astrophysics Data System (ADS)

    Mohan, A.; de Jong, M. M.; Poulios, I.; Schropp, R. E. I.; Rath, J. K.

    2015-09-01

    Dusty plasmas provide a very favorable environment for the growth of silicon nanocrystals. For application of silicon nanocrystals in a solar cell, the fabrication of monodisperse silicon quantum dots has been challenging. We report a single step method to synthesize silicon (Si) nanoparticles in a custom designed dedicated plasma reactor. The nanoparticles produced in the gas phase belong to two different phases exhibiting different structural and optical properties. Particles made in the bulk of the plasma are aggregates of crystalline particles with a mean size of 100 nm. Particles made in locally enhanced plasma regions produced at holes present in the grounded electrode contain free-standing quantum sized particles with crystallites (with mean size of 2.95 nm) embedded within an amorphous matrix. We provide insight on different plasma processes leading to the formation of aggregates and free-standing particles. We hypothesize that the free standing particles are formed due to the excess energetic electrons present in locally enhanced discharges.

  7. 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, 1.5?aa = 2.4227(53) MHz, and 0.25(?bb-?cc) = 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 ? = -0.054 amu 2, 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.

  8. Purification, identification and structural modelling of DPP-IV inhibiting peptides from barbel protein hydrolysate.

    PubMed

    Sila, Assaad; Alvarez, Oscar Martinez; Haddar, Anissa; Frikha, Fakher; Dhulster, Pascal; Nedjar-Arroume, Naima; Bougatef, Ali

    2016-01-01

    Inhibition of DPP-IV may improve glycemic control in diabetics by preventing the rapid breakdown and there by prolonging the physiological action of incretin hormones. Barbel muscle protein hydrolysate (BMPH) was noted to exhibit DPP-IV inhibitory activity, with an IC50 value of 1.94mg/mL. It was fractionated into five major fractions (FI-FV) by size exclusion chromatography using a Superdex peptide. The FIII fraction was noted to display the highest inhibitory activity, with an IC50 value of 1.23mg/mL, and was, therefore, further fractionated by RP-HPLC. Four major peptide sub-fractions were selected. The results revealed that the SF4 sub-fraction showed the highest DPP-IV inhibitory activity, with an IC50 value of 0.21mg/mL. This sub-fraction was submitted to RP-HPLC, ESI-MS, and ESI-MS/MS analyses. The findings indicated that SF4 consisted of two peptides (IC50=96μg/mL), namely PP1 and PP2, whose structures were identified as Trp-Ser-Gly (330Da) and Phe-Ser-Asp (349Da), respectively. This is the first report of these sequences from barbel proteins. The structural modelling through docking simulations results with DPP-IV showed that the Trp-Ser-Gly peptide bound to DPP-IV with high affinity. Overall, the results suggested that BMPH can be considered as a promising natural source of DPP-IV inhibitory peptides. PMID:26687732

  9. Rapid Sampling of Folding Equilibria of ?-Peptides in Methanol Using a Supramolecular Solvent Model.

    PubMed

    Huang, Wei; Riniker, Sereina; van Gunsteren, Wilfred F

    2014-06-10

    Molecular dynamics simulation of biomolecules in solvent using an atomic model for both the biomolecules and the solvent molecules is still computationally rather demanding considering the time scale of the biomolecular motions. The use of a supramolecular coarse-grained (CG) model can speed up the simulation considerably, but it also reduces the accuracy inevitably. Combining an atomic fine-grained (FG) level of modeling for the biomolecules and a supramolecular CG level for the solvent into a hybrid system, the increased computational efficiency may outweigh the loss of accuracy with respect to the biomolecular properties in the hybrid FG/CG simulation. Here, a previously published CG methanol model is reparametrized, and then a 1:1 mixture of FG and CG methanol is used to calibrate the FG-CG interactions using thermodynamic and dielectric screening data for liquid methanol. The FG-CG interaction parameter set is applied in hybrid FG/CG solute/solvent simulations of the folding equilibria of three ?-peptides that adopt different folds. The properties of the peptides are compared with those obtained in FG solvent simulations and with experimental NMR data. The comparison shows that the folding equilibria in the pure CG solvent simulations are different from those in the FG solvent simulations because of the lack of hydrogen-bonding partners in the supramolecular CG solvent. Next, we introduced an FG methanol layer around the peptides in CG solvent to recover the hydrogen-bonding pattern of the FG solvent simulations. The result shows that with the FG methanol layer, the folding equilibria of the three ?-peptides are very similar to those in the FG solvent simulations, while the computational efficiency is at least 3 times higher and the cutoff radius for nonbonded interactions could be increased from 1.4 to 2.0 nm. PMID:26580745

  10. Chemistry in protoplanetary disks: the gas-phase CO/H2 ratio and the carbon reservoir

    NASA Astrophysics Data System (ADS)

    Reboussin, L.; Wakelam, V.; Guilloteau, S.; Hersant, F.; Dutrey, A.

    2015-07-01

    Context. The gas mass of protoplanetary disks and the gas-to-dust ratio are two key elements driving the evolution of these disks and the formation of planetary system. Aims: We explore to what extent CO (or its isotopologues) can be used as a tracer of gas mass. Methods: We use a detailed gas-grain chemical model and study the evolution of the disk composition, starting from a dense prestellar core composition. We explore a range of disk temperature profiles, cosmic-ray ionization rates, and disk ages for a disk model representative of T Tauri stars. Results: At the high densities that prevail in disks, we find that because of fast reactions on grain surfaces, CO can be converted to less volatile forms (principally s-CO2, and to a lesser extent s-CH4) instead of being evaporated over a wide range of temperature. The canonical gas-phase abundance of 10-4 is only reached above about 30-35 K. The dominant carbon bearing entity depends on the temperature structure and age of the disk. The chemical evolution of CO is also sensitive to the cosmic-ray ionization rate. Larger gas phase CO abundances are found in younger disks. Initial conditions, such as parent cloud age and density, have a limited impact. Conclusions: This study reveals that CO gas-phase abundance is heavily dependent on grain surface processes, which remain very incompletely understood so far. The strong dependence on dust temperature profile makes CO a poor tracer of the gas-phase content of disks.

  11. Mimicking and Understanding the Agglutination Effect of the Antimicrobial Peptide Thanatin Using Model Phospholipid Vesicles.

    PubMed

    Robert, Émile; Lefèvre, Thierry; Fillion, Matthieu; Martial, Benjamin; Dionne, Justine; Auger, Michèle

    2015-06-30

    Thanatin is a cationic 21-residue antimicrobial and antifongical peptide found in the spined soldier bug Podisus maculiventris. It is believed that it does not permeabilize membranes but rather induces the agglutination of bacteria and inhibits cellular respiration. To clarify its mode of action, lipid vesicle organization and aggregation propensity as well as peptide secondary structure have been studied using different membrane models. Dynamic light scattering and turbidimetry results show that specific mixtures of negatively charged and zwitterionic phospholipid vesicles are able to mimic the agglutination effect of thanatin observed on Gram-negative and Gram-positive bacterial cells, while monoconstituent ("conventional") models cannot reproduce this phenomenon. The model of eukaryotic cell reveals no particular interaction with thanatin, which is consistent with the literature. Infrared spectroscopy shows that under the conditions under which vesicle agglutination occurs, thanatin exhibits a particular spectral pattern in the amide I' region and in the region associated with Arg side chains. The data suggest that thanatin mainly retains its hairpin structure, Arg residues being involved in strong interactions with anionic groups of phospholipids. In the absence of vesicle agglutination, the peptide conformation and Arg side-chain environment are similar to those observed in solution. The data show that a negatively charged membrane is required for thanatin to be active, but this condition is insufficient. The activity of thanatin seems to be modulated by the charge surface density of membranes and thanatin concentration. PMID:26057537

  12. Optimally-connected hidden markov models for predicting MHC-binding peptides.

    PubMed

    Zhang, Chenhong; Bickis, Mikelis G; Wu, Fang-Xiang; Kusalik, Anthony J

    2006-10-01

    Hidden Markov models (HMMs) are one of various methods that have been applied to prediction of major histo-compatibility complex (MHC) binding peptide. In terms of model topology, a fully-connected HMM (fcHMM) has the greatest potential to predict binders, at the cost of intensive computation. While a profile HMM (pHMM) performs dramatically fewer computations, it potentially merges overlapping patterns into one which results in some patterns being missed. In a profile HMM a state corresponds to a position on a peptide while in an fcHMM a state has no specific biological meaning. This work proposes optimally-connected HMMs (ocHMMs), which do not merge overlapping patterns and yet, by performing topological reductions, a model's connectivity is greatly reduced from an fcHMM. The parameters of ocHMMs are initialized using a novel amino acid grouping approach called "multiple property grouping." Each group represents a state in an ocHMM. The proposed ocHMMs are compared to a pHMM implementation using HMMER, based on performance tests on two MHC alleles HLA (Human Leukocyte Antigen)-A*0201 and HLA-B*3501. The results show that the heuristic approaches can be adjusted to make an ocHMM achieve higher predictive accuracy than HMMER. Hence, such obtained ocHMMs are worthy of trial for predicting MHC-binding peptides. PMID:17099936

  13. 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

  14. Energy and Entropy Effects in Dissociation of Peptide Radical Anions

    SciTech Connect

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

    2012-04-15

    Time- and collision energy-resolved surface-induced dissociation (SID) of peptide radical anions was studied for the first time using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) configured for SID experiments. Peptide radical cations and anions were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes. The effect of the charge, radical, and the presence of a basic residue on the energetics and dynamics of dissociation of peptide ions was examined using RVYIHPF (1) and HVYIHPF (2) as model systems. Comparison of the survival curves for of [M+H]{sup +}, [M-H]{sup -}, M{sup +{sm_bullet}}, and [M-2H]{sup -{sm_bullet}} ions of these precursors demonstrated that even-electron ions are more stable towards fragmentation than their odd-electron counterparts. RRKM modeling of the experimental data demonstrated that the lower stability of the positive radicals is mainly attributed to lower dissociation thresholds while entropy effects are responsible the relative instability of the negative radicals. Substitution of arginine with less basic histidine residue has a strong destabilizing effect on the [M+H]{sup +} ions and a measurable stabilizing effect on the odd-electron ions. Lower threshold energies for dissociation of both positive and negative radicals of 1 are attributed to the presence of lower-energy dissociation pathways that are most likely promoted by the presence of the basic residue.

  15. 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...

  16. DETERMINATION OF GAS-PHASE DIMETHYL SULFATE AND MONOMETHYL HYDROGEN SULFATE

    EPA Science Inventory

    Analytical techniques have been developed for the collection and determination of gas phase dimethyl sulfate and monomethyl sulfuric acid in the flue lines and plumes of power plants and in the ambient atmosphere. The techniques involve the collection of the gas phase species in ...

  17. Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model.

    PubMed

    Nayar, Divya; Chakravarty, Charusita

    2014-06-01

    Hydration of the 16-residue ?-hairpin fragment of the protein in the folded and unfolded ensembles is studied with mTIP3P and TIP4P solvent models using the CHARMM22 protein force-field. mTIP3P is a three-site water model which is used for parameterization of the CHARMM force-field and is known to exhibit liquid-state anomalies of water at temperatures about 80 K lower than the experimental temperature. TIP4P is a four-site water model which gives a better description of the experimental phase diagram and liquid-state anomalies of water. At a temperature of 250 K, where the folded ensemble of the peptide is stable and the unfolded ensemble is metastable, secondary structure metrics are much more sensitive to the choice of solvent model in the unfolded, rather than folded, ensemble. In particular, mean values as well as variation in the positional root mean square displacements (RMSD) and configurational entropy are greater in mTIP3P compared to the TIP4P solvent. The peptide structure is relatively more compact in the TIP4P solvent, which supports unfolded as well as hydrophobic core states. In terms of average local order and binding energy of the water surrounding the peptide, strong deviations from bulk behaviour are restricted to the first hydration shell and differences between the folded and unfolded ensembles in the two solvents are small. The strong coupling between the solvent and the peptide is demonstrated, however, by the dependence of the unfolding temperature on the water model (400 K in mTIP3P and 465 K in TIP4P) and the qualitatively different temperature dependence of the hydration layer occupancy signalling the unfolding transition in the two solvents. A residue-wise decomposition of different contributions to the configurational energy indicates that the TIP4P solvent shows far greater variation in the interaction with charged sidegroups of amino acid residues than the mTIP3P solvent. The implications of sequence-dependent sensitivity of peptide secondary structures to the choice of water models for simulating folding-unfolding equilibria and free energy landscapes are discussed. PMID:24695799

  18. 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

  19. Gas-phase silicon atom densities in the chemical vapor deposition of silicon from silane

    SciTech Connect

    Coltrin, M.E.; Breiland, W.G.; Ho, P.

    1993-12-31

    Silicon atom number density profiles have been measured using laser-induced fluorescence during the chemical vapor deposition of silicon from silane. Measurements were obtained in a rotating-disk reactor as a function of silane partial pressure and the amount of hydrogen added to the carrier gas. Absolute number densities were obtained using an atomic absorption technique. Results were compared with calculated density profiles from a model of the coupled fluid flow, gas-phase and surface chemistry for an infinite-radius rotating disk. An analysis of the reaction mechanism showed that the unimolecular decomposition of SiH{sub 2} is not the dominant source of Si atoms. Profile shapes and positions, and all experimental trends are well matched by the calculations. However, the calculated number density is up to 100 times smaller than measured.

  20. Simulation of gas phase reactions for microcrystalline silicon films fabricated by PECVD

    NASA Astrophysics Data System (ADS)

    He, Bao-hua; Yang, Shi-e.; Chen, Yong-sheng; Lu, Jing-xiao

    2011-05-01

    We present a numerical gas phase reaction model for hydrogenated microcrystalline silicon (μc-Si:H) films from SiH4 and H2 gas mixtures with plasma enhanced chemical vapor deposition (PECVD). Under the typical μc-Si:H deposition conditions, the concentrations of the species in the plasma are calculated and the effects of silane fraction ( SF=[SiH4]/[H2+SiH4]) are investigated. The results show that SiH3 is the key precursor for μc-Si:H films growth, and other neutral radicals, such as Si2H5, Si2H4 and SiH2, may play some roles in the film deposition. With the silane fraction increasing, the precursor concentration increases, but H atom concentration decreases rapidly, which results in the lower H/SiH3 ratio.

  1. Description of liquid-gas phase transition in the frame of continuum mechanics

    NASA Astrophysics Data System (ADS)

    Vilchevskaya, Elena N.; Ivanova, Elena A.; Altenbach, Holm

    2014-03-01

    A new method of describing the liquid-gas phase transition is presented. It is assumed that the phase transition is characterized by a significant change of the particle density distribution as a result of energy supply at the boiling point that leads to structural changes but not to heating. Structural changes are described by an additional state characteristics of the system—the distribution density of the particles which is presented by an independent balance equation. The mathematical treatment is based on a special form of the internal energy and a source term in the particle balance equation. The presented method allows to model continua which have different specific heat capacities in liquid and in gas state.

  2. Identification of Peptides with Targeted Adhesion to Bone-Like Mineral via Phage Display and Computational Modeling

    PubMed Central

    Segvich, Sharon; Biswas, Subhashis; Becker, Udo; Kohn, David H.

    2008-01-01

    The challenges in engineering bone scaffolds reflect the complexity of bone as an organ. The organic-inorganic hybrid system design aims to provide signals within a conductive apatite layer to promote cell adhesion, proliferation and ultimately differentiation into bone tissue. Dual functioning peptides designed to specifically adhere to the apatite layer, while promoting cell adhesion via cell recognition sequences, may increase cell adhesion, leading to increased osteogenesis. The aim of this study is to identify peptide sequences with preferential adsorption towards apatite-based materials. Bone-like mineral films and hydroxyapatite disks were panned with a phage library to elucidate peptide sequences with favorable adsorption. Peptide sequences were analyzed using the web-based biotechnology tool RELIC and validated with a modified ELISA, in addition to being investigated using a newly developed method of high-throughput computational modeling. Peptides having the highest affinity and greatest potential to be incorporated into a dual functioning peptide design are APWHLSSQYSRT, VTKHLNQISQSY and STLPIPHEFSRE. These experiments provide a method of rationally designing peptides that adhere to apatite and that may improve bone tissue regeneration. This work also provides structure for investigating peptide/protein adsorption on apatite substrates with varied carbonate, or other impurity, content. PMID:18701808

  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. 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.

  5. 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.

  6. A viral peptide that targets mitochondria protects against neuronal degeneration in models of Parkinson's disease.

    PubMed

    Szelechowski, Marion; Bétourné, Alexandre; Monnet, Yann; Ferré, Cécile A; Thouard, Anne; Foret, Charlotte; Peyrin, Jean-Michel; Hunot, Stéphane; Gonzalez-Dunia, Daniel

    2014-01-01

    Mitochondrial dysfunction is a common feature of many neurodegenerative disorders, notably Parkinson's disease. Consequently, agents that protect mitochondria have strong therapeutic potential. Here, we sought to divert the natural strategy used by Borna disease virus (BDV) to replicate in neurons without causing cell death. We show that the BDV X protein has strong axoprotective properties, thereby protecting neurons from degeneration both in tissue culture and in an animal model of Parkinson's disease, even when expressed alone outside of the viral context. We also show that intranasal administration of a cell-permeable peptide derived from the X protein is neuroprotective. We establish that both the X protein and the X-derived peptide act by buffering mitochondrial damage and inducing enhanced mitochondrial filamentation. Our results open the way to novel therapies for neurodegenerative diseases by targeting mitochondrial dynamics and thus preventing the earliest steps of neurodegenerative processes in axons. PMID:25333748

  7. 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.

  8. Gas-phase identity nucleophilic substitution reactions of cyclopropenyl halides.

    PubMed

    Kim, Chang Kon; Li, Hong Guang; Lee, Bon-Su; Kim, Chan Kyung; Lee, Hai Whang; Lee, Ikchoon

    2002-03-22

    The gas-phase identity nucleophilic substitution reactions of halide anions (X = F, Cl, and Br) with cyclopropenyl halides, X(-) + (CH)(3)X <= => X(CH)(3) + X(-), are investigated theoretically at four levels of theory, B3LYP/6-311+G**, MP2/6-311+G**, G2(+)MP2//MP2/6-311+G**, and G2(+)//MP2/6-311+G**. Four types of reaction paths, the sigma-attack S(N)2, pi-attack S(N)2'-syn, and S(N)2'-anti and sigmatropic 1,2-shift, are possible for all the halides. In the fluoride anion reactions, two types of stable adducts, syn- and anti-1,2-difluorocyclopropyl anions, can exist on the triple-well-type potential energy surface of the identity substitution reactions with rearrangement of double bond (C=C), S(N)2'-syn, and S(N)2'-anti processes. The TSs for the sigma-attack S(N)2 paths have "open" (loose) structures so that the ring positive charges are high rendering strong aromatic cyclopropenyl (delocalized) cation-like character. In contrast, in the pi-attack S(N)2' paths, a lone pair is formed at the unsubstituted carbon (C3), which stabilizes the 1,2-dihalocyclopropyl (delocalized) anion-like TS by two strong n(C)-sigma*(C-F) vicinal charge-transfer delocalization interactions. The barrier height increases in the order S(N)2'-anti < sigma-attack S(N)2 < S(N)2'-syn for X = Cl and Br, whereas for X = F the order is changed to S(N)2'-anti < S(N)2'-syn < sigma-attack S(N)2 due to the stable difluoro adduct formation. The sigmatropic 1,2-shift (circumambulatory) reactions have high activation barriers and cannot interfere with the substitution reactions. PMID:11895417

  9. 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.

  10. Trimethylsilyl derivatization of nucleic acid anions in the gas phase

    NASA Astrophysics Data System (ADS)

    O'Hair, Richard A. J.; McLuckey, Scott A.

    1997-03-01

    Ion-molecule reactions between nucleic acid anions, [M-nH]n, formed via electrospray ionization, and trimethylsilylchloride have been investigated in an ion trap mass spectrometer at a helium bath gas pressure of 1 mtorr. Three types of reactions are observed: (i) SN2(Si) when n > 1 ; (ii) adduct formation when n = 1 ; and (iii) addition followed by elimination of HCl when n = 1 and where an acidic phosphate proton is present (e.g., 5'-pdA). The kinetics of these reactions have been studied for various anions derived from the following deoxyadenosine species: 5'-pdA; 5'-pppdA, 5'-d(AA)-3'; 5'-d(AAA)-3' and 5'-d(AAAA)-3'. The following reactivity order is observed: [M-2H]2- of 5'-pppdA > [M-2H]2- of 5'-d(AAA)-3' > [M-3H]3- of 5'-d(AAAA)-3' > [M-3H + TMS]2- of 5'-d(AAAA)-3' > [M-2H]2- of 5'-d(AAAA)-3' > [M-H]- of 5'-pdA >> [M-H]- of 5'-d(AA)-3' > [M-H]- of 5'-d(AAA)-3'. In addition, the collision-induced dissociation reactions of the products of these reactions have been studied. Decomposition reactions are consistent with trimethylsilyl attachment on the phosphodiester linkage(s) in oligonucleotides and on the phosphate moieties of 5'-pdA and 5'-pppdA. Comparison of data acquired for modified and unmodified oligonucleotide anions of the same charge state reveal that TMS modification can significantly alter the favored dissociation channels, giving rise to sequence information. The results suggest that gas phase TMS derivatization of oligonucleotide anions, combined with tandem mass spectrometry, can provide sequence information complementary to that derived from unmodified anions.

  11. 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.

  12. 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.

  13. 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.

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

    PubMed

    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. PMID:26049525

  15. 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.

  16. Characterizing the Structures and Folding of Free Proteins Using 2-D Gas-Phase Separations: Observation of Multiple Unfolded Conformers

    SciTech Connect

    Shvartsburg, Alexandre A.; Li, Fumin; Tang, Keqi; Smith, Richard D.

    2006-05-15

    Understanding the 3-D structure and dynamics of proteins and other biological macromolecules in various environments is among the central challenges of chemistry. Electrospray ionization (ESI) can transfer ions from solution to gas phase with only limited structural distortion, allowing their profiling using mass spectrometry and other gas phase approaches. Ion mobility spectrometry (IMS) can be used to separate and characterize macroion conformations with high sensitivity and speed. However, IMS separation power has proven insufficient for full resolution of major structural variants of protein ions and elucidation of their interconversion dynamics. Here we report characterization of macromolecular conformations using field asymmetric waveform IMS (FAIMS) coupled to conventional IMS in conjunction with mass spectrometry. The controlled activation of ions in the electrodynamic funnel trap between FAIMS and IMS stages enables investigating the structural evolution of particular isomeric precursors as a function of the extent and duration of activation that can be varied over a large range. These new capabilities are demonstrated for bovine ubiquitin, a common model for study of structure and folding of gas-phase proteins. For nearly all charge states, two-dimensional FAIMS/IMS separations distinguish many more conformations than either FAIMS or IMS alone, including some species with very low abundance. The unfolding of specific ubiquitin conformers has been studied employing ion heating in the FAIMS/IMS interface.

  17. 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.

  18. 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.

  19. 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.

  20. Empirical parameterization of a model for predicting peptide helix/coil equilibrium populations.

    PubMed

    Andersen, N H; Tong, H

    1997-09-01

    A modification of the Lifson-Roig formulation of helix/coil transitions is presented; it (1) incorporates end-capping and coulombic (salt bridges, hydrogen bonding, and side-chain interactions with charged termini and the helix dipole) effects, (2) helix-stabilizing hydrophobic clustering, (3) allows for different inherent termination probabilities of individual residues, and (4) differentiates helix elongation in the first versus subsequent turns of a helix. Each residue is characterized by six parameters governing helix formation. The formulation of the conditional probability of helix initiation and termination that we developed is essentially the same as one presented previously (Shalongo W, Stellwagen, E. 1995. Protein Sci 4:1161-1166) and nearly the mathematical equivalent of the new capping formulation incorporated in the model presented by Rohl et al. (1996. Protein Sci 5:2623-2637). Side-chain/side-chain interactions are, in most cases, incorporated as context dependent modifications of propagation rather than nucleation parameters. An alternative procedure for converting [theta]221 values to experimental fractional helicities () is presented. Tests of the program predictions suggest this method may have some advantages both for designed peptides and for the analysis of secondary structure preferences that could drive the formation of molten-globule intermediates on protein folding pathways. The model predicts the fractional helicity of 385 peptides with a root-mean-square deviation (RMSD) of 0.050 and locates (with precise definition of the termini in many cases) helices in proteins as well as competing methods. The propagation and nucleation parameters were derived from NMR data and from the CD data for a 79 peptide "learning set" for which an excellent fit resulted (RMSD = 0.0295). The current set of parameter corrections for capping boxes, helix dipole interactions, and side-chain/side-chain interactions (coulombic, hydrogen bonding and hydrophobic clustering), although still under development provide a significant improvement in both helix/coil equilibrium prediction for peptides and helix location in protein sequences. This is clearly evident in the rms deviations between CD measures and calculated values of fractional helicity for different classes of peptides before and after applying the corrections: for peptides lacking capping boxes and i/i + 3 and i/i + 4 side-chain/side-chain interactions RMSD = 0.044 (n = 164) versus RMSD = 0.054 (0.172 without the corrections, n = 221) for peptides that required context-dependent corrections of the parameters. If we restrict the analysis to N-acylated peptides with helix stabilizing side-chain/side-chain interactions (including N-capping boxes), the degree to which our corrections account for the stabilizing interaction can be judged from the change in helicity underestimation, (calc-CD): -0.15 +/- 0.10, which is reduced to -0.018 +/- 0.048 (n = 191) upon applying the corrections. PMID:9300492

  1. A Peptide to Reduce Pulmonary Edema in a Rat Model of Lung Transplantation

    PubMed Central

    Finsterwalder, Richard; Friedl, Heinz P.; Rauscher, Sabine; Gröger, Marion; Kocher, Alfred; Wagner, Christine; Wagner, Stephan N.; Fischer, Gottfried; Schultz, Marcus J.; Wiedemann, Dominik; Petzelbauer, Peter

    2015-01-01

    Background Despite significant advances in organ preservation, surgical techniques and perioperative care, primary graft dysfunction is a serious medical problem in transplantation medicine in general and a specific problem in patients undergoing lung transplantation. As a result, patients develop lung edema, causing reduced tissue oxygenation capacity, reduced lung compliance and increased requirements for mechanical ventilatory support. Yet, there is no effective strategy available to protect the grafted organ from stress reactions induced by ischemia/reperfusion and by the surgical procedure itself. Methods We assessed the effect of a cingulin-derived peptide, XIB13 or a random peptide in an established rat model of allogeneic lung transplantation. Donor lungs and recipients received therapeutic peptide at the time of transplantation and outcome was analyzed 100min and 28 days post grafting. Results XIB13 improved blood oxygenation and reduced vascular leak 100min post grafting. Even after 28 days, lung edema was significantly reduced by XIB13 and lungs had reduced fibrotic or necrotic zones. Moreover, the induction of an allogeneic T cell response was delayed indicating a reduced antigen exchange between the donor and the host. Conclusions In summary, we provide a new tool to strengthen endothelial barrier function thereby improving outcomes in lung transplantation. PMID:26536466

  2. Modeling of Platinum-Aryl Interaction with Amyloid-β Peptide.

    PubMed

    Turner, Matthew; Platts, James A; Deeth, Robert J

    2016-03-01

    Ligand field molecular mechanics (LFMM), density functional theory (DFT), and semiempirical PM7 methods are used to study the binding of two Pt(II)-L systems to an N-terminal fragment of the amyloid-β peptide, where L = 2,2-bipyridyl or 1,10-phenanthroline. Molecular dynamics simulations are used to explore the conformational freedom of the peptide using LFMM combined with AMBER molecular mechanics parameters. We establish a modeling protocol, allowing for identification and analysis of favorable platinum-binding modes and peptide conformations. Preferred binding modes are identified for each ligand investigated; metal coordination occurs via Nε in His residues for both ligands - His6ε-His13ε and His6ε-His14ε for the bipyridyl and phenanthroline ligands, respectively. The observed change in binding mode for the different ligands suggests that the binding mode of these platinum-based structures can be controlled by the choice of ligand. In the bipy systems, Boltzmann population at 310 K is dominated by a single conformer, while in the phenanthroline case, three conformations make significant contributions to the ensemble. The relative stability of these conformations is due to the inherent stability of binding platinum via Nε in addition to subtle H-bonding effects. PMID:26756469

  3. [MODIFICATION OF ALVEOLAR MACROPHAGE POOL UNDER INFLUENCE OF PEPTIDE THERAPY IN THE BLEOMYCIN PNEUMOFIBROSIS MODEL].

    PubMed

    Lebedeva, E S; Dvorakovskava, I V; Kuzubova, N A; Titova, O N

    2015-12-01

    Effect of peptide therapy on morphological and functional characteristics of alveolar macrophages and role of their phenotypic reprogramming in modulation of pulmonary fibrosing process were evaluated on the rat's model of pulmonary fibrosis, initiated by intratracheal administration of bleomycin. Status of alveolar macrophages was evaluated on the basis of electron microscopic studies and phagocytic activity. In lung tissue of control animals widespread diffuse interstitial fibrosis was determined. Alveolar macrophage cytoplasm was filled geterophagosomes with surfactant fragments, lipid droplets and cholesterol crystals; foam cells were a third of macrophage pool. After the course of peptide therapy the young cell with rare geterophagosomes and lipid droplets, without cholesterol crystals and increased phagocytic activity prevailed in macrophage population. There were rare sites of fibrosis in lungs; connective tissue contained much less collagen fibers than in the control; there was a growing proliferation of the bronchial epithelium. It may be assumed that under the influence of the peptide therapy a certain balance in the alveolar macrophage population was established with a predominance of M2 phenotype for the formation of the optimal ratio of cellular and humoral immune response, providing effective remedy of bronchial epithelium and prevention of lung tissue remodeling with the interstitial fibrosis formation. PMID:26987231

  4. 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. PMID:22275089

  5. Novel bioluminescent receptor-binding assays for peptide hormones: using ghrelin as a model.

    PubMed

    Liu, Yu; Shao, Xiao-Xia; Zhang, Lei; Song, Ge; Liu, Ya-Li; Xu, Zeng-Guang; Guo, Zhan-Yun

    2015-10-01

    Peptide hormones perform important biological functions by binding specific cell membrane receptors. For hormone-receptor interaction studies, receptor-binding assays are widely used. However, conventional receptor-binding assays rely on radioactive tracers that have drawbacks. In recent studies, we established novel non-radioactive receptor-binding assays for some recombinant protein hormones based on the ultrasensitive bioluminescence of a newly developed nanoluciferase (NanoLuc) reporter. In the present work, we extended the novel bioluminescent receptor-binding assay to peptide hormones that have small size and can be conveniently prepared by chemical synthesis. Human ghrelin, a 28-amino acid peptide hormone carrying a special O-fatty acid modification, was used as a model. To prepare a bioluminescent ghrelin tracer, a chemically synthesized ghrelin analog with a unique cysteine residue at the C-terminus was site-specifically conjugated with an engineered NanoLuc with a unique exposed cysteine residue at the C-terminus via a reversible disulfide linkage. The NanoLuc-conjugated ghrelin retained high binding affinity with the ghrelin receptor GHSR1a (K d = 1.14 ± 0.13 nM, n = 3) and was able to sensitively monitor the receptor-binding of various GHSR1a ligands. The novel bioluminescent receptor-binding assay will facilitate the interaction studies of ghrelin with its receptor. We also proposed general procedures for convenient conjugation of other peptide hormones with NanoLuc for novel bioluminescent receptor-binding assays. PMID:26002812

  6. 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 functional artificial transmembrane transporters. Our experience to date suggests that the next steps for achieving conceptual devices with better performance and selectivity will derive from the topological control over cyclic peptide assembly and the functionalization of the lumen. PMID:23898935

  7. Probing the Nuclear Liquid-Gas Phase Transition

    NASA Astrophysics Data System (ADS)

    Pochodzalla, Josef

    1996-05-01

    The prospect of creating a state of matter resembling that of the pre-hadronic phase of the early universe or of the core of today's neutron stars is one of the prime motivations to study relativistic heavy ion collisions. Unquestionable, the transition to the quark-gluon plasma represents the most spectacular example of a phase transition in nuclear matter. The complex structure of the hadronic components and the many facets of their interaction, however, offer the opportunity to observe in addition several other, exciting nuclear state transitions. Already two decades ago, the van der Waals behavior of the nucleon - nucleon force inspired the idea of a liquid-gas phase transition in nuclear matter. Looking for signals of this phase transition the ALADIN collaboration studied the decay of projectile spectators produced in relativistic heavy ion collisions. Fragment multiplicities and correlations observed in projectile fragmentation at beam energies between 600 and 1000 MeV per nucleon are found to be invariant with respect to a change of the target mass or the beam energy when plotted as a function of the summed charge of complex fragments, Z_bound. The dependence of the fragment multiplicity on the projectile mass follows a linear scaling law. For Au+Au reactions at E/A=600 MeV, the mass and the excitation energy of the decaying pre-fragments were determined from the measured fragment and neutron distributions. A temperature scale was derived from observed yield ratios of He and Li isotopes. The relation between this isotope temperature and the excitation energy of the system exhibits a behavior which is reminiscent of a phase transition. The nuclear vapor regime takes over at an excitation energy of 10 MeV per nucleon, a temperature of 5 MeV and may be characterized by a density of 0.15-0.3 normal nuclear density. In order to explore the influence of an explosive radial flow, we also investigated central Au+Au collisions in the energy range between 50 and 200 MeV per nucleon. The latter experiment aims at a comparison of isotope temperatures and temperatures extracted from excited state populations. Simultaneously, the space-time extend will be explored by two-particle correlations. Supported by the Deutsche Forschunggemeinschaft under Contract No. Po256/2-1.

  8. 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.

  9. 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

  10. Gas-phase spectroscopy of a vinylheptafulvene chromophore.

    PubMed

    Elm, Jonas; Stockett, Mark; Houmøller, Jørgen; Åxman Petersen, Michael; Mikkelsen, Kurt V; Brøndsted Nielsen, Mogens; Brøndsted Nielsen, Steen

    2015-01-01

    The intrinsic spectral properties of the dihydroazulene (DHA)/vinylheptafulvene (VHF) photo/thermoswitch, free of solvent interactions, were investigated both experimentally and theoretically. A quaternary ammonium group was incorporated via an ethylene bridge to allow for the transfer of charged molecules to the gas phase by electrospray ionization, leaving the chromophore part itself neutral. Absorption by the two isomers was identified from ion dissociation (i.e., action spectroscopy) using a home-built sector instrument. Several fragment ions were observed, and dissociation occurred both at the charge tag side chain and at the chromophore unit itself. We measured an absorption band of VHF with a maximum at 430 ± 20 nm (2.9 eV ± 0.1 eV) but no band was discernible for the DHA in the visible region. This shows that little interconversion between the two isomers occurs during the electrospray and the subsequent trapping in an octopole for 25 ms; the latter is needed to produce ion bunches for spectroscopy where a pulsed laser system is used. For comparison, density functional theoretical calculations predicted lowest-energy vertical excitations of 3.33 eV to 3.48 eV for the DHA and 3.02 eV to 3.08 eV for the VHF (the ranges are based on the use of different functionals), which correspond to a maximal deviation between theory and experiment of 0.1 eV in the case of the VHF. The absorption by the bare ions is significantly blue-shifted compared to that by VHF in acetonitrile solution (2.64 eV), but similar within the experimental uncertainty to that by VHF in cyclohexane (2.78 eV); the transition, therefore has a significant charge-transfer character. Finally, we find that the absorption of two photons is needed to cause fragmentation of the VHF on the microsecond time scale, which indicates that prompt fragmentation from the electronically excited state or prior to the intramolecular vibrational redistribution of the excess energy plays no role. This is of particular importance for the use of the photosystem in advanced materials or molecular electronics where high photostability is required to allow for numerous isomerization cycles. PMID:26307736

  11. 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

  12. A simple model for polyproline II structure in unfolded states of alanine-based peptides

    PubMed Central

    Pappu, Rohit V.; Rose, George D.

    2002-01-01

    The striking similarity between observed circular dichroism spectra of nonprolyl homopolymers and that of regular left-handed polyproline II (PII) helices prompted Tiffany and Krimm to propose in 1968 that unordered peptides and unfolded proteins are built of PII segments linked by sharp bends. A large body of experimental evidence, accumulated over the past three decades, provides compelling evidence in support of the original hypothesis of Tiffany and Krimm. Of particular interest are the recent experiments of Shi et al. who find significant PII structure in a short unfolded alanine-based peptide. What is the physical basis for PII helices in peptide and protein unfolded states? The widely accepted view is that favorable chain-solvent hydrogen bonds lead to a preference for dynamical fluctuations about noncooperative PII helices in water. Is this preference simply a consequence of hydrogen bonding or is it a manifestation of a more general trend for unfolded states which are appropriately viewed as chains in a good solvent? The prevalence of closely packed interiors in folded proteins suggests that under conditions that favor folding, water—which is a better solvent for itself than for any polypeptide chain—expels the chain from its midst, thereby maximizing chain packing. Implicit in this view is a complementary idea: under conditions that favor unfolding, chain-solvent interactions are preferred and in a so-called good solvent, chain packing density is minimized. In this work we show that minimization of chain packing density leads to preferred fluctuations for short polyalanyl chains around canonical, noncooperative PII-like conformations. Minimization of chain packing is modeled using a purely repulsive soft-core potential between polypeptide atoms. Details of chain-solvent interactions are ignored. Remarkably, the simple model captures the essential physics behind the preference of short unfolded alanine-based peptides for PII helices. Our results are based on a detailed analysis of the potential energy landscape which determines the system's structural and thermodynamic preferences. We use the inherent structure formalism of Stillinger and Weber, according to which the energy landscape is partitioned into basins of attraction around local minima. We find that the landscape for the experimentally studied seven-residue alanine-based peptide is dominated by fluctuations about two noncooperative structures: the left-handed polyproline II helix and its symmetry mate. PMID:12237465

  13. 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.

  14. Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique

    NASA Astrophysics Data System (ADS)

    Tianmin, Wu; Tianjun, Wang; Xian, Chen; Bin, Fang; Ruiting, Zhang; Wei, Zhuang

    2016-01-01

    We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide folding landscapes. Project supported by the National Natural Science Foundation of China (Grant No. 21203178), the National Natural Science Foundation of China (Grant No. 21373201), the National Natural Science Foundation of China (Grant No. 21433014), the Science and Technological Ministry of China (Grant No. 2011YQ09000505), and “Strategic Priority Research Program” of the Chinese Academy of Sciences (Grant Nos. XDB10040304 and XDB100202002).

  15. Quantum chemical analysis of the energy of proton transfer from phenol and chlorophenols to H2O in the gas phase and in aqueous solution

    NASA Astrophysics Data System (ADS)

    Schrmann, Gerrit

    1998-12-01

    Proton transfer energies of phenol and 14 chlorophenols with H2O as a base are analyzed in the gas phase and in solution using quantum chemical methods at the semiempirical and ab initio level of computation. The effect of aqueous solution was accounted for by applying the density functional theory (DFT) implementation of the conductor-like screening model (COSMO) as well as semiempirical continuum-solvation models. The results reveal substantial and systematic overestimations of the free energies of proton transfer as derived from experimental solution-phase pKa data. This can be traced back to both deficiencies in the current model parameterization as well as to limitations of the underlying gas-phase quantum chemical models, which is further illustrated by additional complete-basis-set (CBS) calculations for the proton transfer reaction with phenol. In contrast, the relative pKa trend is reflected well by COSMO-DFT calculations with correlation coefficients (adjusted for degrees of freedom) of 0.96. Decomposition of the dissociation energy in aqueous solution into a gas-phase term and a term summarizing the solvation contributions provides new insights into the effect of solvation on proton transfer energies, and yields mechanistic explanations for the observed differences in the gas-phase and solution-phase acidity orders of various subgroups of the compounds.

  16. 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

  17. Interaction(s) of rotavirus non-structural protein 4 (NSP4) C-terminal peptides with model membranes.

    PubMed Central

    Huang, Huan; Schroeder, Friedhelm; Estes, Mary K; McPherson, Tanya; Ball, Judith M

    2004-01-01

    Rotavirus is the major cause of dehydrating gastroenteritis in children and young animals. NSP4 (non-structural protein 4), a rotaviral non-structural glycoprotein and a peptide NSP4(114-135) (DKLTTREIEQVELLKRIYDKLT), corresponding to NSP4 amino acids 114-135, induce diarrhoeal disease in a neonatal mouse model and interact with model membranes that mimic caveolae. Correlation of the mechanisms of diarrhoea induction and membrane interactions by NSP4 protein and peptide remain unclear. Several additional NSP4 peptides were synthesized and their interactions with membranes studied by (i) CD, (ii) a filtration-binding assay and (iii) a fluorescent molecule leakage assay. Model membranes that varied in lipid compositions and radius of curvature were utilized to determine the compositional and structural requirements for optimal interaction with the peptides of NSP4. Similar to the intact protein and NSP4(114-135), peptides overlapping residues 114-135 had significantly higher affinities to membranes rich in negatively charged lipids, rich in cholesterol and with a high radius of curvature. In the leakage assay, small and large unilamellar vesicles loaded with the fluorophore/quencher pair 8-aminonaphthalene-1,3,6-trisulphonic acid disodium salt/p -xylene-bis-pyridinium bromide were incubated with the NSP4 peptides and monitored for membrane disruption by lipid reorganization or by pore formation. At a peptide concentration of 15 microM, none of the NSP4 peptides caused leakage. These results confirm that NSP4 interacts with caveolae-like membranes and the alpha-helical region of NSP4(114-135) comprises a membrane interaction domain that does not induce membrane disruption at physiological concentrations. PMID:15012630

  18. 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.

  19. 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.

  20. Gas phase studies of the competition between substitution and elimination reactions.

    PubMed

    Gronert, Scott

    2003-11-01

    Gas phase studies allow for the examination of organic reaction mechanisms in the absence of solvation effects and therefore probe the intrinsic reactivity of the reaction partners. The competition between substitution and elimination reactions has been a topic of interest for decades, but it has been difficult to examine in the gas phase because both pathways generally lead to the same ionic product and cannot be distinguished by mass spectrometry. By using dianions as nucleophiles, the reactions produce two ionic products, one of which identifies the mechanism. With this approach, we have examined a variety of substituent effects on the gas phase competition between substitution and elimination. In addition, we have found that similar processes occur during collisional activation of salt complexes that contain a dianion and a tetraalkylammonium cation. Overall, the results show that the gas phase studies probe the same fundamental features found in the condensed phase and provide valuable insights into reaction mechanisms. PMID:14622032

  1. On Prognosis of Epitaxy from Gas Phase Process to Improve Properties of Epitaxial Layers

    NASA Astrophysics Data System (ADS)

    Pankratov, E. L.; Bulaeva, E. A.

    2015-12-01

    In this paper we analyzed mass and heat transport in a reactor from gas phase during growth an epitaxial layer. Based on results of the analysis we analyzed dependences of properties of grown layers on parameters of technological process.

  2. GAS PHASE EXPOSURE HISTORY DERIVED FROM MATERIAL PHASE CONCENTRATION PROFILES USING SOLID PHASE MICRO-EXTRACTION

    EPA Science Inventory

    EPA Identifier: F8P31059
    Title: Gas Phase Exposure History Derived from Material Phase Concentration Profiles Using Solid Phase Micro-Extraction
    Fellow (Principal Investigator): Jonathan Lewis McKinney
    Institution: University of Missouri - ...

  3. Molecular modeling approach to explore the role of cathepsin B from Hordeum vulgare in the degradation of Aβ peptides.

    PubMed

    Dhanavade, Maruti J; Parulekar, Rishikesh S; Kamble, Subodh A; Sonawane, Kailas D

    2016-01-01

    The pathological hallmark of Alzheimer's disease is the accumulation of Aβ peptides in human brains. These Aβ peptides can be degraded by several enzymes such as hACE, hECE, hIDE and cathepsin B. Out of which cathepsin B also belongs to the papain super family and has been found in human brains, it has a role in Aβ peptide degradation through limited proteolysis. The Aβ concentrations are maintained properly by its production and clearance via receptor-mediated cellular uptake and direct enzymatic degradation. However, the reduced production of Aβ degrading enzymes as well as their Aβ degrading activity in human brains initiate the process of accumulation of Aβ peptides. So it becomes essential to investigate the molecular interactions involved in the process of Aβ degradation in detail at the atomic level. Hence, homology modeling, molecular docking and molecular dynamics simulation techniques have been used to explore the possible role of cathepsin B from Hordeum vulgare in the degradation of amyloid beta (Aβ) peptides. The homology model of cathepsin B from Hordeum vulgare shows good similarity with human cathepsin B. Molecular docking and MD simulation results revealed that the active site residues Cys32, HIS112, HIS113 are involved in the catalytic activity of cathepsin B. The sulfhydryl group of the Cys32 residue of cathepsin B from Hordeum vulgare cleaves the Aβ peptide from the carboxylic end of Glu11. Hence, this structural study might be helpful in designing alternative strategies for the treatment of AD. PMID:26568474

  4. 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.

  5. 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.

  6. Hemagglutinin fusion peptide mutants in model membranes: structural properties, membrane physical properties, and PEG-mediated fusion.

    PubMed

    Haque, Md Emdadul; Chakraborty, Hirak; Koklic, Tilen; Komatsu, Hiroaki; Axelsen, Paul H; Lentz, Barry R

    2011-09-01

    While the importance of viral fusion peptides (e.g., hemagglutinin (HA) and gp41) in virus-cell membrane fusion is established, it is unclear how these peptides enhance membrane fusion, especially at low peptide/lipid ratios for which the peptides are not lytic. We assayed wild-type HA fusion peptide and two mutants, G1E and G13L, for their effects on the bilayer structure of 1,2-dioleoyl-3-sn-phosphatidylcholine/1,2-dioleoyl-3-sn-phosphatidylethanolamine/Sphingomyelin/Cholesterol (35:30:15:20) membranes, their structures in the lipid bilayer, and their effects on membrane fusion. All peptides bound to highly curved vesicles, but fusion was triggered only in the presence of poly(ethylene glycol). At low (1:200) peptide/lipid ratios, wild-type peptide enhanced remarkably the extent of content mixing and leakage along with the rate constants for these processes, and significantly enhanced the bilayer interior packing and filled the membrane free volume. The mutants caused no change in contents mixing or interior packing. Circular dichroism, polarized-attenuated total-internal-reflection Fourier-transform infrared spectroscopy measurements, and membrane perturbation measurements all conform to the inverted-V model for the structure of wild-type HA peptide. Similar measurements suggest that the G13L mutant adopts a less helical conformation in which the N-terminus moves closer to the bilayer interface, thus disrupting the V-structure. The G1E peptide barely perturbs the bilayer and may locate slightly above the interface. Fusion measurements suggest that the wild-type peptide promotes conversion of the stalk to an expanded trans-membrane contact intermediate through its ability to occupy hydrophobic space in a trans-membrane contact structure. While wild-type peptide increases the rate of initial intermediate and final pore formation, our results do not speak to the mechanisms for these effects, but they do leave open the possibility that it stabilizes the transition states for these events. PMID:21889446

  7. 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.

  8. 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.

  9. Sulfur hexafluoride: Optimal use as a gas-phase, infrared sensitizer

    SciTech Connect

    Stanley, A.E.; Ludwick, L.M.; White, D.; Andrews, D.E.; Godbey, S.E. )

    1992-12-01

    Investigations into the use of sulfur hexafluoride, SF[sub 6], as a gas-phase, infrared photochemical sensitizer have revealed several interesting phenomena. The expedient use of SF[sub 6] can produce an optimal quantity of nitrated product in the gas-phase, laser-induced nitration of cyclopentane. The optimal utilization of sulfur hexafluoride required critical optimization of both frequency and quantity. The results are described herein. 12 refs., 3 figs., 1 tab.

  10. 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.

  11. 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.

  12. Triplet-state energies and substituent effects of excited aroyl compounds in the gas phase

    NASA Astrophysics Data System (ADS)

    Lin, Zhong-Ping; Aue, Walter A.

    2000-01-01

    Triplet-state energy values obtained from the gas phase are still scarce. In this study, the triplet-state energies of 58 aroyl compounds, introduced as gas chromatographic peaks at atmospheric pressure and typically 473 K, have been determined from the 0-0 bands of their n→π* type phosphorescence spectra in excited nitrogen. Correlations of those gas-phase triplet-state energies with Hammett constants could be observed for substituted acetophenones, benzaldehydes and benzophenones.

  13. Detection Of Gas-Phase Polymerization in SiH4 And GeH4

    NASA Technical Reports Server (NTRS)

    Shing, Yuh-Han; Perry, Joseph W.; Allevato, Camillo E.

    1990-01-01

    Inelastic scattering of laser light found to indicate onset of gas-phase polymerization in plasma-enhanced chemical-vapor deposition (PECVD) of photoconductive amorphous hydrogenated silicon/germanium alloy (a-SiGe:H) film. In PECVD process, film deposited from radio-frequency glow-discharge plasma of silane (SiH4) and germane (GeH4) diluted with hydrogen. Gas-phase polymerization undesirable because it causes formation of particulates and defective films.

  14. Energetics and Dynamics of Dissociation of Deprotonated Peptides: Fragmentation of Angiotensin Analogs

    SciTech Connect

    Laskin, Julia; Yang, Zhibo

    2011-12-01

    We present a first study of the energetics and dynamics of dissociation of deprotonated peptides using time- and collision-energy resolved surface-induced dissociation (SID) experiments. SID of four model peptides: RVYIHPF, HVYIHPF, DRVYIHPF, and DHVYIHPF was studied using a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) configured for studying ion-surface collisions. Energy and entropy effects for the overall decomposition of the precursor ion were deduced by modeling the time- and collision energy-resolved survival curves using an RRKM based approach developed in our laboratory. The results were compared to the energetics and dynamics of dissociation of the corresponding protonated species. We demonstrate that acidic peptides are less stable in the negative mode because of the low threshold associated with the kinetically hindered loss of H2O from [M-H]- ions. Comparison between the two basic peptides indicates that the lower stability of the [M-H]- ion of RVYIHPF as compared to HVYIHPF towards fragmentation is attributed to the differences in fragmentation mechanisms. Specifically, threshold energy associated with losses of NH3 and NHCNH from RVYIHPF is lower than the barrier for backbone fragmentation that dominates gas-phase decomposition of HVYIHPF. The results provide a first quantitative comparison between the energetics and dynamics of dissociation of [M+H]+ and [M-H]- ions of acidic and basic peptides.

  15. ESEEM Analysis of Multi-Histidine Cu(II)-Coordination in Model Complexes, Peptides, and Amyloid-?

    PubMed Central

    2015-01-01

    We validate the use of ESEEM to predict the number of 14N nuclei coupled to a Cu(II) ion by the use of model complexes and two small peptides with well-known Cu(II) coordination. We apply this method to gain new insight into less explored aspects of Cu(II) coordination in amyloid-? (A?). A? has two coordination modes of Cu(II) at physiological pH. A controversy has existed regarding the number of histidine residues coordinated to the Cu(II) ion in component II, which is dominant at high pH (?8.7) values. Importantly, with an excess amount of Zn(II) ions, as is the case in brain tissues affected by Alzheimers disease, component II becomes the dominant coordination mode, as Zn(II) selectively substitutes component I bound to Cu(II). We confirm that component II only contains single histidine coordination, using ESEEM and set of model complexes. The ESEEM experiments carried out on systematically 15N-labeled peptides reveal that, in component II, His 13 and His 14 are more favored as equatorial ligands compared to His 6. Revealing molecular level details of subcomponents in metal ion coordination is critical in understanding the role of metal ions in Alzheimers disease etiology. PMID:25014537

  16. Modeling the electrophoresis of peptides and proteins: improvements in the "bead method" to include ion relaxation and "finite size effects".

    PubMed

    Xin, Yao; Hess, Richard; Ho, Nhi; Allison, Stuart

    2006-12-14

    A bead model methodology developed in our lab (Xin et al. J. Phys. Chem. B 2006, 110, 1038) and applicable to modeling the free solution electrophoretic mobility of peptides and proteins is generalized in two significant ways. First, an approximate account is taken of the relaxation effect, which makes the methodology applicable to more highly charged peptides and proteins than was previously possible. Second, a more accurate account is taken of the finite size of the beads making up the model structure. This improvement makes the method applicable at higher salt concentrations and/or to models consisting of larger sized subunits. The relaxation effect is accounted for by correcting "unrelaxed" mobilities on the basis of model size and average electrostatic surface, or zeta potential. Correction factors are estimated using those of spheres with the same hydrodynamic radius and zeta potential as the model structure. The correction factors of spheres are readily determined. The more general methodology is first applied to two sets of peptides (74 different peptides total) varying in size from 2 to 42 amino acids. The sets also cover a wide range of net charges. It is shown that accounting for finite bead size results in a small change in model mobilities under the conditions of the experiments (35 mM monovalent salt). The correction for ion relaxation, however, can be significant for highly charged peptides and improves agreement between model and experimental mobilities. Our correction procedure is also tested by examining the electrophoretic mobility of a particular protein "charge ladder" (Carbeck et al. J. Am. Chem. Soc. 1999, 121, 10,671), where the protein charge is varied over a wide range yet the conformation remains essentially constant. In summary, the effects of ion relaxation can be significant if the absolute electrophoretic mobility of a peptide exceeds approximately 0.20 cm2/(kV s). PMID:17149927

  17. 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.

  18. 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.

  19. Immune response to controlled release of immunomodulating peptides in a murine experimental autoimmune encephalomyelitis (EAE) model.

    PubMed

    Zhao, Hong; Kiptoo, Paul; Williams, Todd D; Siahaan, Teruna J; Topp, Elizabeth M

    2010-01-25

    The effects of controlled release on immune response to an immunomodulating peptide were evaluated in a murine experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis (MS). The peptide, Ac-PLP-BPI-NH(2)-2 (Ac-HSLGKWLGHPDKF-(AcpGAcpGAcp)(2)-ITDGEATDSG-NH(2); Ac = acetyl, Acp = epsilon aminocaproic acid) was designed to suppress T-cell activation in response to PLP(139-151), an antigenic peptide in MS. Poly-lactide-co-glycolide (PLGA) microparticles containing Ac-PLP-BPI-NH(2)-2 (8+/-4 microm, 1.4+/-0.2% (w/w)) were prepared by a powder-in oil-in water emulsion-solvent evaporation method, sterilized and administered subcutaneously (s.c.) to SJL/J (H-2(s)) mice in which EAE had been induced by immunization with PLP(139-151). Treatment groups received Ac-PLP-BPI-NH(2)-2: (i) in solution by repeated i.v. or s.c. injection, (ii) in solution co-administered with blank PLGA microparticles, (iii) in solution co-administered with Ac-PLP-BPI-NH(2)-2 loaded microparticles, and (iv) as Ac-PLP-BPI-NH(2)-2 loaded microparticles. Administration of Ac-PLP-BPI-NH(2)-2 as an s.c. solution produced clinical scores and maintenance of body weight comparable to i.v. solution, but with reduced overall survival, presumably due to anaphylaxis. Administration as s.c. microparticles provided a somewhat less effective reduction in symptoms but with no toxicity during treatment. Thus, the results suggest that s.c. administration of Ac-PLP-BPI-NH(2)-2 microparticles can provide pharmacological efficacy and reduction in dosing frequency without increased toxicity. PMID:19748537

  20. Gas-Phase Synthesis of Gold- and Silica-Coated Nanoparticles

    NASA Astrophysics Data System (ADS)

    Boies, Adam Meyer

    2011-12-01

    Composite nanoparticles consisting of separate core-shell materials are of interest for a variety of biomedical and industrial applications. By combining different materials at the nanoscale, particles can exhibit enhanced or multi-functional behavior such as plasmon resonance combined with superparamagnetism. Gas-phase nanoparticle synthesis processes are promising because they can continuously produce particles with high mass-yield rates. In this dissertation, new methods are investigated for producing gas-phase coatings of nanoparticles in an "assembly-line" fashion. Separate processes are developed to create coatings from silica and gold that can be used with a variety of core-particle chemistries. A photoinduced chemical vapor deposition (photo-CVD) method is used to produce silica coatings from tetraethyl orthosilicate (TEOS) on the surface of nanoparticles (diameter ˜5--70 nm). Tandem differential mobility analysis (TDMA) of the process demonstrates that particle coatings can be produced with controllable thicknesses (˜1--10 nm) by varying system parameters such as precursor flow rate. Electron microscopy and infrared spectroscopy confirm that the photo-CVD films uniformly coat the particles and that the coatings are silica. In order to describe the coating process a chemical mechanism is proposed that includes gas-phase, surface and photochemical reactions. A chemical kinetics model of the mechanism indicates that photo-CVD coating proceeds primarily through the photodecomposition of TEOS which removes ethyl groups, thus creating activated TEOS species. The activated TEOS then adsorbs onto the surface of the particle where a series of subsequent reactions remove the remaining ethyl groups to produce a silica film with an open site for further attachment. The model results show good agreement with the experimentally measured coating trends, where increased TEOS flow increases coating thickness and increased nitrogen flow decreases coating thickness. Gold decoration of nanoparticles is accomplished by evaporation of solid gold in the presence of an aerosol flow. A hot-wire generation method is developed where gold particles are produced from a composite gold-platinum wire. Investigations of the hot-wire generator show that it can produce particles with a range of sizes and that more uniform, non-agglomerated particles are produced when using smaller diameter tubes where gas velocities across the wire are higher and recirculation zones are diminished. When gold is evaporated in the presence of silica nanoparticles, the silica aerosol is decorated by gold through either homogeneous gold nucleation and subsequent scavenging by the silica nanoparticles, or by heterogeneous nucleation on the silica surface in which the gold "balls up" due to the high surface tension of gold on silica. In both cases the resulting particles exhibit a plasmon absorbance resonance typical of gold nanoparticles (lambda˜550 nm). Finally, the silica coating and gold decoration processes are combined with a thermal plasma technique for synthesizing iron-oxide to produce tri-layer nanoparticles.

  1. Development and Validation of Polarized Models for Peptide-Graphene Interactions

    NASA Astrophysics Data System (ADS)

    Heinz, Hendrik; Garley, Amanda; Saikia, Nabanita; Barr, Stephen; Leuty, Gary; Berry, Rajiv

    Biosensor technologies require the understanding of interactions between organic and inorganic materials to tune electric response functions, such as peptide assembly on graphitic substrates. Laboratory characterization of specific interactions and molecular assembly of such biomolecules in atomic resolution remains challenging. These methods can be complemented by molecular simulations and quantum-mechanical analysis of band gaps and expected conductivity. We improved common dispersive interatomic potentials for graphite and graphene to include pi electron density at virtual sites. The new models reproduce experimental X-ray structure, density, cleavage energy, hydration energy, and contact angles. As a result we have improved existing models which gave the wrong sign of hydration energies and deviations on the order of 30% in other properties. The parameters are embedded in CHARMM, CVFF, TEAM-AMBER, and other common force fields as part of the INTERFACE force field. An analysis of binding residues, binding energies, conformations, and dynamic information of molecular mobility on the surfaces will be presented.

  2. The impact of meteorological forcings on gas phase air pollutants over Europe

    NASA Astrophysics Data System (ADS)

    Watson, Laura; Lacressonnière, Gwendoline; Gauss, Michael; Engardt, Magnuz; Andersson, Camilla; Josse, Béatrice; Marécal, Virginie; Nyiri, Agnes; Sobolowski, Stefan; Siour, Guillaume; Vautard, Robert

    2015-10-01

    The impact of meteorological forcings on gas phase air pollutants (ozone and nitrogen dioxide) over Europe was studied using four offline chemistry transport models (CTMs) as part of the IMPACT2C project. This study uses long (20- and 30-year) simulations to evaluate the present-day performance of the CTMs, which is a necessary first step before undertaking any analysis of future air quality impacts. Two sets of meteorological forcings were used for each model: reanalysis of past observation data (ERA-Interim) and Global Climate Model (GCM) output. The results for the simulations forced by reanalysis data were assessed in relation to AirBase v7 measurement data, and it was determined that all four models slightly overpredict annual O3 values (mean biases range between 0.7 and 6.6 ppb) and three out of the four models underpredict observed annual NO2 (mean biases range between -3.1 and -5.2 ppb). The simulations forced by climate models result in spatially averaged monthly concentrations of O3 that are generally between 0 and 5 ppb higher than the values obtained from simulations forced by reanalysis data; therefore it was concluded that the use of climate models introduces an additional bias to the results, but this bias tends not to be significant in the majority of cases. The bias in O3 results appears to be correlated mainly to differences in temperature and boundary layer height between the two types of simulations, whereas the less significant bias in NO2 is negatively correlated to temperature and boundary layer height. It is also clear that the selection of chemical boundary conditions is an important factor in determining the variability of O3 model results. These results will be used as a baseline for the interpretation of future work, which will include an analysis of future climate scenarios upon European air quality.

  3. The Synthetic Parasite-Derived Peptide GK1 Increases Survival in a Preclinical Mouse Melanoma Model

    PubMed Central

    Vera-Aguilera, Jesús; Hernaiz-Leonardo, Juan Carlos; Moreno-Aguilera, Eduardo; Monteverde-Suarez, Diego; Vera-Aguilera, Carlos; Estrada-Bárcenas, Daniel

    2013-01-01

    Abstract Purpose The therapeutic efficacy of a synthetic parasite-derived peptide GK1, an immune response booster, was evaluated in a mouse melanoma model. This melanoma model correlates with human stage IIb melanoma, which is treated with wide surgical excision; a parallel study employing a surgical treatment was carried out as an instructive goal. Experimental Design C57BL/6 mice were injected subcutaneously in the flank with 2×105 B16-F10 murine melanoma cells. When the tumors reached 20 mm3, mice were separated into two different groups; the GK1 group, treated weekly with peritumoral injections of GK1 (10 μg/100 μL of sterile saline solution) and the control group, treated weekly with an antiseptic peritumoral injection of 100 μL of sterile saline solution without further intervention. All mice were monitored daily for clinical appearance, tumor size, and survival. Surgical treatment was performed in parallel when the tumor size was 20 mm3 (group A), 500 mm3 (group B), and >500 mm3 (group C). Results The GK1 peptide effectively increased the mean survival time by 9.05 days, corresponding to an increase of 42.58%, and significantly delayed tumor growth from day 3 to 12 of treatment. In addition, tumor necrosis was significantly increased (p<0.05) in the treated mice. The overall survival rates obtained with surgical treatment at 6 months were 83.33% for group A, 40% for group B, and 0% for group C, with significant differences (p<0.05) among the groups. Conclusions The GK1 peptide demonstrated therapeutic properties in a mouse melanoma model, as treatment resulted in a significant increase in the mean survival time of the treated animals (42.58%). The potential for GK1 to be used as a primary or adjuvant component of chemotherapeutic cocktails for the treatment of experimental and human cancers remains to be determined, and surgical removal remains a challenge for any new experimental treatment of melanoma in mouse models. PMID:23841709

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Visser, Robert-Jan; Schellekens, Jack P.; Reuhman-Huisken, Marian E.; Van Ijzendoorn, Leo J.

    1987-08-01

    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 controlling 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 indenecarboxylic acids cannot. Due to the high content of silicon after the treatment these resists become highly etch-resistant towards oxygen plasmas.

  6. 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.

  7. Implications of aromatic-aromatic interactions: From protein structures to peptide models.

    PubMed

    Madhusudan Makwana, Kamlesh; Mahalakshmi, Radhakrishnan

    2015-12-01

    With increasing structural information on proteins, the opportunity to understand physical forces governing protein folding is also expanding. One of the significant non-covalent forces between the protein side chains is aromatic-aromatic interactions. Aromatic interactions have been widely exploited and thoroughly investigated in the context of folding, stability, molecular recognition, and self-assembly processes. Through this review, we discuss the contribution of aromatic interactions to the activity and stability of thermophilic, mesophilic, and psychrophilic proteins. Being hydrophobic, aromatic amino acids tend to reside in the protein hydrophobic interior or transmembrane segments of proteins. In such positions, it can play a diverse role in soluble and membrane proteins, and in α-helix and β-sheet stabilization. We also highlight here some excellent investigations made using peptide models and several approaches involving aryl-aryl interactions, as an increasingly popular strategy in protein and peptide engineering. A recent survey described the existence of aromatic clusters (trimer, tetramer, pentamer, and higher order assemblies), revealing the self-associating property of aryl groups, even in folded protein structures. The application of this self-assembly of aromatics in the generation of modern bionanomaterials is also discussed. PMID:26402741

  8. Antimicrobial peptide Cathelicidin-BF prevents intestinal barrier dysfunction in a mouse model of endotoxemia.

    PubMed

    Song, Deguang; Zong, Xin; Zhang, Haiwen; Wang, Tenghao; Yi, Hongbo; Luan, Chao; Wang, Yizhen

    2015-03-01

    Intestinal barrier functions are altered during the development of sepsis. Cathelicidin antimicrobial peptides, such as LL-37 and mCRAMP, can protect animals against intestinal barrier dysfunction. Cathelicidin-BF (C-BF), a new cathelicidin peptide purified from the venom of the snake Bungarus fasciatus, has been shown to have both antimicrobial and anti-inflammatory properties. This study investigated whether C-BF pretreatment could protect the intestinal barrier against dysfunction in a mouse model of endotoxemia, induced by intraperitoneal injection of LPS (10mg/kg). Mice were treated with low or high dose C-BF before treatment with LPS, and samples were collected 5h after LPS treatment. C-BF reduced LPS induced intestinal histological damage and gut permeability to 4 KD Fluorescein-isothiocyanate-conjugated dextran. Pretreatment with C-BF prevented LPS induced intestinal tight junction disruption and epithelial cell apoptosis. Moreover, C-BF down regulated the expression and secretion of TNF-α, a process involving the NF-κB signaling pathway. C-BF also reduced LPS induced TNF-α expression through the NF-κB signaling pathway in mouse RAW 264.7 macrophages. These findings indicate that C-BF can prevent gut barrier dysfunction induced by LPS, suggesting that C-BF may be used to develop a prophylactic agent for intestinal injury in endotoxemia. PMID:25639228

  9. Antimicrobial Peptides in 2014

    PubMed Central

    Wang, Guangshun; Mishra, Biswajit; Lau, Kyle; Lushnikova, Tamara; Golla, Radha; Wang, Xiuqing

    2015-01-01

    This article highlights new members, novel mechanisms of action, new functions, and interesting applications of antimicrobial peptides reported in 2014. As of December 2014, over 100 new peptides were registered into the Antimicrobial Peptide Database, increasing the total number of entries to 2493. Unique antimicrobial peptides have been identified from marine bacteria, fungi, and plants. Environmental conditions clearly influence peptide activity or function. Human α-defensin HD-6 is only antimicrobial under reduced conditions. The pH-dependent oligomerization of human cathelicidin LL-37 is linked to double-stranded RNA delivery to endosomes, where the acidic pH triggers the dissociation of the peptide aggregate to release its cargo. Proline-rich peptides, previously known to bind to heat shock proteins, are shown to inhibit protein synthesis. A model antimicrobial peptide is demonstrated to have multiple hits on bacteria, including surface protein delocalization. While cell surface modification to decrease cationic peptide binding is a recognized resistance mechanism for pathogenic bacteria, it is also used as a survival strategy for commensal bacteria. The year 2014 also witnessed continued efforts in exploiting potential applications of antimicrobial peptides. We highlight 3D structure-based design of peptide antimicrobials and vaccines, surface coating, delivery systems, and microbial detection devices involving antimicrobial peptides. The 2014 results also support that combination therapy is preferred over monotherapy in treating biofilms. PMID:25806720

  10. Predicting antitumor activity of peptides by consensus of regression models trained on a small data sample.

    PubMed

    Radman, Andreja; Gredičak, Matija; Kopriva, Ivica; Jerić, Ivanka

    2011-01-01

    Predicting antitumor activity of compounds using regression models trained on a small number of compounds with measured biological activity is an ill-posed inverse problem. Yet, it occurs very often within the academic community. To counteract, up to some extent, overfitting problems caused by a small training data, we propose to use consensus of six regression models for prediction of biological activity of virtual library of compounds. The QSAR descriptors of 22 compounds related to the opioid growth factor (OGF, Tyr-Gly-Gly-Phe-Met) with known antitumor activity were used to train regression models: the feed-forward artificial neural network, the k-nearest neighbor, sparseness constrained linear regression, the linear and nonlinear (with polynomial and Gaussian kernel) support vector machine. Regression models were applied on a virtual library of 429 compounds that resulted in six lists with candidate compounds ranked by predicted antitumor activity. The highly ranked candidate compounds were synthesized, characterized and tested for an antiproliferative activity. Some of prepared peptides showed more pronounced activity compared with the native OGF; however, they were less active than highly ranked compounds selected previously by the radial basis function support vector machine (RBF SVM) regression model. The ill-posedness of the related inverse problem causes unstable behavior of trained regression models on test data. These results point to high complexity of prediction based on the regression models trained on a small data sample. PMID:22272081

  11. Predicting Antitumor Activity of Peptides by Consensus of Regression Models Trained on a Small Data Sample

    PubMed Central

    Radman, Andreja; Gredičak, Matija; Kopriva, Ivica; Jerić, Ivanka

    2011-01-01

    Predicting antitumor activity of compounds using regression models trained on a small number of compounds with measured biological activity is an ill-posed inverse problem. Yet, it occurs very often within the academic community. To counteract, up to some extent, overfitting problems caused by a small training data, we propose to use consensus of six regression models for prediction of biological activity of virtual library of compounds. The QSAR descriptors of 22 compounds related to the opioid growth factor (OGF, Tyr-Gly-Gly-Phe-Met) with known antitumor activity were used to train regression models: the feed-forward artificial neural network, the k-nearest neighbor, sparseness constrained linear regression, the linear and nonlinear (with polynomial and Gaussian kernel) support vector machine. Regression models were applied on a virtual library of 429 compounds that resulted in six lists with candidate compounds ranked by predicted antitumor activity. The highly ranked candidate compounds were synthesized, characterized and tested for an antiproliferative activity. Some of prepared peptides showed more pronounced activity compared with the native OGF; however, they were less active than highly ranked compounds selected previously by the radial basis function support vector machine (RBF SVM) regression model. The ill-posedness of the related inverse problem causes unstable behavior of trained regression models on test data. These results point to high complexity of prediction based on the regression models trained on a small data sample. PMID:22272081

  12. Speciation of gas-phase and fine particle emissions from burning of foliar fuels.

    PubMed

    Hays, Michael D; Geron, Christopher D; Linna, Kara J; Smith, N Dean; Schauer, James J

    2002-06-01

    Fine particle matter with aerodynamic diameter <2.5 microm (PM2.5) and gas-phase emissions from open burning of six fine (foliar) fuels common to fire-prone U.S. ecosystems are investigated. PM2.5 distribution is unimodal within the 10-450 nm range, indicative of an accumulation mode. Smoldering relative to flaming combustion shows smaller particle number density per unit time and median size. Over 100 individual organic compounds in the primarily carbonaceous (>70% by mass) PM2.5 are chemically speciated by gas chromatography/mass spectrometry. Expressed as a percent of PM2.5 mass, emission ranges by organic compound class are as follows: n-alkane (0.1-2%), polycyclic aromatic hydrocarbon (PAH) (0.02-0.2%), n-alkanoic acid (1-3%), n-alkanedioic acid (0.06-0.3%), n-alkenoic acid (0.3-3%), resin acid (0.5-6%), triterpenoid (0.2-0.5%), methoxyphenol (0.5-3%), and phytosterol (0.2-0.6%). A molecular tracer of biomass combustion, the sugar levoglucosan is abundant and constitutes a remarkably narrow PM2.5 mass range (2.8-3.6%). Organic chemical signatures in PM2.5 from open combustion of fine fuels differ with those of residential wood combustion and other related sources, making them functional for source-receptor modeling of PM. Inorganic matter [PM2.5 - (organic compounds + elemental carbon)] on average is estimated to make up 8% of the PM2.5. Wavelength dispersive X-ray fluorescence spectroscopy and ion chromatography identify 3% of PM2.5 as elements and water-soluble ions, respectively. Compared with residential wood burning, the PM2.5 of fine fuel combustion is nitrate enriched but shows lower potassium levels. Gas-phase C2-C13 hydrocarbon and C2-C9 carbonyl emissions are speciated by respective EPA Methods T0-15 and T0-11A. They comprise mainly low molecular weight C2-C3 compounds and hazardous air pollutants (48 wt % of total quantified volatile organic carbon). PMID:12075778

  13. 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.

  14. Metabolic cleavage of cell-penetrating peptides in contact with epithelial models: human calcitonin (hCT)-derived peptides, Tat(47–57) and penetratin(43–58)

    PubMed Central

    2004-01-01

    We assessed the metabolic degradation kinetics and cleavage patterns of some selected CPP (cell-penetrating peptides) after incubation with confluent epithelial models. Synthesis of N-terminal CF [5(6)-carboxyfluorescein]-labelled CPP, namely hCT (human calcitonin)-derived sequences, Tat(47–57) and penetratin(43–58), was through Fmoc (fluoren-9-ylmethoxycarbonyl) chemistry. Metabolic degradation kinetics of the tested CPP in contact with three cell-cultured epithelial models, MDCK (Madin–Darby canine kidney), Calu-3 and TR146, was evaluated by reversed-phase HPLC. Identification of the resulting metabolites of CF-hCT(9–32) was through reversed-phase HPLC fractionation and peak allocation by MALDI–TOF-MS (matrix-assisted laser-desorption ionization–time-of-flight mass spectrometry) or direct MALDI–TOF-MS of incubates. Levels of proteolytic activity varied highly between the investigated epithelial models and the CPP. The Calu-3 model exhibited the highest proteolytic activity. The patterns of metabolic cleavage of hCT(9–32) were similar in all three models. Initial cleavage of this peptide occurred at the N-terminal domain, possibly by endopeptidase activity yielding both the N- and the C-terminal counterparts. Further metabolic degradation was by aminopeptidase, endopeptidase and/or carboxypeptidase activities. In conclusion, when in contact with epithelial models, the studied CPP were subject to efficient metabolism, a prerequisite of cargo release on the one hand, but with potential for premature cleavage and loss of the cargo as well on the other. The results, particularly on hCT(9–32), may be used as a template to suggest structural modifications towards improved CPP performance. PMID:15193145

  15. The gas-phase metallicity of central and satellite galaxies in the Sloan Digital Sky Survey

    NASA Astrophysics Data System (ADS)

    Pasquali, Anna; Gallazzi, Anna; van den Bosch, Frank C.

    2012-09-01

    We exploit the galaxy groups catalogue of Yang et al. and the galaxy properties measured in the Sloan Digital Sky Survey Data Releases 4 and 7 to study how the gas-phase metallicities of star-forming galaxies depend on environment. We find that satellite and central galaxies follow a qualitatively similar stellar mass (M★)-gas-phase metallicity relation, whereby their gas-phase metallicity increases with M★. Satellites, though, have higher gas-phase metallicities than equally massive centrals, and this difference increases with decreasing stellar mass. We find a maximum offset of 0.06 dex at log(M★/h-2 M⊙) ≃ 8.25. At fixed halo mass, centrals are more metal rich than satellites by ˜0.5 dex on average. This is simply due to the fact that, by definition, centrals are the most massive galaxies in their groups, and the fact that gas-phase metallicity increases with stellar mass. More interestingly, we also find that the gas-phase metallicity of satellites increases with halo mass (Mh) at fixed stellar mass. This increment is more pronounced for less massive galaxies, and, at M★ ≃ 109 h-2 M⊙, corresponds to ˜0.15 dex across the range 11 < log (Mh/h-1 M⊙) < 14. We also show that low-mass satellite galaxies have higher gas-phase metallicities than central galaxies of the same stellar metallicity. This difference becomes negligible for more massive galaxies of roughly solar metallicity. We demonstrate that the observed differences in gas-phase metallicity between centrals and satellites at fixed M★ are not a consequence of stellar mass stripping (advocated by Pasquali et al. in order to explain similar differences but in stellar metallicity), nor to the past star formation history of these galaxies as quantified by their surface mass density or gas mass fraction. Rather, we argue that these trends probably originate from a combination of three environmental effects: (i) strangulation, which prevents satellite galaxies from accreting new, low-metallicity gas which would otherwise dilute their interstellar medium; (ii) ram pressure stripping of the outer gas disc, thereby inhibiting radial inflows of low-metallicity gas and (iii) external pressure provided by the hot gas of the host halo which prevents metal-enriched outflows from escaping the galaxies. Each of these three mechanisms naturally explains why the difference in gas-phase metallicity between centrals and satellites increases with decreasing stellar mass and with increasing host halo mass, at least qualitatively. However, more detailed simulations and observations are required in order to discriminate between these mechanisms, and to test, in detail, whether they are consistent with the data.

  16. Fusion of cell-penetrating peptides to thermally responsive biopolymer improves tumor accumulation of p21 peptide in a mouse model of pancreatic cancer.

    PubMed

    Walker, Leslie R; Ryu, Jung Su; Perkins, Eddie; McNally, Lacey R; Raucher, Drazen

    2014-01-01

    Current therapies for the treatment of pancreatic cancer are limited. The limitations of this type of treatment are abundant. The majority of chemotherapeutic agents used in clinics are highly toxic to both tumor cells and normal tissues due to the lack of specificity. Resistance can develop due to overexposure of these agents. To address these issues, these agents must be made more exclusive toward the tumor site. We have developed a macromolecular carrier based on the sequence of the biopolymer elastin-like polypeptide (ELP) that is able to aggregate upon reaching the externally heated tumor environment. This carrier is specific to the tumor as it only aggregates at the heated tumor site. ELP is soluble below its transition temperature but will aggregate when the temperature is raised above its transition temperature. ELP was modified by p21, a cell cycle inhibitory peptide, and the addition of Bac, a cell-penetrating peptide with nuclear localization capabilities. In this study, p21-ELP-Bac and its control, ELP-p21, were used in cell proliferation studies using the pancreatic cancer cell lines Panc-1, MiaPaca-2, and S2013. ELP-p21 had little effect on proliferation, while the half maximal inhibitory concentration of p21-ELP-Bac was ∼30 μM. As translocation across the plasma membrane is a limiting step for delivery of macromolecules, these polypeptides were utilized in a pancreatic xenograft model to study the plasma clearance, biodistribution, tumor accumulation, and tumor reduction capabilities of the polypeptide with and without a cell-penetrating peptide. PMID:25336913

  17. 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).

  18. Organic acids enhanced decoloration of azo dye in gas phase surface discharge plasma system.

    PubMed

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

    2016-01-25

    A gas phase surface discharge plasma combined with organic acids system was developed to enhance active species mass transfer and dye-containing wastewater treatment efficacy, with Acid Orange II (AO7) as the model pollutant. The effects of discharge voltage and various organic acid additives (acetic acid, lactic acid and nonoic acid) on AO7 decoloration efficiency were evaluated. The experimental results showed that an AO7 decoloration efficiency of approximately 69.0% was obtained within 4 min of discharge plasma treatment without organic acid addition, which was improved to 82.8%, 83.5% and 88.6% within the same treatment time with the addition of acetic acid, lactic acid and nonoic acid, respectively. The enhancement effects on AO7 decoloration efficiency could be attributed to the decrease in aqueous surface tension, improvement in bubble distribution and shape, and increase in ozone equivalent concentration. The AO7 wastewater was biodegradable after discharge plasma treatment with the addition of organic acid. AO7 decomposition intermediates were analyzed by UV-vis spectrometry and GC-MS; 2-naphthol, 1,4-benzoquinone, phthalic anhydride, coumarin, 1,2-naphthoquinone, and 2-formyl-benzoic acid were detected. A possible pathway for AO7 decomposition in this system was proposed. PMID:26444488

  19. 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. PMID:26624519

  20. 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

  1. 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.

  2. Investigation of the gas-phase emitter effect of dysprosium in ceramic metal halide lamps

    NASA Astrophysics Data System (ADS)

    Langenscheidt, O.; Westermeier, M.; Reinelt, J.; Mentel, J.; Awakowicz, P.

    2008-07-01

    The behaviour of electrodes operated with ac-currents in ceramic metal halide lamps containing Hg + NaTlDy iodide has been investigated experimentally. Using transparent YAG lamp tubes with the so-called Bochum model lamp as an outer bulb phase resolved measurements were performed of the electrode temperature and Dy density in dependence on the cold-spot temperature of the salt filling. The electrode tip temperature and electrode power loss are deduced from the temperature profile measured along the electrode axis. The Dy density in front of the electrode is determined by spatially resolved spectroscopic measurements of absolute line intensities. It is found that doping of a mercury lamp only with Dy iodide generates at low operation frequencies a pronounced emitter effect at the cathode but it declines with increasing frequency. In a lamp doped with NaTlDy iodide the formation and movement of Dy ions are hampered by Na ions accumulated in front of the cathode due to cataphoresis. As a consequence the lowering of the power loss by Dy is in part diminished. It is shown that a gas-phase emitter effect of Dy is effective for standard operation conditions of lamps in spite of the counteracting effects of a long time constant of the emitter effect and Na accumulation.

  3. Characterization of gas-phase adsorption on metal oxide thin films using a magnetoelastic resonance microbalance.

    PubMed

    Zorn, Michael E; Rahne, Kari A; Tejedor-Tejedor, M Isabel; Anderson, Marc A; Grimes, Craig A

    2003-11-15

    In this study, a magnetoelastic resonance microbalance (MERM) was used to directly measure the gas-phase adsorption behavior of water vapor, isopropyl alcohol, and acetone on a sol-gel-derived titanium dioxide sensor coating. The nature of the MERM platform enables chemical measurements in situations in which wires or physical connections are undesired (or not possible) or in which sensor cost is a major issue. The underlying MERM technique (with an uncoated sensor) showed excellent day-to-day stability, a linear calibration over a 1 kHz change in frequency (or a 1.5-mg change in mass), and the ability to detect a mass change of 15 microg without any efforts at sensitivity optimization. The titanium dioxide coated sensor yielded excellent response to each of the analytes; however, the response did not follow a simple linear calibration function. A more complex calibration model or utilization of the coated sensor in a limited concentration range would be required for quantitative analysis. The process of applying the metal oxide coatings onto the magnetic substrate altered the structure of the thin film layer, resulting in a relatively loose packing of the porous primary titanium dioxide particles to create an open overall honeycomb structure, thereby affecting the adsorption behavior at high relative concentration. PMID:14616005

  4. Gas-phase formation of the prebiotic molecule formamide: insights from new quantum computations

    NASA Astrophysics Data System (ADS)

    Barone, V.; Latouche, C.; Skouteris, D.; Vazart, F.; Balucani, N.; Ceccarelli, C.; Lefloch, B.

    2015-10-01

    New insights into the formation of interstellar formamide, a species of great relevance in prebiotic chemistry, are provided by electronic structure and kinetic calculations for the reaction NH2 + H2CO → NH2CHO + H. Contrarily to what previously suggested, this reaction is essentially barrierless and can, therefore, occur under the low temperature conditions of intestellar objects thus providing a facile formation route of formamide. The rate coefficient parameters for the reaction channel leading to NH2CHO + H have been calculated to be A = 2.6 × 10-12 cm3 s-1, β = -2.1 and γ = 26.9 K in the range of temperatures 10-300 K. Including these new kinetic data in a refined astrochemical model, we show that the proposed mechanism can well reproduce the abundances of formamide observed in two very different interstellar objects: the cold envelope of the Sun-like protostar IRAS16293-2422 and the molecular shock L1157-B2. Therefore, the major conclusion of this Letter is that there is no need to invoke grain-surface chemistry to explain the presence of formamide provided that its precursors, NH2 and H2CO, are available in the gas phase.

  5. Functional and metabolic properties of alveolar macrophages in response to the gas phase of tobacco smoke

    SciTech Connect

    Drath, D.B.; Shorey, J.M.; Huber, G.L.

    1981-10-01

    The effect of whole tobacco smoke and the gas phase of tobacco smoke on the metabolism and phagocytic ability of alveolar macrophages was monitored over a 30-day exposure period. It was demonstrated that both the gas phase and whole tobacco smoke induced a weight loss in exposed rats. Alveolar macrophage oxygen consumption was markedly increased by both exposure regimens. Superoxide generation was not affected by whole tobacco smoke exposure but was increased in response to the filtered gas phase. Hexose monophosphate shunt activity was not altered by either treatment. When metabolic alterations were seen in response to the separate exposures, they were seen only after a phagocytic challenge to the macrophage and not when the cell was unchallenged. Neither whole tobacco smoke nor the gas phase had any significant effect on the ability of alveolar macrophages to phagocytize a viable challenge of Staphylococcus aureus. Our results suggest that many of the metabolic and functional effects of tobacco smoke on alveolar macrophages can be attributed to the gas-phase component of whole tobacco smoke.

  6. Gas-Phase Oxidation Products From the Photooxidation of Fifteen Biogenic Terpenes

    NASA Astrophysics Data System (ADS)

    Lee, A.; Goldstein, A. H.; Ng, N. L.; Kroll, J. H.; Varutbangkul, V.; Flagan, R. C.; Seinfeld, J. H.

    2005-12-01

    Biogenic emissions of terpene compounds influence atmospheric chemistry through the formation of tropospheric ozone and the production of secondary organic aerosol (SOA). We conducted photooxidation experiments at the Caltech Indoor Chamber Facility to examine the gas-phase products and secondary aerosol yields from isoprene, eight monoterpenes, four sesquiterpenes, and three oxygenated C10 terpenes. Terpenes were reacted with OH in the presence of NOx, with hydrocarbon to NOx ratios consistent with ratios typically observed in the ambient forested environments. The real-time formation of gas-phase oxidation products was monitored using a Proton Transfer Reaction Mass Spectrometer (PTR-MS), which identified compounds by their mass to charge ratio and showed multi-step oxidation pathways from these reactions. The photooxidation of terpenes resulted in the formation of numerous gas-phase oxidation products that were not observed from our previous ozonolysis experiments, as well as the formation of gas-phase organic nitrogen compounds. These gas-phase oxidation products can contribute to tropospheric chemistry through further oxidation reactions in the atmosphere, or may influence the biosphere through the deposition of organic nitrogen compounds downwind. Possible reaction mechanisms and products from the photooxidation of these terpene compounds will be presented, and the relevance of these laboratory experiments to recent observations of rapid within-canopy chemistry will be discussed.

  7. Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin.

    PubMed

    Voronina, Liudmila; Rizzo, Thomas R

    2015-10-21

    Understanding the relation between the gas-phase structure of biological molecules and their solution-phase structure is important when attempting to use gas-phase techniques to address biologically relevant questions. Directly after electrospray ionization, molecules can be kinetically trapped in a state that retains some "memory" of its conformation in solution and is separated from the lowest-energy gas-phase structure by barriers on the potential energy surface. In order to identify and characterize kinetically trapped structures, we have explored the conformational space of triply protonated bradykinin in the gas phase by combining field-asymmetric ion mobility spectrometry (FAIMS) with cold ion spectroscopy. We isolate three distinct conformational families and characterize them by recording their UV-photofragment spectra and vibrational spectra. Annealing of the initial conformational distribution produced by electrospray reveals that one of the conformational families is kinetically trapped, while two others are stable, gas-phase structures. We compare our results to previously published results obtained using drift-tube ion mobility spectrometry (IMS) and propose a correspondence between the conformational families separated by FAIMS and those by IMS. PMID:25940085

  8. 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)

  9. Stabilization of Collagen-Model, Triple-Helical Peptides for In Vitro and In Vivo Applications

    PubMed Central

    Bhowmick, Manishabrata; Fields, Gregg B.

    2014-01-01

    The triple-helical structure of collagen has been accurately reproduced in numerous chemical and recombinant model systems. Triple-helical peptides and proteins have found application for dissecting collagen-stabilizing forces, isolating receptor- and protein-binding sites in collagen, mechanistic examination of collagenolytic proteases, and development of novel biomaterials. Introduction of native-like sequences into triple-helical constructs can reduce the thermal stability of the triple-helix to below that of the physiological environment. In turn, incorporation of nonnative amino acids and/or templates can enhance triple-helix stability. We presently describe approaches by which triple-helical structure can be modulated for use under physiological or near-physiological conditions. PMID:24014440

  10. Protein matrices for improved wound healing: elastase inhibition by a synthetic peptide model.

    PubMed

    Vasconcelos, Andreia; Pêgo, Ana Paula; Henriques, Lara; Lamghari, Meriem; Cavaco-Paulo, Artur

    2010-09-13

    The unique properties of silk fibroin were combined with keratin to develop new wound-dressing materials. Silk fibroin/keratin (SF/K) films were prepared to reduce high levels of elastase found on chronic wounds. This improved biological function was achieved by the incorporation of a small peptide synthesized based on the reactive-site loop of the Bowman-Birk Inhibitor (BBI) protein. In vitro degradation and release were evaluated using porcine pancreatic elastase (PPE) solution as a model of wound exudate. It was found that biological degradation and release rate are highly dependent on film composition. Furthermore, the level of PPE activity can be tuned by changing the film composition, thus showing an innovative way of controlling the elastase-antielastase imbalance found on chronic wounds. PMID:20690591

  11. Conformationally specific enhancement of receptor-mediated LDL binding and internalization by peptide models of a conserved anionic N-terminal domain of human apolipoprotein E.

    PubMed

    Braddock, D T; Mercurius, K O; Subramanian, R M; Dominguez, S R; Davies, P F; Meredith, S C

    1996-11-01

    In this paper, we test the hypothesis that peptide models of a highly conserved domain of apolipoprotein E (amino acids 41-60 in human apo E) modulate the binding and internalization of LDL to cell surface receptors in a conformationally specific manner. Three peptides were compared: peptide I containing the natural sequence of amino acids 41-60 of human apo E; peptide III containing side-chain lactam cross-links designed to enhance alpha-helical structure; and peptide II containing cross-links designed to prevent formation of alpha-helices. Peptide III was shown previously to consist of two short alpha-helical domains linked by a turn and to have more alpha-helical content than peptide I, while peptide II was shown to have less helical content than either peptide III or I(Luo et al., 1994). Peptide III induced a 30-fold increase in the specific binding of 125I-LDL to normal human skin fibroblasts and a 60-fold increase in the binding to fibroblasts lacking the LDL-R. This same peptide also restored the binding to normal fibroblasts of 125I-LDL from a patient with familial defective apolipoprotein B, the R3500-->Q mutation. Analysis of binding indicated an increase in the apparent number of binding sites, with little effect on the affinity of 125I-LDL for the cell surface. Heparinase treatment of the cells did not abrogate this effect, suggesting that the increased binding is not mediated by cell surface glycans. LDL internalization but not degradation was also increased by peptide III. Similar but smaller effects were also induced by peptide I. Peptide II was much less active than peptide I or III. Thus, the order of biological activity was the same as the order of alpha-helical content, i.e., peptide III > peptide I > peptide II. These results suggest a hitherto unknown biological function for a highly conserved domain of apolipoprotein E, and this bioactivity was shown by peptide models to be specific to the alpha-helical conformation. PMID:8909295

  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. Biofunctionalization of electrospun PCL-based scaffolds with perlecan domain IV peptide to create a 3-D pharmacokinetic cancer model

    PubMed Central

    Hartman, Olga; Zhang, Chu; Adams, Elizabeth L.; Farach-Carson, Mary C.; Petrelli, Nicholas J.; Chase, Bruce D.; Rabolt, John F.

    2010-01-01

    Because prostate cancer cells metastasize to bone and exhibit osteoblastic features (osteomimicry), the interrelationships between bone-specific microenvironment and prostate cancer cells at sites of bone metastasis are critical to disease progression. In this work the bone marrow microenvironment in vitro was recreated both by tailoring scaffolds physical properties and by functionalizing electrospun polymer fibers with a bioactive peptide derived from domain IV of perlecan heparan sulfate proteoglycan. Electrospun poly (?-caprolactone) (PCL) fibers and PCL/gelatin composite scaffolds were modified covalently with perlecan domain IV (PlnDIV) peptide. The expression of tight junction protein (E-cadherin) and focal adhesion kinase (FAK) phosphorylation on tyrosine 397 also were investigated. The described bioactive motif significantly enhanced adherence and infiltration of the metastatic prostate cancer cells on all modified electrospun substrates by day 5 post-seeding. Cells cultured on PlnDIV-modified matrices organized stress fibers and increased proliferation at statistically significant rates. Additional findings suggest that presence of PlnDIV peptide in the matrix reduced expression of tight junction protein and binding to PlnDIV peptide was accompanied by increased focal adhesion kinase (FAK) phosphorylation on tyrosine 397. We conclude that PlnDIV peptide supports key signaling events leading to proliferation, survival, and migration of C4-2B cancer cells; hence its incorporation into electrospun matrix is a key improvement to create a successful three-dimensional (3-D) pharmacokinetic cancer model. PMID:20417554

  15. Peptide inhibitors of botulinum neurotoxin serotype A: design, inhibition, cocrystal structures, structure-activity relationship and pharmacophore modeling

    SciTech Connect

    Kumar G.; Swaminathan S.; Kumaran, D.; Ahmed, S. A.

    2012-05-01

    Clostridium botulinum neurotoxins are classified as Category A bioterrorism agents by the Centers for Disease Control and Prevention (CDC). The seven serotypes (A-G) of the botulinum neurotoxin, the causative agent of the disease botulism, block neurotransmitter release by specifically cleaving one of the three SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins and induce flaccid paralysis. Using a structure-based drug-design approach, a number of peptide inhibitors were designed and their inhibitory activity against botulinum serotype A (BoNT/A) protease was determined. The most potent peptide, RRGF, inhibited BoNT/A protease with an IC{sub 50} of 0.9 {micro}M and a K{sub i} of 358 nM. High-resolution crystal structures of various peptide inhibitors in complex with the BoNT/A protease domain were also determined. Based on the inhibitory activities and the atomic interactions deduced from the cocrystal structures, the structure-activity relationship was analyzed and a pharmacophore model was developed. Unlike the currently available models, this pharmacophore model is based on a number of enzyme-inhibitor peptide cocrystal structures and improved the existing models significantly, incorporating new features.

  16. 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.

  17. OMVPE growth and gas-phase reactions of AlGaN for UV emitters

    SciTech Connect

    Han, J.; Figiel, J.J.; Crawford, M.H.; Banas, M.A.; Bartram, M.E.; Biefeld, R.M.; Song, Y.K.; Nurmikko, A.V.

    1998-06-01

    Gas-phase parasitic reactions among TMG, TMA, and NH3, are investigated by monitoring of the growth rate/incorporation efficiency of GaN and AlN using an in-situ optical reflectometer. It is suggested that gas phase adduct (TMA: NH{sub 3}) reactions not only reduce the incorporation efficiency of TMA but also affect the incorporation behavior of TMGa. The observed phenomena can be explained by either a synergistic gas-phase scavenging effect or a surface site-blocking effect. Relatively low reactor pressures (30--50 Torr) are employed to grow an AlGaN/GaN QW p-n diode structure. The UV emission at 354 nm (FWHM {approximately} 6 nm) represents the first report of LED operation from an indium-free GaN QW diode.

  18. Recent radiolytic studies on the mechanism of gas-phase ionic reactions

    NASA Astrophysics Data System (ADS)

    Cacace, Fulvio

    Recent mechanistic applications of radiolytic techniques to gas-phase ion-molecule reactions are reviewed. In particular, attention is focused on the following typical research areas: (i) structural and stereochemical characterization of gaseous ions, and study of their isomerization in a wide pressure range, (ii) stereochemical course of selected ion-molecule reactions, (iii) mechanistic features of gas-phase aromatic substitution, in particular evaluation of the substrate and positional selectivity of gaseous cations, and (iv) competition between proton-transfer and condensation reactions of gaseous cations with n-type nucleophilic centers. The results reviewed underline the mechanistic value of current radiolytic techniques, whose application does extend to the gas phase the degree of structural and stereochemical specificity typical of solution-chemistry studies.

  19. A Survey of Peptides with Effective Therapeutic Potential in Alzheimer’s Disease Rodent Models or in Human Clinical Studies

    PubMed Central

    Sun, N; Funke, SA; Willbold, D

    2012-01-01

    Alzheimer’s disease (AD) is a devastating neurodegenerative disorder and the most common cause of dementia. Today, only palliative therapies are available. The pathological hallmarks of AD are the presence of neurofibrillary tangles and amyloid plaques, mainly composed of the amyloid-β peptide (Aβ), in the brains of the patients. Several lines of evidence suggest that the increased production and/or decreased cleavage of Aβ and subsequent accumulation of Aβ oligomers and aggregates play a fundamental role in the disease progress. Therefore, substances which bind to Aβ and influence aggregation thereof are of great interest. A wide range of Aβ binding peptides were investigated to date for therapeutic purposes. Only very few were shown to be effective in rodent AD models or in clinical studies. Here, we review those peptides and discuss their possible mechanisms of action. PMID:22303971

  20. Conformational characterization of the 1-aminocyclobutane-1-carboxylic acid residue in model peptides.

    PubMed

    Gatos, M; Formaggio, F; Crisma, M; Toniolo, C; Bonora, G M; Benedetti, Z; Di Blasio, B; Iacovino, R; Santini, A; Saviano, M; Kamphuis, J

    1997-01-01

    A series of N- and C-protected, monodispersed homo-oligopeptides (to the dodecamer level) from the small-ring alicyclic C alpha, alpha-dialkylated glycine 1-aminocyclobutane-1-carboxylic acid (Ac4c) and two Ala/Ac4c tripeptides were synthesized by solution methods and fully characterized. The conformational preferences of all the model peptides were determined in deuterochloroform solution by FT-IR absorption and 1H-NMR. The molecular structures of the amino acid derivatives Z-Ac4c-OH and Z2-Ac4c-OH, the tripeptides Z-(Ac4c)3-OtBu, Z-Ac4c-(L-Ala)2-OMe and Z-L-Ala-Ac4c-L-Ala-OMe, and the tetrapeptide Z-(Ac4c)4-OtBu were determined in the crystal state by X-ray diffraction. The average geometry of the cyclobutyl moiety of the Ac4c residue was assessed and the tau(N-C alpha-C') bond angle was found to be significantly expanded from the regular tetrahedral value. The conformational data are strongly in favour of the conclusion that the Ac4c residue is an effective beta-turn and helix former. A comparison with the structural propensities of alpha-aminoisobutyric acid, the prototype of C alpha, alpha-dialkylated glycines, and the other extensively investigated members of the family of 1-aminocycloalkane-1-carboxylic acids (Acnc, with n = 3, 5-8) is made and the implications for the use of the Ac4c residue in conformationally constrained peptide analogues are briefly examined. PMID:9230476

  1. A Colloidal Description of Intermolecular Interactions Driving Fibril-Fibril Aggregation of a Model Amphiphilic Peptide.

    PubMed

    Owczarz, Marta; Motta, Anna C; Morbidelli, Massimo; Arosio, Paolo

    2015-07-14

    We apply a kinetic analysis platform to study the intermolecular interactions underlying the colloidal stability of dispersions of charged amyloid fibrils consisting of a model amphiphilic peptide (RADA 16-I). In contrast to the aggregation mechanisms observed in the large majority of proteins and peptides, where several elementary reactions involving both monomers and fibrils are present simultaneously, the system selected in this work allows the specific investigation of the fibril-fibril aggregation process. We examine the intermolecular interactions driving the aggregation reaction at pH 2.0 by changing the buffer composition in terms of salt concentration, type of ion as well as type and concentration of organic solvent. The aggregation kinetics are followed by dynamic light scattering, and the experimental data are simulated by Smoluchowski population balance equations, which allow to estimate the energy barrier between two colliding fibrils in terms of the Fuchs stability ratio (W). When normalized on a dimensionless time weighted on the Fuchs stability ratio, the aggregation profiles under a broad range of conditions collapse on a single master curve, indicating that the buffer composition modifies the aggregation kinetics without affecting the aggregation mechanism. Our results show that the aggregation process does not occur under diffusion-limited conditions. Rather, the reaction rate is limited by the presence of an activation energy barrier that is largely dominated by electrostatic repulsive interactions. Such interactions could be reduced by increasing the concentration of salt, which induces charge screening, or the concentration of organic solvent, which affects the dielectric constant. It is remarkable that the dependence of the activation energy on the ionic strength can be described quantitatively in terms of charge screening effects in the frame of the DLVO theory, although specific anion and cation effects are also observed. While anion effects are mainly related to the binding to the positive groups of the fibril surface and to the resulting decrease of the surface charge, cation effects are more complex and involve additional solvation forces. PMID:26125620

  2. Infrared Reflection Absorption Spectroscopy of Amphipathic Model Peptides at the Air/Water Interface

    PubMed Central

    Kerth, Andreas; Erbe, Andreas; Dathe, Margitta; Blume, Alfred

    2004-01-01

    The linear sequence KLAL (KLALKLALKALKAALKLA-NH2) and its corresponding d,l-isomers k9a10-KLAL (KLALKLALkaLKAALKLA-NH2) and l11k12-KLAL (KLALKLALKAlkAALKLA-NH2) are model compounds for potentially amphipathic α-helical peptides which are able to bind to membranes and to increase the membrane permeability in a structure- and target-dependent manner (Dathe and Wieprecht, 1999) We first studied the secondary structure of KLAL and its analogs bound to the air/water using infrared reflection absorption spectroscopy. For the peptide films the shape and position of the amide I and amide II bands indicate that the KLAL adopts at large areas per molecule an α-helical secondary structure, whereas at higher surface pressures or smaller areas it converts into a β-sheet structure. This transition could be observed in the compression isotherm as well as during the adsorption at the air/water interface from the subphase as a function of time. The secondary structures are essentially orientated parallel to the air/water interface. The analogs with d-amino acids in two different positions of the sequence, k9a10-KLAL and l11k12-KLAL, form only β-sheet structures at all surface pressures. The observed results are interpreted using a comparison of hydrophobic moments calculated for α-helices and β-sheets. The differences between the hydrophobic moments calculated using the consensus scale are not large. Using the optimal matching hydrophobicity scale or the whole-residue hydrophobicity scale the β-sheet even has the larger hydrophobic moment. PMID:15189871

  3. Enantiomer-Selective Photolysis of Cold Gas-Phase Tryptophan in L-Serine Clusters with Linearly Polarized Light

    NASA Astrophysics Data System (ADS)

    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. Effect of Proton Substitution by Alkali Ions on the Fluorescence Emission of Rhodamine B Cations in the Gas Phase.

    PubMed

    Greisch, Jean-François; Harding, Michael E; Klopper, Wim; Kappes, Manfred M; Schooss, Detlef

    2014-05-14

    The photophysics of chromophores is strongly influenced by their environment. Solvation, charge state, and adduct formation significantly affect ground and excited state energetics and dynamics. The present study reports on fluorescence emission of rhodamine B cations (RhBH(+)) and derivatives in the gas phase. Substitution of the acidic proton of RhBH(+) by alkali metal cations, M(+), ranging from lithium to cesium leads to significant and systematic blue shifts of the emission. The gas-phase structures and singlet transition energies of RhBH(+) and RhBM(+), M = Li, Na, K, Rb, and Cs, were investigated using Hartree-Fock theory, density functional methods, second-order Møller-Plesset perturbation theory, and the second-order approximate coupled-cluster model CC2. Comparison of experimental and theoretical results highlights the need for improved quantum chemical methods, while the hypsochromic shift observed upon substitution appears best explained by the Stark effect due to the inhomogeneous electric field generated by the alkali ions. PMID:24786781

  5. 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. PMID:25351685

  6. 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.