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Sample records for model gas-phase peptide

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

    PubMed

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

    2015-07-14

    The distance-dependence of excitation energy transfer, e.g., being described by Förster theory (Förster resonance energy transfer (FRET)), allows the use of optical techniques for the direct observation of structural properties. Recently, this technique has been successfully applied in the gas phase. The detailed interpretation of the experimental FRET results, however, relies on the comparison with structural modeling. We therefore present a complete first-principles modeling approach that explores the gas-phase structure of chromophore-grafted peptides and achieves accurate predictions of FRET efficiencies. We apply the approach to amyloid-? 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

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

  3. Aldehyde complexes with protonated peptides in the gas phase.

    PubMed

    Shi, Xiangguo; Ren, Jianhua; Parks, Joel H

    2011-09-29

    This Article presents a study of aldehyde complexes with peptide ions formed by bimolecular collisions in the gas phase. Desolvated ions generated by electrospray ionization are stored within a radio frequency (RF) ion trap and exposed to aldehyde vapor. Mass spectrometry measurements were performed on the resulting aldehyde complexes formed with single amino acids (LysH(+), HisH(+), and ArgH(+)) and polypeptides [Pro(n)-Lys+2H](2+) and [(Gly-Ser)(m)-Lys+2H](2+). These data identify several interesting and unexpected aspects of the aldehyde complex kinetics. It is observed that the formation of stable complexes requires the presence of water vapor. The formation kinetics of aldehyde-peptide complexes exhibits multiexponential time dependence that is modeled by interactions in the presence of structural heterogeneity. Aldehyde binding appears to involve a competition between conformers with unhindered access to protonation sites and conformers with intramolecular solvation of these sites. Proton transfer to the aldehyde ligand is responsible for the loss of the complexes. This is supported by proton affinity calculations and identified by reaction products exhibiting loss of protonation by the parent ion accompanied by the appearance of aldehyde cations. PMID:21834583

  4. 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

  5. Volumes of Individual Amino Acid Residues in Gas-Phase Peptide Ions

    E-print Network

    Clemmer, David E.

    Volumes of Individual Amino Acid Residues in Gas-Phase Peptide Ions Anne E. Counterman and David E calculations have been combined to extract average volumes of amino acid residues in gas-phase peptide ions [XxxnLys+H]+ (where Xxx is any amino acid except Lys, Arg, His, and Cys, and n ) 4 to 8). The results

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

    NASA Astrophysics Data System (ADS)

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

    2005-02-01

    Recent developments in sample introduction of biologically relevant molecules have heralded a new era for gas-phase methods of structural determination. One of the biggest challenges is to relate gas-phase structures, often measured in the absence of water and counter ions, with in vivo biologically active structures. An advantage of gas-phase based techniques is that a given peptide can be analysed in a variety of different forms, for example, as a function of charge state, or with additional water molecules. Molecular modelling can provide insight into experimental findings and help elucidate the differences between structural forms. Combining experiment and theory provides a thorough interrogation of candidate conformations. Here two important naturally occurring peptide systems have been examined in detail and results are assessed in terms of their biological significance. The first of these is gonadotropin-releasing hormone (GnRH), a decapeptide which is the central regulator of the reproductive system in vertebrates. We have examined several naturally occurring variants of this peptide using Ion Mobility Mass Spectrometry and Electron Capture Dissociation (ECD) in conjunction with Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR-MS). Candidate conformations are modelled using the AMBER force field. Single amino acid changes, for example Gly6 --> Ala6, or Ala6 --> D-Ala6, have observable effects on the gas phase structure of GnRH. It has been shown that evolutionary primary sequence variations are key to the biological activity of GnRH, and it is thought that this is due to different binding affinities at target receptors. This work provides strong evidence that this activity is structurally based. The second system examined is the relationship between the quaternary structure and activity of two novel [beta]-defensins. FT-ICR mass spectrometry has been employed to characterize di-sulphide bridging and dissociation based experiments utilised to investigate their structural core. Defr1, with five cysteines, exists as a covalently bound disulphide linked dimer; Defr1 Y5C with six cysteines also is observed as a dimer, but non-covalently bound, suggesting that this defensin has a tendency to aggregate. The activity of Defr1 is 10 times higher than that of Defr1 Y5C when tested against the pathogen Pseudomonas aeruginosa. The results from these studies could inform future design of novel GnRH type ligands and anti-microbial agents, and illustrate the power of gas-phase based techniques for solving peptide structures.

  7. Photosynthesis of a Combinatorial Peptide Library in the Gas Phase Sunyoung Lee,

    E-print Network

    Clemmer, David E.

    Photosynthesis of a Combinatorial Peptide Library in the Gas Phase Sunyoung Lee, Matthew S. Glover. The solutions were infused at a flow rate of 3.0 L min-1 using a syringe pump. A potential of 3.0 kV was applied

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

    PubMed Central

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

    1999-01-01

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

  9. 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

  10. 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.

  11. 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

  12. Probing the Gas Phase Folding Kinetics of Peptide Ions by IR Activated DR-ECD

    PubMed Central

    Lin, Cheng; Cournoyer, Jason J.; O’Connor, Peter B.

    2011-01-01

    The effect of infrared (IR) irradiation on the electron capture dissociation (ECD) fragmentation pattern of peptide ions was investigated. IR heating increases the internal energy of the precursor ion, which often amplifies secondary fragmentation, resulting in the formation of w-type ions as well as other secondary fragments. Improved sequence coverage was observed with IR irradiation before ECD, likely due to the increased conformational heterogeneity upon IR heating, rather than faster breakdown of the initially formed product ion complex, as IR heating after ECD did not have similar effect. Although the ECD fragment ion yield of peptide ions does not typically increase with IR heating, in double resonance (DR) ECD experiments, fragment ion yield may be reduced by fast resonant ejection of the charge reduced molecular species, and becomes dependent on the folding state of the precursor ion. In this work, the fragment ion yield was monitored as a function of the delay between IR irradiation and the DR-ECD event to study the gas phase folding kinetics of the peptide ions. Furthermore, the degree of intra-complex hydrogen transfer of the ECD fragment ion pair was used to probe the folding state of the precursor ion. Both methods gave similar refolding time constants of ~1.5 s?1, revealing that gaseous peptide ions often refold in less than a second, much faster than their protein counterparts. It was also found from the IR-DR-ECD study that the intra-molecular H• transfer rate can be an order of magnitude higher than that of the separation of the long-lived c/z product ion complexes, explaining the common observation of c• and z type ions in ECD experiments. PMID:18400512

  13. Metal-Mediated Peptide Ion Conformations in the Gas Phase John A. Taraszka, Jianwei Li, and David E. Clemmer*

    E-print Network

    Clemmer, David E.

    Metal-Mediated Peptide Ion Conformations in the Gas Phase John A. Taraszka, Jianwei Li, and David E, 1999; In Final Form: February 24, 2000 The influence of metal cations and source temperature-resolution ion mobility techniques. Cross sections for non-metalated [ICA-nH]n- (n ) 2-6) ions show a distinct

  14. 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

  15. 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.

  16. 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 (?S(‡) ?=?-30 to -25?eu) suggested that the transition structure was stabilized by multiple intramolecular interactions. PMID:24863621

  17. 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.

  18. Cis-Trans Signatures of Proline-Containing Tryptic Peptides in the Gas Phase

    E-print Network

    Clemmer, David E.

    . No other amino acids were common to all sequences. The appearance of multiple features only for sequences digest peptide ions obtained from digestion of common proteins. Here, we report a mobility signature-terminal carboxylic acid group. Several studies of fragmentation patterns of proline-containing proteins and peptides

  19. Structure-property relationships in gas-phase protonated and metalated peptide ions 

    E-print Network

    Slaton, James Garrett

    2009-05-15

    amino acid is either arginine, histidine, lysine, aspartic acid or tryptophan and the Z amino acid is proline, glycine, serine, or histidine. These homologous peptide ions have been carefully selected to probe the effects of charge site location...

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  1. 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.

  2. Combining UV photodissociation action spectroscopy with electron transfer dissociation for structure analysis of gas-phase peptide cation-radicals.

    PubMed

    Shaffer, Christopher J; Pepin, Robert; Ture?ek, František

    2015-12-01

    We report the first example of using ultraviolet (UV) photodissociation action spectroscopy for the investigation of gas-phase peptide cation-radicals produced by electron transfer dissociation. z-Type fragment ions (?) Gly-Gly-Lys(+) , coordinated to 18-crown-6-ether (CE), are generated, selected by mass and photodissociated in the 200-400?nm region. The UVPD action spectra indicate the presence of valence-bond isomers differing in the position of the C? radical defect, (?-Gly)-Gly-Lys(+) (CE), Gly-(?-Gly)-Lys(+) (CE) and Gly-Gly-(?-Lys(+) )(CE). The isomers are readily distinguishable by UV absorption spectra obtained by time-dependent density functional theory (TD-DFT) calculations. In contrast, conformational isomers of these radical types are calculated to have similar UV spectra. UV photodissociation action spectroscopy represents a new tool for the investigation of transient intermediates of ion-electron reactions. Specifically, z-type cation radicals are shown to undergo spontaneous hydrogen atom migrations upon electron transfer dissociation. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26634979

  3. A Model of Gas-Phase Transport During the Initial Stages of Sintering of Silicon Carbide

    E-print Network

    Matthewson, M. John

    A Model of Gas-Phase Transport During the Initial Stages of Sintering of Silicon Carbide Anil Kaza used as an additive to silicon carbide powder, is thought to facilitate densification during sintering pressureless sintering of silicon carbide (SiC) was first discovered by Prochazka in 1977,1 using boron

  4. Liquid Gas Phase Transition for Asymmetric Nuclear Matter in the Zimanyi Moszkowski Model

    NASA Astrophysics Data System (ADS)

    Zhang, Xu-Ming; Qian, Wei-Liang; Su, Ru-Keng

    2004-07-01

    By using the improved Zimanyi-Moszkowski (ZM) model including the freedom of nucleons, sigma mesons, omega mesons and rho mesons, we investigate the liquid-gas phase transition for asymmetric nuclear matter. It is found that the phase transition for asymmetric nuclear matter in the improved ZM model with the isospin vector rho meson degree of freedom is well defined. The binodal surface, which is essential in the study of the phase transition process, is addressed.

  5. Gas-phase abundances of refractory elements in planetary nebulae - A hot-wind model

    NASA Astrophysics Data System (ADS)

    Shields, G. A.

    1980-08-01

    Planetary nebulae (PN) characteristically show large gas-phase depletions of some refractory elements, with Fe/H and Ca/H concentration ratios approximately equal to -1.5. In contrast, the gas-phase abundance of carbon is large, with a C/H concentration ratio greater than approximately +0.3. This pattern is difficult to understand in terms of grain formation and destruction during PN formation. However, these abundances are consistent with a model (Kwok, Purton, and FitzGerald, 1978) in which the PN shell consists of material expelled as a wind during the red-giant phase and subsequently compressed and accelerated by the impact of a hot stellar wind from the central star.

  6. From Solution to the Gas Phase: Stepwise Dehydration and Kinetic Trapping of Substance P Reveals the Origin of Peptide

    E-print Network

    Clemmer, David E.

    From Solution to the Gas Phase: Stepwise Dehydration and Kinetic Trapping of Substance P Reveals+ , the results demonstrate that a compact dehydrated conformer population can be kinetically trapped on the time intramolecular interactions in the absence of complicating solvation effects.4-7 However, a potential concern

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

    E-print Network

    James R. Torres; Francesca Gulminelli; Débora P. Menezes

    2015-10-26

    Background: The advent of new dedicated experimental programs on hyperon physics is rapidly boosting the field, and the possibility of synthetizing 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 $\\Lambda$ 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 hyper-clusters. Conclusions: More quantitative results within the RMF model need improved functionals at low density, possibly fitted to ab-initio calculations of nuclear and $\\Lambda$ matter.

  8. Gas-Phase Separations of Electrosprayed Peptide Catherine A. Srebalus, Jianwei Li, William S. Marshall, and David E. Clemmer*,

    E-print Network

    Clemmer, David E.

    over 26 residues including 10 naturally occur- ring amino acids and 16 synthetic forms) were ionized-70% of the expected peptides is found. Variation in ion abundance for different components indicates. Mass spectrometry (MS)-based methods can be used to rapidly assess abundance information for ions

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

    The aim of this work was to develop a model suited for detailed studies of aerosol dynamics, gas and particle phase chemistry within urban plumes, from local scale (1 × 1 km2) to regional scale. This article describes and evaluates the trajectory model for Aerosol Dynamics, gas and particle phase CHEMistry and radiative transfer (ADCHEM). The model treats both vertical and horizontal dispersion perpendicular to an air mass trajectory (2-space dimensions). The Lagrangian approach enables a more detailed representation of the aerosol dynamics, gas and particle phase chemistry and a finer spatial and temporal resolution compared to that of available regional 3D-CTMs. These features make it among others well suited for urban plume studies. The aerosol dynamics model includes Brownian coagulation, dry deposition, wet deposition, in-cloud processing, condensation, evaporation, primary particle emissions and homogeneous nucleation. The organic mass partitioning was either modeled with a 2-dimensional volatility basis set (2D-VBS) or with the traditional two-product model approach. In ADCHEM these models consider the diffusion limited and particle size dependent condensation and evaporation of 110 and 40 different organic compounds respectively. The gas phase chemistry model calculates the gas phase concentrations of 61 different species, using 130 different chemical reactions. Daily isoprene and monoterpene emissions from European forests were simulated separately with the vegetation model LPJ-GUESS, and included as input to ADCHEM. ADCHEM was used to simulate the ageing of the urban plumes from the city of Malmö in southern Sweden (280 000 inhabitants). Several sensitivity tests were performed concerning the number of size bins, size structure method, aerosol dynamic processes, vertical and horizontal mixing, coupled or uncoupled condensation and the secondary organic aerosol formation. The simulations show that the full-stationary size structure gives accurate results with little numerical diffusion when more than 50 size bins are used between 1.5 and 2500 nm, while the moving-center method is preferable when only a few size bins are selected. The particle number size distribution in the center of the urban plume from Malmö was mainly affected by dry deposition, coagulation and vertical dilution. The modeled PM2.5 mass was dominated by organic material, nitrate, sulfate and ammonium. If the condensation of HNO3 and NH3 was treated as a coupled process (pH independent) the model gave lower nitrate PM2.5 mass than if considering uncoupled condensation. Although the time of ageing from that SOA precursors are emitted until condensable products are formed is substantially different with the 2D-VBS and two product model, the models gave similar total organic mass concentrations.

  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. A reaction class approach for modeling gas phase reaction rates Thanh N. Truong,* Wendell T. Duncan and Max Tirtowidjojo

    E-print Network

    Truong, Thanh N.

    A reaction class approach for modeling gas phase reaction rates Thanh N. Truong,* Wendell T. Duncan present a series of new tunneling models based on a reaction class approach. Reaction class consists of all reactions that have the same reactive moiety. One can expect that reactions in the same class

  12. Liquid-gas phase transition in hot asymmetric nuclear matter with density-dependent relativistic mean-field models

    E-print Network

    Guang-Hua Zhang; Wei-Zhou Jiang

    2013-02-14

    The liquid-gas phase transition in hot asymmetric nuclear matter is studied within density-dependent relativistic mean-field models where the density dependence is introduced according to the Brown-Rho scaling and constrained by available data at low densities and empirical properties of nuclear matter. The critical temperature of the liquid-gas phase transition is obtained to be 15.7 MeV in symmetric nuclear matter falling on the lower edge of the small experimental error bars. In hot asymmetric matter, the boundary of the phase-coexistence region is found to be sensitive to the density dependence of the symmetry energy. The critical pressure and the area of phase-coexistence region increases clearly with the softening of the symmetry energy. The critical temperature of hot asymmetric matter separating the gas phase from the LG coexistence phase is found to be higher for the softer symmetry energy.

  13. Gas-Phase Lubrication of ta-C by Glycerol and Hydrogen Peroxide. Experimental and Computer Modeling

    E-print Network

    Goddard III, William A.

    Gas-Phase Lubrication of ta-C by Glycerol and Hydrogen Peroxide. Experimental and Computer Modeling and hydrogen peroxide. The experiments were complemented by computer simulations using the ReaxFF reactive. Sliding simulations show that the carbon surface atoms react with glycerol and hydrogen peroxide to form

  14. Modeling of Gas Phase Transport and Composition Evolution during the Initial Stage Sintering of Boron Carbide with Carbon Additions

    E-print Network

    Matthewson, M. John

    C and holding the powder compact at an intermediate temperature below the normal sintering1 Modeling of Gas Phase Transport and Composition Evolution during the Initial Stage Sintering, Piscataway, New Jersey 08854 Abstract Densification of 4B C during sintering can be aided by removing

  15. 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

  16. 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.

  17. 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...

  18. Gas-phase models for the evolved planetary nebulae NGC 6781, M4-9 and O. M. Shalabiea,1,2

    E-print Network

    Millar, Tom

    Gas-phase models for the evolved planetary nebulae NGC 6781, M4-9 and NGC 7293 A. Ali,1 O. M planetary nebulae. Three pseudo-time-dependent gas-phase models have been constructed for dense ð104 ­105 cm23 � and cool ðT , 15 K� clumpy envelopes of the evolved nebulae NGC 6781, M4-9 and NGC 7293

  19. SHORT COMMUNICATION Gas-Phase Separations of Protease Digests

    E-print Network

    Clemmer, David E.

    SHORT COMMUNICATION Gas-Phase Separations of Protease Digests Stephen J. Valentine, Anne E University, Bloomington, Indiana, USA A mixture of peptides from a complete tryptic digest of ubiquitin has and identify peptides from a tryptic digest of ubiquitin. The mixture was electrosprayed into the gas phase

  20. 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.

  1. Assessing Intrinsic Side Chain Interactions between i and i + 4 Residues in Solvent-Free Peptides: A Combinatorial Gas-Phase Approach

    E-print Network

    Clemmer, David E.

    Assessing Intrinsic Side Chain Interactions between i and i + 4 Residues in Solvent-Free Peptides-(Ala)7-Xxx-(Ala)3-Yyy-(Ala)3, where residues 8 and 12 are randomized. In total, 160 different peptide ions (80 related NH2-terminated and -acetylated sequences) have been studied. Substitutions of residues

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

    SciTech Connect

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

    2012-05-22

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

  3. Gas Phase Nanoparticle Synthesis

    NASA Astrophysics Data System (ADS)

    Granqvist, Claes; Kish, Laszlo; Marlow, William

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

  4. The statistical multifragmentation model for liquid-gas phase transition with a compressible nuclear liquid

    E-print Network

    V. V. Sagun; A. I. Ivanytskyi; K. A. Bugaev; I. N. Mishustin

    2013-06-10

    We propose a new formulation of the statistical multifragmentation model based on the analysis of the virial expansion for a system of the nuclear fragments of all sizes. The developed model not only enables us to account for short-range repulsion, but also to calculate the surface free energy which is induced by the interaction between the fragments. We propose a new parameterization for the liquid phase pressure which allows us to introduce a compressible nuclear liquid into the statistical multifragmentation model. The resulting model is exactly solvable and has no irregular behavior of the isotherms in the mixed phase region that is typical for mean-field models. The general conditions for the 1-st and 2-nd (or higher) order phase transitions are formulated. It is shown that all endpoints of the present model phase diagram are the tricritical points, if the Fisher exponent $\\tau$ is in the range $\\{3}{2} \\le \\tau \\le 2$. The treatment of nuclear liquid compressibility allows us to reduce the tricritical endpoint density of the statistical multifragmentation model to one third of the normal nuclear density. A specific attention is paid to of the fragment size distributions in the region of a negative surface tension at supercritical temperatures.

  5. DSMC Simulations Assessing the ES-BGK Kinetic Model for Gas-Phase Transport between Parallel Walls

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

    Bird's Direct Simulation Monte Carlo (DSMC) method is used to simulate gas-phase diffusive transport at near-continuum conditions. The molecules collide using either the Boltzmann collision term or the ellipsoidal-statistical Bhatnagar-Gross-Krook (ES-BGK) kinetic model. Momentum, heat, and mass transport between parallel walls (i.e., Couette, Fourier, and Fickian flows) are investigated. The ES-BGK model produces values of the viscosity and the thermal conductivity outside the Knudsen layers that agree closely with the corresponding values from the Boltzmann collision term (also implemented in DSMC). However, the ES-BGK model produces less accurate values for the mass self-diffusivity, with a modest difference for the Maxwell interaction but a large difference for the hard-sphere interaction. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  6. SIMS analysis of xenon and krypton in uranium dioxide: A comparison of two models of gas-phase ionisation

    NASA Astrophysics Data System (ADS)

    Wittmaack, K.

    2008-12-01

    Reasonable detection limits in secondary ion mass spectrometry (SIMS) analysis of inert gases in solids may be achieved by gas-phase ionisation. For Xe in UO 2 Desgranges and Pasquet (D&P) have recently reported that the ion intensity IXe+ can be enhanced significantly using O2+ ion bombardment in combination with an oxygen jet directed at the sputtered area. A similar effect was reported by Portier et al. for Kr in UO 2. The enhancement was attributed to ionisation by an interaction with oxygen atoms and molecules (D&P model). The proposed mechanism is at variance with a recently outlined model of gas-phase ionisation involving charge transfer between the ejected atoms and the incoming primary ions. The purpose of this study was to clarify these contradictory views by a reanalysis of the original data. Access to all relevant original data was kindly provided by L. Desgranges. In contrast to expectation based on the D&P model, step-wise increases in the flow rate of the oxygen jet did not result in an immediate response of IXe+. Instead, transient yield changes were observed, with characteristic rise times that were even longer for Xe + than for uranium specific signals. This observation invalidates the idea that ionisation of Xe atoms is due to interaction with oxygen molecules of the jet. Recalling well known transient phenomena in ion-bombardment induced photon emission, it is argued that the enhancement effect may be associated with the increase in the oxidation state of the sample, as a result of which the fraction of Xe (or Kr) atoms leaving the sample in an electronically excited state is presumably increasing, thus enlarging the effective cross section for charge transfer. Alternatively, the enhancement may be due to a lowering of the ejection velocity of rare gas atoms, possibly caused by the increase in near-surface sample oxidation. A second problem with the D&P study is the use of IU+ as a reference signal. Literature data as well as new results reveal that UO2+ and UO + secondary ions dominate the SIMS spectrum of oxidised uranium at energies <60 eV, the U + fraction amounting to only 1% or less. Other issues are (i) the significant variation of the sample erosion rate that occurred upon deliberate changes of the mean primary ion current density, (ii) the associated bombardment induced, progressive oxygen depletion of the sample, (iii) the presence of a background superimposed on the Xe + signals, a significant effect at low current densities and (iv) the space-charge broadening of the primary ion beam at high beam currents. Eliminating all these interfering factors, the (reduced) ionisation probabilities of Xe + were found to be in accordance with gas-phase ionisation by charge exchange, even in the pressure of excessive oxygen flooding.

  7. Modeling Gas Phase RDX Combustion with Intrinsic Low Dimensional Manifolds 1 Sandeep Singh2

    E-print Network

    detailed kinetics model which accounts for 45 species and 232 elementary reaction steps; while the ILDM of the slowest reactions to those of the fastest reactions to reach values near 1010 , which indicates severe a prohibitive amount of computational resources for all but the simplest of flows. While the addition of species

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

    EPA Science Inventory

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

  9. Sensitivity and uncertainty analysis of the mechanism of gas-phase chlorine production from NaCl aerosols in the MAGIC model

    E-print Network

    Dabdub, Donald

    Sensitivity and uncertainty analysis of the mechanism of gas-phase chlorine production from Na Chlorine chemistry a b s t r a c t This paper presents a global sensitivity and uncertainty analyses of the chlorine chemistry included in the Model of Aqueous, Gaseous and Interfacial Chemistry (MAGIC). Uncertainty

  10. 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

  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. Intercomparison of the gas-phase chemistry in several chemistry and transport models

    NASA Astrophysics Data System (ADS)

    Kuhn, M.; Builtjes, P. J. H.; Poppe, D.; Simpson, D.; Stockwell, W. R.; Andersson-Sko¨ld, Y.; Baart, A.; Das, M.; Fiedler, F.; Hov, Ø.; Kirchner, F.; Makar, P. A.; Milford, J. B.; Roemer, M. G. M.; Ruhnke, R.; Strand, A.; Vogel, B.; Vogel, H.

    An intercomparison of nine chemical mechanisms (e.g. ADOM, CBM-IV, EMEP, RADM2) as used by 12 contributing groups was conducted. The results for three scenarios are presented covering remote situations with a net O 3 loss of around 2.7 ppb (LAND and FREE) and a moderately polluted situation with O 3 formation of around 100 ppb (PLUMEI) over a 5 day simulation period. The overall tendencies (i.e. the total net production/loss over 5 days) for O 3 show a r.m.s. error of 38, 15 and 16%; for H 2O 2 the errors are 76, 23 and 30% (for LAND, FREE, PLUMEI). In terms of ozone production in PLUME1, the most productive mechanisms are EMEP and IVL, the RADM-type mechanisms lie in the mid-range and the CBM-1V type mechanisms fall at the bottom of the range. The differences in H 2O 2 can partly be explained by an incorrect use of the HO 2 + HO 2 rate constant and by differences in the treatment of the peroxy radical interactions. In the PLUME1 case the r.m.s. error of the PAN tendency was found to be 29%. Differences between mechanisms for the HO radical are 10, 15 and 19% and for the NO 3 radical 35, 16 and 40% (for LAND, FREE, PLUME1) in terms of the r.m.s. error of the results for a 12 h time period centred around the last noon (HO), respectively, a 8 h time period centred around the last midnight (NO 3) of simulation. Especially for NO 3 some differences are due to different numerical treatment of photolytic processes in the models. Large differences between mechanisms are observed for higher organic peroxides and higher aldehydes with a r.m.s. error of around 50% for the final concentration in PLUME1. The protocol of the intercomparison is given in the appendix, so that the comparison could be repeated for the purpose of mechanism development and sensitivity studies.

  13. 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.

  14. 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.

    2013-03-01

    The Unified Partitioning-Aerosol phase Reaction (UNIPAR) model has been developed to predict the secondary organic aerosol (SOA) formation through multiphase reactions. An explicit gas-kinetic model was employed to express gas-phase oxidation of aromatic hydrocarbons. Gas-phase products are grouped based on volatility (6 levels) and reactivity (5 levels) and used to construct the stoichiometric coefficients (?i,j) matrix, the set of parameters used to describe the concentrations of organic compounds in multiphase. Weighting of the ?i,j matrix as a function of NOx improved the evaluation of NOx effects on 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. OMP is estimated using the SOA partitioning model that has been used in a regional air quality model (CMAQ 5.0.1). OMAR predicts multiphase reactions of organic compounds, such as oligomerization, acid-catalyzed reactions, and organosulfate (OS) formation. The model was evaluated with the SOA data produced from the photooxidation of toluene and 1,3,5-trimethylbenzene using an outdoor reactor (UF-APHOR chamber). The model reasonably simulates SOA formation under various aerosol acidities, NOx concentrations, humidities and temperatures. Furthermore, the OS fraction in the SOA predicted by the model was in good agreement with the experimentally measured OS fraction.

  15. Aerosol formation from the reaction of {alpha}pinene and ozone using a gas-phase kinetics-aerosol partitioning model

    SciTech Connect

    Kamens, R.; Jang, M.; Chien, C.J.; Leach, K.

    1999-05-01

    As a result of new aerosol compositional information, the authors have implemented an exploratory model for predicting aerosol yields from the reaction of {alpha}-pinene with ozone in the atmosphere. This new approach has the ability to embrace a range of different atmospheric chemical conditions, which bring about biogenic aerosol formation. A kinetic mechanism was used to describe the gas-phase reactions of {alpha}-pinene with ozone. This reaction scheme produces low vapor pressure reaction products that distribute between gas and particle phases. Some of the products have subcooled liquid vapor pressures which are low enough to initiate self-nucleation. More volatile products such as pinonic acid and pinonaldehyde will not self-nucleate but will partition onto existing particle surfaces. Partitioning was treated as an equilibrium between the rate of particle uptake and rate of particle loss of semivolatile terpene reaction products. Given estimated liquid vapor pressures and activation energies of desorption, it was possible to calculate gas-particle equilibrium constants with aerosol desorption rate constants at different temperatures. This permitted an estimate of the rate of absorption from the gas phase. Gas- and aerosol-phase reactions were linked together in one chemical mechanism, and a chemical kinetics solver was used to predict reactant and product concentrations over time. Aerosol formation from the model was then compared with aerosol production observed from outdoor chamber experiments.

  16. 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).

  17. Development and implementation of a FT-ICR mass spectrometer for the investigation of ion conformations of peptide sequence isomers containing basic amino acid residues by gas-phase hydrogen/deuterium exchange 

    E-print Network

    Marini, Joseph Thomas

    2004-09-30

    The gas-phase hydrogen/deuterium (H/D) exchange of protonated di- and tripeptides containing a basic amino acid residue has been studied with a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Bimolecular ...

  18. 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

  19. 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 (?i,j) matrix, the set of parameters used to describe the concentrations of organic compounds in multiphase. Weighting of the ?i,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.

  20. 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...

  1. 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...

  2. OZONE CALIBRATION AND AUDIT BY GAS PHASE TITRATION IN EXCESS OZONE. BENDIX (TRADE NAME) TRANSPORTABLE FIELD CALIBRATION SYSTEM, MODELS 8861D AND 8861DA

    EPA Science Inventory

    Detailed procedures for the dynamic calibration and audit of chemiluminescence ozone analyzers are presented. The calibrations and audits are performed by means of a gas phase titration technique using the rapid gas phase reaction between nitric oxide and ozone with excess ozone ...

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

    PubMed Central

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

    2009-01-01

    Diabatic models are widely employed for studying chemical reactivity in condensed phases and enzymes, but there has been little discussion of the pros and cons of various diabatic representations for this purpose. Here we discuss and contrast six different schemes for computing diabatic potentials for a charge rearrangement reaction. They include (i) the variational diabatic configurations (VDC) constructed by variationally optimizing individual valence bond structures and (ii) the consistent diabatic configurations (CDC) obtained by variationally optimizing the ground-state adiabatic energy, both in the nonorthogonal molecular orbital valence bond (MOVB) method, along with the orthogonalized (iii) VDC-MOVB and (iv) CDC-MOVB models. In addition, we consider (v) the fourfold way (based on diabatic molecular orbitals and configuration uniformity), and (vi) empirical valence bond (EVB) theory. To make the considerations concrete, we calculate diabatic electronic states and diabatic potential energies along the reaction path that connects the reactant and the product ion-molecule complexes of the gas-phase bimolecular nucleophilic substitution (SN2) reaction of 1,2-dichloethane (DCE) with acetate ion, which is a model reaction corresponding to the reaction catalyzed by haloalkane dehalogenase. We utilize ab initio block-localized molecular orbital theory to construct the MOVB diabatic states and ab initio multi-configuration quasidegenerate perturbation theory to construct the fourfold-way diabatic states; the latter are calculated at reaction path geometries obtained with the M06-2X density functional. The EVB diabatic states are computed with parameters taken from the literature. The MOVB and fourfold-way adiabatic and diabatic potential energy profiles along the reaction path are in qualitative but not quantitative agreement with each other. In order to validate that these wave-function-based diabatic states are qualitatively correct, we show that the reaction energy and barrier for the adiabatic ground state, obtained with these methods, agree reasonably well with the results of high-level calculations using the composite G3SX and G3SX(MP3) methods and the BMC-CCSD multi-coefficient correlation method. However, a comparison of the EVB gas-phase adiabatic ground-state reaction path with those obtained from MOVB and with the fourfold way reveals that the EVB reaction path geometries show a systematic shift towards the products region, and that the EVB lowest-energy path has a much lower barrier. The free energies of solvation and activation energy in water reported from dynamical calculations based on EVB also imply a low activation barrier in the gas phase. In addition, calculations of the free energy of solvation using the recently proposed SM8 continuum solvation model with CM4M partial atomic charges lead to an activation barrier in reasonable agreement with experiment only when the geometries and the gas-phase barrier are those obtained from electronic structure calculations, i.e., methods i–v. These comparisons show the danger of basing the diabatic states on molecular mechanics without the explicit calculation of electronic wave functions. Furthermore, comparison of schemes i–v with one another shows that significantly different quantitative results can be obtained by using different methods for extracting diabatic states from wave function calculations, and it is important for each user to justify the choice of diabatization method in the context of its intended use. PMID:20047005

  4. 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.

  5. 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

  6. Peptide-Ligand Binding Modeling of siRNA with Cell-Penetrating Peptides

    PubMed Central

    García-Sosa, Alfonso T.; Langel, Ülo

    2014-01-01

    The binding affinity of a series of cell-penetrating peptides (CPP) was modeled through docking and making use of the number of intermolecular hydrogen bonds, lipophilic contacts, and the number of sp3 molecular orbital hybridization carbons. The new ranking of the peptides is consistent with the experimentally determined efficiency in the downregulation of luciferase activity, which includes the peptides' ability to bind and deliver the siRNA into the cell. The predicted structures of the complexes of peptides to siRNA were stable throughout 10?ns long, explicit water molecular dynamics simulations. The stability and binding affinity of peptide-siRNA complexes was related to the sidechains and modifications of the CPPs, with the stearyl and quinoline groups improving affinity and stability. The reranking of the peptides docked to siRNA, together with explicit water molecular dynamics simulations, appears to be well suited to describe and predict the interaction of CPPs with siRNA. PMID:25147791

  7. Mon. Not. R. Astron. Soc. 000, 000{000 (0000) Printed 13 March 2001 (MN L A T E X style le v1.4) Gas-Phase Models for the Evolved Planetary Nebulae

    E-print Network

    Millar, Tom

    .4) Gas-Phase Models for the Evolved Planetary Nebulae NGC 6781, M4-9, and NGC 7293 A. Ali 1 , O of the evolved nebulae NGC 6781 , M 4-9, and NGC 7293. The three nebulae are modelled as carbon-rich stars evolved from the asymptotic giant branch to the late plane- tary nebulae phase. The clumpy neutral

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

    PubMed

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

    2014-03-30

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

  9. Bistability in Interstellar Gas-Phase Chemistry

    E-print Network

    Gai I. Boger; Amiel Sternberg

    2006-01-16

    We present an analysis of "bistability" in gas-phase chemical models of dark interstellar clouds. We identify the chemical mechanisms that allow high- and low-ionization solutions to the chemical rate-equations to coexist. We derive simple analytic scaling relations for the gas densities and ionization rates for which the chemistry becomes bistable. We explain why bistability is sensitive to the H3+ dissociative recombination rate coefficient, and why it is damped by gas-grain neutralization.

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

  12. Characterization of a pilot plant airlift tower loop reactor: III. Evaluation of local properties of the dispersed gas phase during yeast cultivation and in model media.

    PubMed

    Fröhlich, S; Lotz, M; Larson, B; Lübbert, A; Schügerl, K; Seekamp, M

    1991-06-01

    The local properties of the dispersed gas phase (gasholdup, bubble diamater, and bubble velocity) were measured and evaluated at different positions in the riser and downcomer of a pilot plant reactor and, for comparison, in a laboratory reactor. These were described in Parts I and II of this series of articles during yeast cultivation and with model media. In the riser of the pilot plant reactor, the local gas holdup and bubble velocities varied only slightly in axial direction. The gas holdup increased considerably, while the bubble velocity increased only slightly with aeration rate. The bubble size diminished with increasing distance from the aerator in the riser, since the primary bubble size was larger than the equilibrium bubble size. In the downcomer, the mean bubble size was smaller than in the riser. The mean bubble size varied only slightly, the bubble velocity was accelerated, and the gas holdup decreased from top to bottom in the downcomer. In pilot plant at constant aeration rate, the properties of the dispersed phase were nearly constant during the batch cultivation, i.e., they depended only slightly on the cell concentration. In the laboratory reactor, the mean bubble sizes were much larger than in the pilot plant reactor. In the laboratory reactor, the bubble velocities in the riser and downcomer increased, and the mean gas holdup and bubble diameter in the downcomer remained constant as the aeration rate was increased. PMID:18600698

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

    EPA Science Inventory

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

  15. Fission and Nuclear Liquid-Gas Phase Transition

    E-print Network

    E. A. Cherepanov; V. A. Karnaukhov

    2007-03-30

    The temperature dependence of the liquid-drop fission barrier is considered, the critical temperature for the liquid-gas phase transition in nuclear matter being a parameter. Experimental and calculated data on the fission probability are compared for highly excited $^{188}$Os. The calculations have been made in the framework of the statistical model. It is concluded that the critical temperature for the nuclear liquid--gas phase transition is higher than 16 MeV.

  16. Modelling water molecules inside cyclic peptide nanotubes

    NASA Astrophysics Data System (ADS)

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2015-03-01

    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[(-uc(D)-Ala-uc(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.

  17. Gas-phase photolysis of tungsten hexachloride

    NASA Astrophysics Data System (ADS)

    Kullmer, R.

    1994-07-01

    The laser-induced decomposition of WCl6 in the gas-phase is investigated by means of absorption, Raman and laser-induced fluorescence spectroscopy. With visible Ar+-laser radiation dissociation of WCl6 into WCl4 and Cl2 has been observed. Further decomposition can be achieved in the presence of H2 employing ultraviolet Ar+-laser radiation at 360 nm. A complete reduction to W requires even shorter wavelengths. The experimental results are analyzed on the basis of model calculations. Implications on the Laser-induced Chemical Vapor Deposition (LCVD) of W are discussed.

  18. Gas Phase Detection of Benzocyclopropenyl.

    PubMed

    Maity, Surajit; Steglich, Mathias; Maier, John P

    2015-11-01

    The gas phase detection of benzocyclopropenyl is reported. In this aromatic resonance stabilized radical, a large angular strain is present due to a three-membered ring annelated to a benzene. The resonant two-color two-photon ionization technique is used to record the D1((2)A2) ? D0((2)B1) electronic transition of this radical after the in situ synthesis in a discharge source. The spectrum features absorptions up to 3300 cm(-1) above the origin band at 19?305 cm(-1). Benzocyclopropenyl is possibly the major product of the bimolecular reaction of benzene and an atomic carbon at low temperatures. PMID:26463227

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

    PubMed

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

    2015-09-01

    Two synthetic strategies for incorporating diiron analogues of [FeFe]-hydrogenases into short peptides via phosphine functional groups are described. First, utilizing the amine side chain of lysine as an anchor, phosphine carboxylic acids can be coupled via amide formation to resin-bound peptides. Second, artificial, phosphine-containing amino acids can be directly incorporated into peptides via solution phase peptide synthesis. The second approach is demonstrated using three amino acids each with a different phosphine substituent (diphenyl, diisopropyl, and diethyl phosphine). In total, five distinct monophosphine-substituted, diiron model complexes were prepared by reaction of the phosphine-peptides with diiron hexacarbonyl precursors, either (?-pdt)Fe2(CO)6 or (?-bdt)Fe2(CO)6 (pdt = propane-1,3-dithiolate, bdt = benzene-1,2-dithiolate). Formation of the complexes was confirmed by UV/Vis, FTIR and (31)P NMR spectroscopy. Electrocatalysis by these complexes is reported in the presence of acetic acid in mixed aqueous-organic solutions. Addition of water results in enhancement of the catalytic rates. PMID:26223293

  20. 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.

  1. Oxygen Gas Phase Abundance Revisited

    E-print Network

    M. K. André; C. M. Oliveira; J. C. Howk; R. Ferlet; J. -M. Désert; G. Hébrard; S. Lacour; A. Lecavelier des Étangs; A. Vidal-Madjar; H. W. Moos

    2003-03-26

    We present new measurements of the interstellar gas-phase oxygen abundance along the sight lines towards 19 early-type galactic stars at an average distance of 2.6 kpc. We derive O {\\small I} column densities from {\\it HST}/STIS observations of the weak 1355 \\AA intersystem transition. We derive total hydrogen column densities [N(H {\\small I})+2N(H$_2$)] using {\\it HST}/STIS observations of \\lya and {\\it FUSE} observations of molecular hydrogen. The molecular hydrogen content of these sight lines ranges from f(H$_2$) = 2N(H$_2$)/[N(H {\\small I})+2N(H$_2$)] = 0.03 to 0.47. The average $$ of 6.3$\\times10^{21}$ cm$^{-2}$ mag$^{-1}$ with a standard deviation of 15% is consistent with previous surveys. The mean oxygen abundance along these sight lines, which probe a wide range of galactic environments in the distant ISM, is 10$^6$ \\oh = $408 \\pm 13$ (1 $\\sigma$ in the mean). %$({\\rm O/H})_{gas} = 408 \\pm 14$(1 $\\sigma$). We see no evidence for decreasing gas-phase oxygen abundance with increasing molecular hydrogen fraction and the relative constancy of \\oh suggests that the component of dust containing the oxygen is not readily destroyed. We estimate that, if 60% of the dust grains are resilient against destruction by shocks, the distant interstellar total oxygen abundance can be reconciliated with the solar value derived from the most recent measurements %by Holweger and by Allende Prieto, Lambert & Asplund: of 10$^6$ \\oh$_\\odot$ = 517 $\\pm$ 58 (1 $\\sigma$). We note that the smaller oxygen abundances derived for the interstellar gas within 500 pc %by Meyer, Cardelli & Jura or from nearby B star surveys are consistent with a local elemental deficit.

  2. Interaction of Arginine-Rich Peptides with Model Cell Membranes

    NASA Astrophysics Data System (ADS)

    Mishra, Abhijit; Schmidt, Nathan; Gordon, Vernita; Cheng, Jianjun; Deming, Timothy; Wong, Gerard

    2008-03-01

    Cell-penetrating peptides have the ability to traverse the plasma membrane of eukaryotic cells. Furthermore, these peptides can transport cargo across a range of cell membranes, implying they have many potential biotechnological applications. In this study we compare the interaction of three commonly used arginine-rich cell-penetrating peptides, TAT, Penetratin, and pVEC, with model cell membranes of variable charge density and intrinsic curvature, using synchrotron small angle x-ray scattering (SAXS). To better understand the respective roles of arginine and hydrophobic residues in membrane reorganization we also examine the interaction of arginine-leucine (R60L20) block copolypeptides with model membranes, as well as the relationship between membrane composition and peptide induced changes in membrane topology.

  3. 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

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

    PubMed

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

    2015-10-01

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

  5. 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.

  6. Evolutionary Sequence Modeling for Discovery of Peptide Hormones

    PubMed Central

    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

  7. 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.

  8. Gas-phase magnetohydrodynamic disk accelerator

    NASA Astrophysics Data System (ADS)

    Pozdnyakov, G. A.

    2007-06-01

    A pulsed gas-phase magnetohydrodynamic (MHD) disk accelerator with a radial initial gas flow and radial electric current direction is described. Some working regime parameters and characteristics of the accelerated natural gas flow are reported. MHD accelerators of this type can be used for the investigation of chemical kinetics. Another promising application is related to the development of supersonic gas-phase endothermal chemical reactors with gasdynamic control.

  9. Phase behavior and the partitioning of caveolin-1 scaffolding domain peptides in model lipid bilayers

    E-print Network

    Rädler, Joachim

    The membrane binding and model lipid raft interaction of synthetic peptides derived from the caveolin scaffolding domain (CSD) of the protein caveolin-1 have been investigated. CSD peptides bind preferentially to ...

  10. 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.

  11. Mechanism of unfolding of a model helical peptide.

    PubMed

    Pastrana-Rios, B

    2001-08-01

    Synthetic model helical peptides, Acetyl-W(EAAAR)(5)A-amide with (13)C=O specifically labeled alanine segments in repeats n = 1,2 or 4,5 were studied in aqueous D(2)O solution as a function of temperature using Fourier transform infrared spectroscopy and two-dimensional correlation analysis. The (13)C==O provided a probe which was sensitive to the carbonyl stretch in the peptide bonds of the alanine residues at the amino terminal end in one peptide as compared to the probe in the carboxy terminal end of the other peptide during thermal perturbation. The relative stability of each terminal end was examined; the more stable terminal was determined to be the amino terminal end. Also studied were the glutamate and arginine side-chain modes involved in the salt bridging interaction. Two-dimensional correlation analysis enabled enhanced resolution in the spectral region of 1520--1700 cm(-1), and thus, the order in which these vibrational modes were perturbed as a function of increasing temperature were established. PMID:11478873

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

    E-print Network

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

    2005-01-27

    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 $f_s$ 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.

  13. 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

  14. Model for the Peptide-Free Conformation of Class II MHC Proteins

    PubMed Central

    López, Gustavo E.; Stern, Lawrence J.; Zavala-Ruiz, Zarixia

    2008-01-01

    Background Major histocompatibility complex proteins are believed to undergo significant conformational changes concomitant with peptide binding, but structural characterization of these changes has remained elusive. Methodology/Principal Findings Here we use molecular dynamics simulations and experimental probes of protein conformation to investigate the peptide-free state of class II MHC proteins. Upon computational removal of the bound peptide from HLA-DR1-peptide complex, the ?50-59 region folded into the P1-P4 region of the peptide binding site, adopting the same conformation as a bound peptide. Strikingly, the structure of the hydrophobic P1 pocket is maintained by engagement of the side chain of Phe ?54. In addition, conserved hydrogen bonds observed in crystal structures between the peptide backbone and numerous MHC side chains are maintained between the ?51-55 region and the rest of the molecule. The model for the peptide-free conformation was evaluated using conformationally-sensitive antibody and superantigen probes predicted to show no change, moderate change, or dramatic changes in their interaction with peptide-free DR1 and peptide-loaded DR1. The binding observed for these probes is in agreement with the movements predicted by the model. Conclusion/Significance This work presents a molecular model for peptide-free class II MHC proteins that can help to interpret the conformational changes known to occur within the protein during peptide binding and release, and can provide insight into possible mechanisms for DM action. PMID:18545669

  15. Gas-Phase IR Spectroscopy of Nucleobases.

    PubMed

    de Vries, Mattanjah S

    2015-01-01

    IR spectroscopy of nucleobases in the gas phase reflects simultaneous advances in both experimental and computational techniques. Important properties, such as excited state dynamics, depend in subtle ways on structure variations, which can be followed by their infrared signatures. Isomer specific spectroscopy is a particularly powerful tool for studying the effects of nucleobase tautomeric form and base pair hydrogen-bonding patterns. PMID:25663555

  16. 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.

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

    PubMed

    Rankovi?, M Lj; Canon, F; Nahon, L; Giuliani, A; Milosavljevi?, 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

  18. Investigation on Gas-phase Structures of Biomolecules Using Ion Mobility-mass Spectrometry 

    E-print Network

    Tao, Lei

    2011-08-08

    , David H. Russell May 2010 Major Subject: Chemistry iii ABSTRACT Investigation on Gas-phase Ion Structures of Biomolecules Using Ion Mobility-mass Spectrometry. (May 2010) Lei Tao, B.A., Fudan University, Shanghai, China; M.S... the measured collision cross-section (?meas) by calculating the collision cross- sections (?calc) of candidates generated by molecular dynamics (MD) and compared with the experiment results. A database of ?s for singly-charged peptide ions is presented...

  19. 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 ?g/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

  20. Peptide immunotherapy in models of allergic airways disease 

    E-print Network

    MacKenzie, Karen Joan

    2011-11-25

    Allergen-reactive CD4+ T cells are implicated in the pathogenesis of allergic disease. Peptide immunotherapy (PIT) involves therapeutic administration of short immunodominant peptides from within the protein allergen to ...

  1. 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.

  2. The lipid dependence of antimicrobial peptide activity is an unreliable experimental test for different pore models.

    PubMed

    Bobone, Sara; Roversi, Daniela; Giordano, Lorenzo; De Zotti, Marta; Formaggio, Fernando; Toniolo, Claudio; Park, Yoonkyung; Stella, Lorenzo

    2012-12-21

    Antimicrobial peptides usually kill bacteria by making their membranes permeable. Two main models (barrel-stave and Shai-Matsuzaki-Huang) have been proposed to describe the peptide-induced pores. Although several experimental tests can be exploited to discriminate between these two models, the dependence of peptide activity on lipid properties (intrinsic curvature and membrane thickness) is routinely used for this purpose. Here, we show that, contrary to what is currently accepted, this criterion is unreliable. PMID:23228161

  3. Gas-phase unsteadiness and its inuence on droplet vaporization in sub-and super-critical environments

    E-print Network

    Aggarwal, Suresh K.

    Gas-phase unsteadiness and its in¯uence on droplet vaporization in sub- and super quantitatively the in¯uence of gas-phase unsteadiness on the droplet vaporization process in sub- and super-critical environments. Two comprehensive models of high-pressure droplet vaporization, including a transient model

  4. 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.

  5. 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 ?s, 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.

  6. Isospin dependence of liquid-gas phase transition in hot asymmetric nuclear matter

    E-print Network

    W. L. Qian; Ru-Keng Su; Ping Wang

    2000-08-30

    By using the Furnstahl, Serot and Tang's model, the effect of density dependence of the effective nucleon-nucleon-rho-meson (NN-rho) coupling on the liquid-gas phase transition in hot asymmetric nuclear matter is investigated. A limit pressure p_lim has been found. We found that the liquid-gas phase transition cannot take place if p>p_lim. The binodal surface for density dependent NN-rho coupling situation is addressed.

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

    NASA Astrophysics Data System (ADS)

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

    1998-05-01

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

  8. Gas-phase electron diffraction studies of unstable molecules 

    E-print Network

    Noble-Eddy, Robert

    2009-01-01

    Gas-phase electron diffraction (GED) is the only viable technique for the accurate structural study of gas-phase molecules that contain more than ~10 atoms. Recent advances in Edinburgh have made it possible to study ...

  9. 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.

  10. Biophysical properties of membrane-active peptides based on micelle modeling: a case study of cell-penetrating and antimicrobial peptides.

    PubMed

    Wang, Qian; Hong, Gongyi; Johnson, Glenn R; Pachter, Ruth; Cheung, Margaret S

    2010-11-01

    We investigated the molecular mechanisms of short peptides interacting with membrane-mimetic systems. Three short peptides were selected for this study: penetratin as a cell-penetrating peptide (CPP), and temporin A and KSL as antimicrobial peptides (AMP). We investigated the detailed interactions of the peptides with dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles, and the subsequent peptide insertion based on free energy calculations by using all-atomistic molecular dynamics simulations with the united atom force field and explicit solvent models. First, we found that the free energy barrier to insertion for the three peptides is dependent on the chemical composition of the micelles. Because of the favorable electrostatic interactions between the peptides and the headgroups of lipids, the insertion barrier into an SDS micelle is less than a DPC micelle. Second, the peptides' secondary structures may play a key role in their binding and insertion ability, particularly for amphiphilic peptides such as penetratin and KSL. The secondary structures with a stronger ability to bind with and insert into micelles are the ones that account for a smaller surface area of hydrophobic core, thus offering a possible criterion for peptide design with specific functionalities. PMID:20939546

  11. 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

  12. Zipf's Law in the Liquid Gas Phase Transition of Nuclei

    E-print Network

    Y. G. Ma

    2000-11-03

    Zipf's law in the field of linguistics is tested in the nuclear disassembly within the framework of isospin dependent lattice gas model. It is found that the average cluster charge (or mass) of rank $n$ in the charge (or mass) list shows exactly inversely to its rank, i.e., there exists Zipf's law, at the phase transition temperature. This novel criterion shall be helpful to search the nuclear liquid gas phase transition experimentally and theoretically. In addition, the finite size scaling of the effective phase transition temperature at which the Zipf's law appears is studied for several systems with different mass and the critical exponents of $\

  13. 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.

  14. Folding of gas-phase polyalanines in a static electric field: alignment, deformations, and polarization effects.

    PubMed

    Calvo, F; Dugourd, P

    2008-07-01

    Monte Carlo simulations of the temperature-induced unfolding of small gas-phase polyalanines in a static, homogeneous electric field are reported, based on the AMBER ff96 force field. The peptides exhibit a structural transition from the native alpha-helix state to entropically favored beta-sheet conformations, before eventually turning to extended coil at higher temperatures. Upon switching the electric field, the molecules undergo preferential alignment of their dipole moment vector toward the field axis and a shift of the alpha-beta transition to higher temperatures. At higher field strengths (>10(8) V/m) the molecules stretch and the alpha-beta and beta-coil transitions merge. A simple three-state model is shown to account for the observed behavior. Under even higher fields, density functional theory calculations and a polarizable force field both show that electronic rearrangements tend to further increase the dipole moment, polarization effects being approximately half in magnitude with respect to stretching effect. Finally a tentative (temperature, field-strength) phase diagram is sketched. PMID:18223004

  15. Predictive Bayesian neural network models of MHC class II peptide binding.

    PubMed

    Burden, Frank R; Winkler, David A

    2005-06-01

    We used Bayesian regularized neural networks to model data on the MHC class II-binding affinity of peptides. Training data consisted of sequences and binding data for nonamer (nine amino acid) peptides. Independent test data consisted of sequences and binding data for peptides of length peptides depends only on the highest ranked embedded nonamer and that reverse sequences of active nonamers are inactive. We also internally validated the models by using 30% of the training data in an internal test set. We obtained robust models, with near identical statistics for multiple training runs. We determined how predictive our models were using statistical tests and area under the Receiver Operating Characteristic (ROC) graphs (A(ROC)). Most models gave training A(ROC) values close to 1.0 and test set A(ROC) values >0.8. We also used both amino acid indicator variables (bin20) and property-based descriptors to generate models for MHC class II-binding of peptides. The property-based descriptors were more parsimonious than the indicator variable descriptors, making them applicable to larger peptides, and their design makes them able to generalize to unknown peptides outside of the training space. None of the external test data sets contained any of the nonamer sequences in the training sets. Consequently, the models attempted to predict the activity of truly unknown peptides not encountered in the training sets. Our models were well able to tackle the difficult problem of correctly predicting the MHC class II-binding activities of a majority of the test set peptides. Exceptions to the assumption that nonamer motif activities were invariant to the peptide in which they were embedded, together with the limited coverage of the test data, and the fuzziness of the classification procedure, are likely explanations for some misclassifications. PMID:15878832

  16. Design and Spectroscopic Characterization of Peptide Models for the Plastocyanin Copper-Binding Loop

    E-print Network

    Gibney, Brian R.

    of the remainder of the folded protein but, by itself, cannot stabilize a type 1 copper site, emphasizing the roleDesign and Spectroscopic Characterization of Peptide Models for the Plastocyanin Copper of two peptides, designed on the basis of the active site sequence and structure of the blue copper

  17. Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics

    E-print Network

    Clemmer, David E.

    Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics Brian C. Bohrer to complex proteome analysis, replicate study of individual libraries identified additional unique peptides heterogeneity. Whole organism or blood serum proteomes are complexsboth in terms of total number of proteins

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

    SciTech Connect

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

    2005-09-01

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

  19. Gas phase methylation of methyl acetoacetate. Experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Morizur, J.-P.; Martigny, I.; Taphanel, M.-H.; Tortajada, J.; Geribaldi, S.; Decouzon, M.

    1992-04-01

    Fourier transform ion cyclotron resonance and tandem mass spectrometry, complemented by semiempirical molecular orbital calculations, have been used to study gas phase methylation of methyl acetoacetate as a mixture of the keto form 1 and the enol form 2. The daughter ion spectra of the ion/molecule reaction products were compared with those of model ions generated by electron impact or chemical ionization, in order to determine the site(s) of nucleophilic reaction for the mixture. The data indicate that the site of attachment in the keto form 1 is the keto-carbonyl oxygen. For the enol form 2, no C-methylation occurs in the gas phase; the only product corresponds to O-alkylation. The results derived from D- and 13C-labelled precursors have been used to study the fragmentation mechanisms of model ions a, CH3C+ (OCH3)CH2CO2CH3; and b, CH3COCH2C+(OCH3)2. Experimental results indicate that an irreversible isomerization a --> b occurs under collisional conditions. Unimolecularly both a and b ions eliminate a neutral molecule of ketene but by different pathways. Calculations of charge distributions in 1 and 2 as well as the enthalpies of the neutral and the adduct ions are discussed.

  20. 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.

  1. Mechanical unfolding pathway of a model ?-peptide foldamer

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  2. Patterns of diamond nucleation from the gas phase

    NASA Astrophysics Data System (ADS)

    Molinari, E.; Polini, R.; Tomellini, M.

    1993-04-01

    On the basis of an analysis of experimental data on nucleation rates, patterns of the process of diamond nucleation from the gas phase on Si(100) substrates have been drawn. A kinetic scheme is proposed which is apparently able to describe the complex behavior of the system in the temperature range 750-1225 K, at (CH4/H2) ratios between 0.5 and 2 percent and at a total pressure of 100 mbar. The model postulates a distribution function of the nucleation centers over the heats of adsorption of active gaseous species and introduces a cutoff criterion based on the necessary condition that adjacent active sites coexist for times longer than the characteristic time of germ growth. Nucleation centers, active sites, germs, and nuclei have been defined by simple molecular models and their rates of transformation discussed, using available literature data.

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

    PubMed

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

    2014-07-01

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

  4. 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

  5. Peptide Pores in Lipid Bilayers: Voltage Facilitation Pleads for a Revised Model

    NASA Astrophysics Data System (ADS)

    Fadda, G. C.; Lairez, D.; Guennouni, Z.; Koutsioubas, A.

    2013-07-01

    We address the problem of antimicrobial peptides that create pores in lipid bilayers, focusing on voltage-temperature dependence of pore opening. Two novel experiments (voltage clamp with alamethicin as an emblematic representative of these peptides and neutron reflectivity of lipid monolayer at solid-water interface under electric field) serve to revise the only current theoretical model. We introduce a general contribution of peptide adsorption and electric field as being responsible for an unbalanced tension of the two bilayer leaflets and we claim that the main entropy cost of one pore opening is due to the corresponding excluded area for lipid translation.

  6. Peptide pores in lipid bilayers: voltage facilitation pleads for a revised model.

    PubMed

    Fadda, G C; Lairez, D; Guennouni, Z; Koutsioubas, A

    2013-07-12

    We address the problem of antimicrobial peptides that create pores in lipid bilayers, focusing on voltage-temperature dependence of pore opening. Two novel experiments (voltage clamp with alamethicin as an emblematic representative of these peptides and neutron reflectivity of lipid monolayer at solid-water interface under electric field) serve to revise the only current theoretical model. We introduce a general contribution of peptide adsorption and electric field as being responsible for an unbalanced tension of the two bilayer leaflets and we claim that the main entropy cost of one pore opening is due to the corresponding excluded area for lipid translation. PMID:23889447

  7. 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.

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

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

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

  9. 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.

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

    E-print Network

    Balucani, Nadia; Taquet, Vianney

    2015-01-01

    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 synthetized in the gas phase from methanol, which is desorbed by a non-thermal process from the ices. Our new model reproduces fairy well the observations towards L1544. It also...

  11. Gas-phase reactions in extraterrestrial environments: laboratory investigations by crossed molecular beams.

    PubMed

    Balucani, Nadia; Casavecchia, Piergiorgio

    2006-12-01

    We have investigated gas-phase reactions of N((2)D) with the most abundant hydrocarbons in the atmosphere of Titan by the crossed molecular beam technique. In all cases, molecular products containing a novel CN bond are formed, thus suggesting possible routes of formation of gas-phase nitriles in the atmosphere of Titan and primordial Earth. The same approach has been recently extended to the study of radical-radical reactions, such as the reaction of atomic oxygen with the CH(3) and C(3)H(5) radicals. Products other than those already considered in the modeling of planetary atmospheres and interstellar medium have been identified. PMID:17131088

  12. Nuclear symmetry energy effects on liquid-gas phase transition in hot asymmetric nuclear matter

    E-print Network

    Bharat K. Sharma; Subrata Pal

    2010-01-14

    The liquid-gas phase transition in hot asymmetric nuclear matter is investigated within relativistic mean-field model using the density dependence of nuclear symmetry energy constrained from the measured neutron skin thickness of finite nuclei. We find symmetry energy has a significant influence on several features of liquid-gas phase transition. The boundary and area of the liquid-gas coexistence region, the maximal isospin asymmetry and the critical values of pressure and isospin asymmetry all of which systematically increase with increasing softness in the density dependence of symmetry energy. The critical temperature below which the liquid-gas mixed phase exists is found higher for a softer symmetry energy.

  13. Peptides 26 (2005) 197206 Protegrin structureactivity relationships: using homology models

    E-print Network

    Minnesota, University of

    2005-01-01

    to be unaffected by the antibiotic resistance that renders small drug molecules 0196-9781/$ ­ see front matter active against a variety of microorganisms. The major goal of this study is to characterize easily therapeutic agents in fighting a wide range of microorganisms. Some antimicro- bial peptides (AMPs) have been

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

    PubMed

    Fang, Yigang; Bennett, Andrew; Liu, Jianbo

    2011-01-28

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

  15. Models of Membrane-bound Alzheimer’s Abeta Peptide Assemblies

    PubMed Central

    Shafrir, Yinon; Durell, Stewart; Arispe, Nelson; Guy, H. Robert

    2010-01-01

    Although it is clear that amyloid beta (A?) peptides play a pivotal role in the development of Alzheimer’s disease, the precise molecular model of action remains unclear. A? peptides form assemble both in aqueous solution and in lipid membranes. It has been proposed that deleterious effects occur when the peptides interact with membranes, possibly by forming Ca2+ permeant ion channels. In the accompanying manuscript, we propose models in which the C-terminus third of six A?42 peptides forms a six-stranded ?-barrel in highly toxic soluble oligomers. Here we extend this hypothesis to membrane-bound assemblies. In these A? models, the hydrophobic ?-barrel of a hexamer may either reside on the surface of the bilayer, or span the bilayer. Transmembrane pores are proposed to form between several hexamers. Once the ?-barrels of six hexamers have spanned the bilayer, they may merge to form a more stable 36-stranded ?-barrel. We favor models in which parallel ?-barrels formed by N-terminus segments comprise the lining of the pores. These types of models explain why the channels are selective for cations and how metal ions, such as Zn2+, synthetic peptides that contain histidines, and some small organic cations may block channels or inhibit formation of channels. Our models were developed to be consistent with microscopy studies of A? assemblies in membranes, one of which is presented here for the first time. PMID:20939098

  16. Ultrafast gas-phase electron diffraction

    NASA Astrophysics Data System (ADS)

    Williamson, Joseph Charles

    1998-03-01

    The temporal resolution of pump-probe, gas-phase electron diffraction (GED) has been extended to the picosecond time scale, a three order-of-magnitude improvement. With such resolution, GED can now be applied to structural studies of fundamental chemical dynamics, providing complementary information to conventional time-resolved spectroscopy techniques. This thesis gives a thorough theoretical and experimental treatment of ultrafast GED. Simulations of coherent chemical dynamics demonstrated that the evolution of molecular spatial coordinates can be determined with fs GED. Similarly, ps GED can reveal the structure of short-lived intermediates in kinetic processes, and the circular symmetries of GED patterns were predicted to break during ps rotational coherences. 620-nm output from an amplified femtosecond laser (2.5 mJ; 300 fs) was split into pump and probe arms and frequency-doubled. 95% of the laser intensity was focused onto a molecular beam. The remaining 5% was directed onto a back-illuminated 450-A silver cathode, where ultrafast electron pulses were created via the photoelectric effect and accelerated to 18 keV. Space-charge effects forced a compromise between electron number density and temporal resolution: streaking experiments revealed that the pulse duration increased by 1 ps for every 1,000 electrons. The electrons intersected the pump laser directly underneath the molecular beam orifice. Approximately 10% of the electrons scattered elastically from sample molecules within the interaction region, and the resulting diffraction pattern was recorded with a scintillator/fused fiber optic/image intensifier/charge- coupled device imaging system. Single-electron sensitivity across two-dimensions was necessary because of the extremely low electron flux, and the measured detective quantum efficiency of the imaging system was better than 0.5. Ground-state GED patterns of several molecules were recorded using ps electron pulses. Time zero for the pump-probe experiment was identified to within 1 ps using photoionization-induced lensing (PIL) of the unscattered electron beam. The first ultrafast GED investigation studied diiodomethane, and diffraction patterns were recorded at several time steps around time zero. The resulting structural transients showed that 10% of the CH2I2 dissociated into CH2I + I following excitation with the 310-nm pump laser. The estimated temporal resolution was 5 to 10 ps.

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

    PubMed

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

    2014-01-01

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

  18. 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.

  19. 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

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

    PubMed

    Kuczera, Krzysztof; Kursula, Petri

    2012-01-01

    We have studied the interactions between calmodulin (CaM) and three target peptides from the death-associated protein kinase (DAPK) protein family using both experimental and modeling methods, aimed at determining the details of the underlying biological regulation mechanisms. Experimentally, calorimetric binding free energies were determined for the complexes of CaM with peptides representing the DAPK2 wild-type and S308D mutant, as well as DAPK1. The observed affinity of CaM was very similar for all three studied peptides. The DAPK2 and DAPK1 peptides differ significantly in sequence and total charge, while the DAPK2 S308D mutant is designed to model the effects of DAPK2 Ser308 phosphorylation. The crystal structure of the CaM-DAPK2 S308D mutant peptide is also reported. The structures of CaM-DAPK peptide complexes present a mode of CaM-kinase interaction, in which bulky hydrophobic residues at positions 10 and 14 are both bound to the same hydrophobic cleft. To explain the microscopic effects underlying these interactions, we performed free energy calculations based on the approximate MM-PBSA approach. For these highly charged systems, standard MM-PBSA calculations did not yield satisfactory results. We proposed a rational modification of the approach which led to reasonable predictions of binding free energies. All three complexes are strongly stabilized by two effects: electrostatic interactions and buried surface area. The strong favorable interactions are to a large part compensated by unfavorable entropic terms, in which vibrational entropy is the largest contributor. The electrostatic component of the binding free energy followed the trend of the overall peptide charge, with strongest interactions for DAPK1 and weakest for the DAPK2 mutant. The electrostatics was dominated by interactions of the positively charged residues of the peptide with the negatively charged residues of CaM. The nonpolar binding free energy was comparable for all three peptides, the largest contribution coming from the Trp305. About two-thirds of the buried surface area corresponds to nonpolar residues, showing that hydrophobic interactions play an important role in these CaM-peptide complexes. The simulation results agree with the experimental data in predicting a small effect of the S308D mutation on CaM interactions with DAPK2, suggesting that this mutation is not a good model for the S308 phosphorylation. PMID:22571432

  1. Equilibrium structures from gas-phase electron-diffraction data 

    E-print Network

    McCaffrey, Philip D

    2007-01-01

    For the past 75 years gas-phase electron diffraction (GED) has remained the most valuable technique for determining structures of small molecules, free from intermolecular interactions. Throughout this period many ...

  2. Cell selectivity and anti-inflammatory activity of a Leu/Lys-rich alpha-helical model antimicrobial peptide and its diastereomeric peptides.

    PubMed

    Wang, Peng; Nan, Yong Hai; Yang, Sung-Tae; Kang, Shin Won; Kim, Yangmee; Park, Il-Seon; Hahm, Kyung-Soo; Shin, Song Yub

    2010-07-01

    To investigate the effect of the number and distribution of d-amino acids introduced into non-cell-selective alpha-helical antimicrobial peptides on the cell selectivity, protease stability and anti-inflammatory activity, we synthesized an 18-meric Leu/Lys-rich alpha-helical model peptide (K(9)L(8)W) and d-amino acid-containing diastereomeric peptides. Increasing in cell selectivity of the peptides was increased in parallel with increasing in the number of d-amino acids introduced. Despite having the same number of d-amino acids, D(9)-K(9)L(8)W-1 had better cell selectivity than D(9)-K(9)L(8)W-2, indicating that a dispersed distribution of d-amino acids in diastereomeric peptides is more effective for cell selectivity than their segregated distribution. D(3)-K(9)L(8)W-2, D(6)-K(9)L(8)W, D(9)-K(9)L(8)W-1 and D(9)-K(9)L(8)W-2 showed complete resistance to tryptic digestion. Furthermore, K(9)L(8)W and all of its diastereomeric peptides significantly inhibited nitric oxide (NO) production, inducible nitric oxide synthase (iNOS) mRNA expression and tumor necrosis factor-alpha (TNF-alpha) release in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells at a lower concentration than bactericidal concentration. The order of anti-inflammatory activity for the peptides was K(9)L(8)W approximately D(3)-K(9)L(8)W-1 approximately D(3)-K(9)L(8)W-2 approximately D(6)-K(9)L(8)W approximately D(9)-K(9)L(8)W-2>D(4)-K(9)L(8)W>D(9)-K(9)L(8)W-1. Increasing in hydrophobicity or alpha-helicity of the peptides was more closely correlated with increasing in hemolytic activity and anti-inflammatory activity than antimicrobial and LPS-disaggregation activities. Collectively, we successfully developed several d-amino acid-containing antimicrobial peptides (D(4)-K(9)L(8)W, D(6)-K(9)L(8)W and D(9)-K(9)L(8)W-1) with good cell selectivity, protease stability and potent anti-inflammatory activity. These antimicrobial peptides could serve as templates for the development of peptide antibiotics for the treatment of sepsis, as well as microbial infection. PMID:20363271

  3. Atomic and molecular physics in the gas phase

    SciTech Connect

    Toburen, L.H.

    1990-09-01

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

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

    PubMed

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

    2015-07-30

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

  5. 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.

  6. 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)

  7. 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

  8. 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

  9. 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.

  10. 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.

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

    PubMed

    Canon, Francis; Milosavljevi?, 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

  12. Exxon gains gas-phase patent, makes LLDPE

    SciTech Connect

    Rotman, D.

    1995-04-26

    Exxon chemical says it has made linear low-density polyethylene (LLDPE) using metallocene catalysts at its world-scale gas-phase plant in Mont Belvieu, TX. Exxon also says it has received a broad US patent that covers the use of metallocenes in gas-phase reactors that use condensing mode technology and that it plans to license the know-how. The moves, say industry experts, greatly strengthen Exxon`s position in metallocenes, particularly in pushing metallocene-based PE into commodity markets. The use of gas-phase technology {open_quotes}had to happen{close_quotes} to allow metallocene polymers to compete as commodities, says David Highfield, v.p. at Catalyst Consultants (Spring House, PA). {open_quotes}It`s very important and very significant in widening the scope of [metallocene] technology.{close_quotes}

  13. 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 d

  14. Molecular Dynamics Simulations of Model Trans-Membrane Peptides in Lipid Bilayers: A Systematic Investigation of Hydrophobic Mismatch

    E-print Network

    Nielsen, Steven O.

    Molecular Dynamics Simulations of Model Trans-Membrane Peptides in Lipid Bilayers: A Systematic the hydrophobic length of trans-membrane segments of a protein and the hydrophobic width of the surrounding lipid simulations of trans-membrane KALP peptides (sequence: GKK(LA)nLKKA) in phos- pholipid bilayers to investigate

  15. 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.

  16. 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.

  17. 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

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

    PubMed Central

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

    2007-01-01

    Ion mobility spectrometry (IMS) has been explored for decades, and its versatility in separation and identification of gas-phase ions 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. Implementation of FAIMS/IMS and IMS/MS interfaces using electrodynamic ion funnels greatly improves sensitivity. Evaluation of FAIMS/IMS/TOF performance for 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 peak capacities in analyses of tryptic peptides are ~500 for FAIMS/IMS separations and ~106 for 3-D FAIMS/IMS/MS, providing a potential platform for ultrahigh-throughput analyses of complex mixtures. PMID:16194103

  19. MOVPE GaN gas phase chemistry for reactor design and optimization

    SciTech Connect

    Safvi, S.A.; Thon, A.; Kuech, T.F.; Redwing, J.M.; Flynn, J.S.; Tischler, M.A.

    1997-12-31

    The results of gas phase decomposition studies are used to construct a chemistry model which is compared to data obtained from an experimental MOVPE reactor. A flow tube reactor is used to study gas phase reactions between trimethylgallium (TMG) and ammonia at high temperatures, characteristic to the metalorganic vapor phase epitaxy (MOVPE) of GaN. Experiments were performed to determine the effect of the mixing of the Group III precursors and Group V precursors on the growth rate, growth uniformity and film properties. Growth rates are predicted for simple reaction mechanisms and compared to those obtained experimentally. Quantification of the loss of reacting species due to oligomerization is made based on experimentally observed growth rates. The model is used to obtain trends in growth rate and uniformity with the purpose of moving towards better operating conditions.

  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 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.

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

    PubMed

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

    2015-10-26

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

  3. 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

  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. Routes for Drug Delivery to the Retina: Topical, Transscleral, Suprachoroidal and Intravitreal Gas Phase Delivery.

    PubMed

    Yamada, Norihiro; Olsen, Timothy W

    2016-01-01

    Local drug delivery to the posterior segment, particularly the macula, represents a significant challenge. In this chapter, we review current challenges, barriers and limitations. Due to the local drug delivery to the retina and macula, systemic side effects are limited. In this chapter, we also discuss the historical approaches, key aspects of ideal drug delivery systems, the use of animal models to study pharmacokinetics, and the principles of transscleral, suprachoroidal and gas phase drug delivery. PMID:26501685

  6. Isospin and momentum dependence of liquid-gas phase transition in hot asymmetric nuclear matter

    E-print Network

    Jun Xu; Lie-Wen Chen; Bao-An Li; Hong-Ru Ma

    2007-11-12

    The liquid-gas phase transition in hot neutron-rich nuclear matter is investigated within a self-consistent thermal model using different interactions with or without isospin and/or momentum dependence. The boundary of the phase-coexistence region is shown to be sensitive to the density dependence of the nuclear symmetry energy as well as the isospin and momentum dependence of the nuclear interaction.

  7. QSAR modeling of the antimicrobial activity of peptides as a mathematical function of a sequence of amino acids.

    PubMed

    Toropova, Mariya A; Veselinovi?, Aleksandar M; Veselinovi?, Jovana B; Stojanovi?, Dušica B; Toropov, Andrey A

    2015-12-01

    Antimicrobial peptides have emerged as new therapeutic agents for fighting multi-drug-resistant bacteria. However, the process of optimizing peptide antimicrobial activity and specificity using large peptide libraries is both tedious and expensive. Therefore, computational techniques had to be applied for process optimization. In this work, the representation of the molecular structure of peptides (mastoparan analogs) by a sequence of amino acids has been used to establish quantitative structure-activity relationships (QSARs) for their antibacterial activity. The data for the studied peptides were split three times into the training, calibration and test sets. The Monte Carlo method was used as a computational technique for QSAR models calculation. The statistical quality of QSAR for the antibacterial activity of peptides for the external validation set was: n=7, r(2)=0.8067, s=0.248 (split 1); n=6, r(2)=0.8319, s=0.169 (split 2); and n=6, r(2)=0.6996, s=0.297 (split 3). The stated statistical parameters favor the presented QSAR models in comparison to 2D and 3D descriptor based ones. The Monte Carlo method gave a reasonably good prediction for the antibacterial activity of peptides. The statistical quality of the prediction is different for three random splits. However, the predictive potential is reasonably well for all cases. The presented QSAR modeling approach can be an attractive alternative of 3D QSAR at least for the described peptides. PMID:26454621

  8. Molecular Interactions between Cell Penetrating Peptide Pep-1 and Model Cell Membranes

    PubMed Central

    Ding, Bei; Chen, Zhan

    2012-01-01

    We investigated the molecular interactions of a cell penetrating peptide (CPP) Pep-1 with model cell membranes using sum frequency generation (SFG) vibrational spectroscopy, supplemented by attenuated total reflectance - Fourier transform infrared spectroscopy (ATR-FTIR). Hydrogenated and deuterated 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG and dDPPG) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1?-rac-glycerol) (POPG), were used in the experiments to represent gel-phase and fluid-phase lipid bilayers, respectively. Our SFG results indicated that Pep-1 molecules adopted a ?-sheet conformation when adsorbed to the surface of gel-phase DPPG lipid bilayers. When interacting with fluid-phase POPG lipid bilayers, Pep-1 adopted a mix of ?-helical and ?-sheet structures over a broad range of peptide concentrations. The orientation distribution of the ?-helical Pep-1 segment associated with the fluid-phase bilayers was found to depend on the peptide concentration. SFG orientation analysis showed that Pep-1 molecules adopted an orientation nearly perpendicular to the plane of the bilayer for peptide concentrations of 0.28 ?M and 1.4 ?M. When the Pep-1 concentration was increased to 7.0 ?M, combined SFG and ATR-FTIR measurements showed that Pep-1 molecules were associated with the bilayer with a broad orientation distribution. Our results demonstrated that lipid bilayer phase and peptide concentration affect the conformation and orientation of Pep-1 molecules associated with model cell membranes, which is crucial to the translocation process of CPPs. A combination of SFG and ATR-FTIR studies can be used to determine the conformation and orientation of CPPs interacting with model cell membranes in situ. PMID:22292835

  9. 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.

  10. 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.

  11. A model of the peptide triazole entry inhibitor binding to HIV-1 gp120 and mechanism of bridging sheet disruption

    PubMed Central

    Emileh, Ali; Tuzer, Ferit; Yeh, Herman; Umashankara, Muddegowda; Moreira, Diogo R. M.; LaLonde, Judith M.; Bewley, Carole A.; Abrams, Cameron F.; Chaiken, Irwin M.

    2013-01-01

    Peptide-triazole (PT) entry inhibitors prevent HIV-1 infection by blocking viral gp120 binding to both HIV-1 receptor and coreceptor on target cells. Here, we used all-atom explicit solvent molecular dynamics (MD) to propose a model for the encounter complex of the peptide-triazoles with gp120. Saturation Transfer Difference NMR (STD NMR) and single-site mutagenesis experiments were performed to test the simulation results. We found that docking of the peptide to a conserved patch of residues lining the “F43 pocket” of gp120 in a bridging sheet naïve gp120 conformation of the glycoprotein, led to a stable complex. This pose prevents formation of the bridging sheet minidomain, which is required for receptor/coreceptor binding, providing a mechanistic basis for dual-site antagonism of this class of inhibitors. Burial of the peptide triazole at gp120 inner/outer domain interface significantly contributed to complex stability and rationalizes the significant contribution of hydrophobic triazole groups to peptide potency. Both the simulation model and STD NMR experiments suggest that the I-X-W (where X=(2S, 4S)-4-(4-phenyl-1H-1, 2, 3-triazol-1-yl) pyrrolidine) tripartite hydrophobic motif in the peptide is the major contributor of contacts at the gp120/PT interface. Since the model predicts that the peptide Trp side chain hydrogen bonding with gp120 S375 contributes to stability of the PT/gp120 complex, we tested this prediction through analysis of peptide binding to gp120 mutant S375A. The results showed that a peptide triazole KR21 inhibits S375A with 20-fold less potency versus WT, consistent with predictions of the model. Overall, the PT/gp120 model provides a starting point for both rational design of higher affinity peptide triazoles and development of structure-minimized entry inhibitors that can trap gp120 into an inactive conformation and prevent infection. PMID:23470147

  12. Ion Trap/Ion Mobility/Quadrupole/Time-of-Flight Mass Spectrometry for Peptide Mixture Analysis

    E-print Network

    Clemmer, David E.

    Ion Trap/Ion Mobility/Quadrupole/Time-of-Flight Mass Spectrometry for Peptide Mixture Analysis for the analysis of peptide mixtures. In this approach, a mixture of peptides is electrosprayed into the gas phase. The mixture of ions that is created is accumulated in an ion trap and periodi- cally injected into a drift

  13. Molecular dynamics simulations of small peptides: dependence on dielectric model and pH.

    PubMed

    Daggett, V; Kollman, P A; Kuntz, I D

    1991-02-15

    There has been much interest recently in the structure of small peptides in solution. A recent study by Bradley and co-workers [(1989) in Techniques of Protein Chemistry, Hugli, T.E., Ed., Academic Press, Orlando, FL, pp. 531-546; (1990) Journal of Molecular Biology, 215, pp. 607-622] describes a 17-residue peptide that is stable as a monomeric helix in aqueous solution at low pH, as determined by two-dimensional nmr and CD spectroscopy. They also have determined the helix content of the peptide as a function of pH using CD. We performed molecular dynamics simulations, with an empirical force field, of this peptide at low pH, with three different dielectric models: a linear distance-dependent dielectric function (epsilon = R); a modified form [J. Ramstein and R. Lavery (1988) Proceedings of the National Academy of Science, USA, Vol. 85, pp. 7231-7235] of the sigmoidal distance-dependent dielectric function of Hingerty and co-workers [(1985) Biopolymers, Vol. 24, pp. 427-439]; and epsilon = 1 with the peptide immersed in a bath of water molecules. We found that simulations with the sigmoidal dielectric function and the model with explicit water molecules resulted in average distances for particular interactions that were consistent with the experimental nmr results, with the sigmoidal function best representing the data. However, these models exhibited very different helix-stabilizing interactions. We also performed simulations using the sigmoidal function at moderate and high pH to compare to experimental determinations of the pH dependence of helix content. Helix content did not decrease with increases in pH, as shown experimentally. We did, however, observe changes in a specific side chain-helix dipole interaction that was implicated in determining the pH-dependent behavior of this peptide. Overall, the sigmoidal dielectric function was a reasonable alternative to adding explicit water molecules. In comparing 100 ps molecular dynamics simulations, the sigmoidal function was much less computer intensive and sampled more of conformational space than the treatment using explicit water molecules. Sampling is especially important for this system since the peptide has been shown experimentally to populate both helical and nonhelical conformations. PMID:1868159

  14. Conformational Changes and Association of Membrane-Interacting Peptides in Myelin Membrane Models: A Case of the C-Terminal Peptide of Proteolipid Protein and the Antimicrobial Peptide Melittin.

    PubMed

    Appadu, Ashtina; Jelokhani-Niaraki, Masoud; DeBruin, Lillian

    2015-11-25

    Model membranes composed of various lipid mixtures can segregate into liquid-ordered (Lo) and liquid-disordered (Ld) phases. In this study, lipid vesicles composed of mainly Lo or Ld phases as well as complex lipid systems representing the cytosolic leaflet of the myelin membrane were characterized by fluorescence resonance energy transfer with a donor/acceptor pair that preferentially partitioned into Lo or Ld phases, respectively. The fluidity of the lipid systems containing >30% cholesterol was modulated in the presence of the amphipathic peptide melittin. With all the studied lipid systems, melittin attained an ?-helical conformation as determined by CD spectroscopy and attained varying degrees of membrane association and penetration as determined by intrinsic Trp fluorescence. The other protein domain utilized was a putative amphipathic helical peptide derived from the cytosolic C-terminal sequence of proteolipid protein (PLP) which is the most abundant protein in the myelin membrane. The C-terminal PLP peptide transitioned from a random coil to an ?-helix in the presence of trifluoroethanol. Upon interacting with each of lipid vesicle system, the PLP peptide also folded into a helix; however, at high concentrations of the peptide with fluid lipid systems, associated helices transmuted into a ?-sheet conformer. The membrane-associated aggregation of the cytosolic C-termini could be a mechanism by which the transmembrane PLP multimerizes in the myelin membrane. PMID:26561987

  15. 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

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2002-03-01

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

  18. Tropospheric Measurements of Gas-Phase and Aerosol Chemistry

    E-print Network

    Meskhidze, Nicholas

    .s.l. BI Bear Island 74.5 N 19.0 E bp Browning Pass, Ross Sea, Antarctica 74 36' S 163 56' E BS BeaufortTropospheric Measurements of Gas-Phase and Aerosol Chemistry in Polar Regions (Version from 2007 in polar boundary-layer ozone depletion" by Simpson et al., Atmos. Chem. Phys., 2007, available at: http

  19. Multimaterial nanostructures Mimicking Electrodeposition in the Gas Phase

    E-print Network

    Jacobs, Heiko O.

    , and Heiko O. Jacobs* An in situ gas-phase process that produces charged streams of Au, Si, TiO2, ZnO, and Ge applies is discussed and it is demonstrated that particles can be plated into pores vertically (minimum of pumpless operation and parallel nozzle-free deposition provides a scalable tool for printable flexible

  20. NEUTRAL PRODUCTS FROM GAS PHASE REARRANGEMENTS OF SIMPLE

    E-print Network

    Morton, Thomas Hellman

    NEUTRAL PRODUCTS FROM GAS PHASE REARRANGEMENTS OF SIMPLE CARBOCATIONS Thomas Hellman Morton OUTLINE . . . . . . . . . . . . . . . . . . . . . . 217 C. Distinguishing Transposition from Randomization . . . . . . . . . 221 D. Formation of Ion­Neutral Elsevier Science B.V. All rights reserved. #12;ABSTRACT Analyzing the neutral products from ionic reactions

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

    ERIC Educational Resources Information Center

    Willis, Clive

    1981-01-01

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

  2. 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

  3. 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...

  4. Probing Gas Phase Chemistry above Ice Surfaces with Millimeter/submillimeter Spectrosocpy

    NASA Astrophysics Data System (ADS)

    Mesko, AJ; Wagner, Ian C.; Milam, Stefanie N.; Widicus Weaver, Susanna L.

    2014-06-01

    Chemical reactions involving the icy mantles of interstellar dust grains have been invoked in astrochemical models to explain the formation of complex organic molecules in interstellar clouds. Interstellar ices can act as a substrate to encourage reactions in three ways: reactions within the bulk ice, reactions between mobile species on the ice surface, or gas-phase reactions that are initiated by thermal desorption or photodesorption of the ice. We are building a new experiment that uses millimeter/submillimeter absorption spectroscopy to probe the gas-phase chemistry directly above the ice surface during thermal- or photo-processing. We will present the experimental design and preliminary results for pure water ices and water+ methanol ice mixtures.

  5. Nuclear liquid-gas phase transition studied with antisymmetrized molecular dynamics

    E-print Network

    Takuya Furuta; Akira Ono

    2006-02-23

    The nuclear liquid-gas phase transition of the system in ideal thermal equilibrium is studied with antisymmetrized molecular dynamics. The time evolution of a many-nucleon system confined in a container is solved for a long time to get a microcanonical ensemble of a given energy and volume. The temperature and the pressure are extracted from this ensemble and the caloric curves are constructed. The present work is the first time that a microscopic dynamical model which describes nuclear multifragmentation reactions well is directly applied to get the nuclear caloric curve. The obtained constant pressure caloric curves clearly show the characteristic feature of the liquid-gas phase transition, namely negative heat capacity (backbending), which is expected for the phase transition in finite systems.

  6. 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.

  7. 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.

  8. A Quantitative Model for the All-or-None Permeabilization of Phospholipid Vesicles by the Antimicrobial Peptide Cecropin A?

    PubMed Central

    Gregory, Sonia M.; Cavenaugh, Allison; Journigan, Velvet; Pokorny, Antje; Almeida, Paulo F.F.

    2008-01-01

    The mechanism of the all-or-none release of the contents of phospholipid vesicles induced by the antimicrobial peptide cecropin A was investigated. A detailed experimental study of the kinetics of dye release showed that the rate of release increases with the ratio of peptide bound per vesicle and, at constant concentration, with the fraction of the anionic lipid phosphatidylglycerol in neutral, phosphatidylcholine membranes. Direct measurement of the kinetics of peptide binding and dissociation from vesicles revealed that the on-rate is almost independent of vesicle composition, whereas the off-rate decreases by orders of magnitude with increasing content of anionic lipid. A simple, exact model fits all experimental kinetic data quantitatively. This is the first time that an exact kinetic model is implemented for a peptide with an all-or-none mechanism. In this model, cecropin A binds reversibly to vesicles, which at a certain point enter an unstable state. In this state, a pore probably opens and all vesicle contents are released, consistent with the all-or-none mechanism. This pore state is a state of the whole vesicle, but does not necessarily involve all peptides on that vesicle. No peptide oligomerization on the vesicle is involved; alternative models that assume oligomerization are inconsistent with the experimental data. Thus, formation of well-defined, peptide-lined pores is unlikely. PMID:17921201

  9. Aromatic interactions in model peptide ?-hairpins: ring current effects on proton chemical shifts.

    PubMed

    Rajagopal, Appavu; Aravinda, Subrayashastry; Raghothama, Srinivasarao; Shamala, Narayanaswamy; Balaram, Padmanabhan

    2012-01-01

    Crystal structures of eight peptide ?-hairpins in the sequence Boc-Leu-Phe-Val-Xxx-Yyy-Leu-Phe-Val-OMe revealed that the Phe(2) and Phe(7) aromatic rings are in close spacial proximity, with the centroid-centroid distance (R(cen)) of 4.4-5.4 Å between the two phenyl rings. Proton NMR spectra in chloroform and methanol solution reveal a significant upfield shift of the Phe(7) C(?,?') H(2) protons (6.65-7.04 ppm). Specific assignments of the aromatic protons have been carried out in the peptide Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (6). The anticipated ring current shifts have been estimated from the aromatic ring geometrics observed in crystals for all eight peptides. Only one of the C(?,?') H proton lies in the shielding zone with rapid ring flipping, resulting in averaging between the two extreme chemical shifts. An approximate estimate of the population of conformations, which resemble crystal state orientation, may be obtained. Key nuclear Overhauser effects (NOEs) between facing Phe side chains provide support for close similarity between the solid state and solution conformation. Temperature dependence of aromatic ring proton chemical shift and line widths for peptide 6 (Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe) and the control peptide Boc-Leu-Val-Val-(D)Pro-Gly-Leu-Phe-Val-OMe establish an enhanced barrier to ring flipping when the two Phe rings are in proximity. Modeling studies suggest that small, conformational adjustment about C(?)-C(?) (?(1) ) and C(?)-C(?) (?(2) ) bonds of both the Phe residues may be required in order to permit unhindered, uncorrelated flipping of both the Phe rings. The maintenance of the specific aromatic ring orientation in organic solvents provides evidence for significant stabilizing interaction. PMID:22782561

  10. 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.

  11. Small interacting peptides. Part II: Interaction of cyclohexapeptides with immobilised model peptides. Comparison of infrared investigations, principal components analysis and force field calculations.

    PubMed

    Palmer, Frauke; Stingel, Christiane; Tünnemann, Rolf; Mack, Hans-Georg; Jung, Günther; Hoffmann, Volker

    2004-07-01

    The interaction of cyclic peptides with surface-bound model peptides was investigated by ATR-FTIR spectroscopy, principal components analysis and force field calculations. Information about the interacting functional COOH, COO-, and NH3+ groups and the peptide backbone was gained through a set of cyclohexapeptides (seven of the type c(X1KX2KX3K) (K = L-lysine) and one of the type c(X1KX2KX3k) (k = D-lysine), which are interacting with L-arginine- or tripeptide-coated Si-ATR crystals. All measurements were performed in aqueous solutions. Spectra evaluation in the range 1800-1500 cm(-1) was done by band and principal components analysis (PCA). Only adsorbed molecules were present in these spectra. The coatings were investigated by ATR-FTIR spectroscopy too in order to characterise their functional groups. Based on this knowledge, the spectra of the interacting partners could be evaluated in relation to cyclohexapeptides and coatings. As a result, it was possible to identify the distinct differences in the bonding behaviour of the various peptides. PMID:15248946

  12. 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) ?-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

  13. 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

  14. 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.

  15. 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

  16. 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 (± 1?) 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.

  17. Testing the diffusing boundary model for the helix–coil transition in peptides

    PubMed Central

    Neumaier, Sabine; Reiner, Andreas; Büttner, Maren; Fierz, Beat; Kiefhaber, Thomas

    2013-01-01

    The dynamics of peptide ?-helices have been studied extensively for many years, and the kinetic mechanism of the helix–coil dynamics has been discussed controversially. Recent experimental results have suggested that equilibrium helix–coil dynamics are governed by movement of the helix/coil boundary along the peptide chain, which leads to slower unfolding kinetics in the helix center compared with the helix ends and position-independent helix formation kinetics. We tested this diffusion of boundary model in helical peptides of different lengths by triplet-triplet energy transfer measurements and compared the data with simulations based on a kinetic linear Ising model. The results show that boundary diffusion in helical peptides can be described by a classical, Einstein-type, 1D diffusion process with a diffusion coefficient of 2.7?107 (amino acids)2/s or 6.1?10?9 cm2/s. In helices with a length longer than about 40 aa, helix unfolding by coil nucleation in a helical region occurs frequently in addition to boundary diffusion. Boundary diffusion is slowed down by helix-stabilizing capping motifs at the helix ends in agreement with predictions from the kinetic linear Ising model. We further tested local and nonlocal effects of amino acid replacements on helix–coil dynamics. Single amino acid replacements locally affect folding and unfolding dynamics with a ?f-value of 0.35, which shows that interactions leading to different helix propensities for different amino acids are already partially present in the transition state for helix formation. Nonlocal effects of amino acid replacements only influence helix unfolding (?f = 0) in agreement with a diffusing boundary mechanism. PMID:23878243

  18. Title: Protective effects of C-type natriuretic peptide on linear growth and articular cartilage integrity in an inflammatory arthritis mouse model.

    E-print Network

    ). Patients with homozygous loss-of-function mutations in the CNP receptor Natriuretic Peptide Receptor B (NPRTitle: Protective effects of C-type natriuretic peptide on linear growth and articular cartilage integrity in an inflammatory arthritis mouse model. Short title: C-type natriuretic peptide protects

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

    PubMed

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

    2015-01-01

    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

  20. 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, ?-sheet struture. Our study provides an insight into the principles of how the formation of amyloid can be governed by amino acid sequence.

  1. 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...

  2. 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.

  3. Gas-phase clustering of protonated amino acids with acetonitrile

    NASA Astrophysics Data System (ADS)

    Wincel, Henryk

    2010-03-01

    The gas-phase clustering reactions of protonated amino acids, AAH + (AA = Ala, Val, Ser, Phe, Pro, Gln, Lys and Arg) with acetonitrile were studied with a pulsed ion-beam high-pressure mass spectrometer. The bond energies of the AAH +·(CH 3CN) complexes range from 20 to 11 kcal/mol. While for AlaH +, ValH +, SerH +, PheH +, ProH + and GlnH +, the solvation free energies decrease linearly with increasing gas-phase basicity of AA, deviations from the correlation are observed for LysH + and ArgH +. The bonding free energies for AAH +·(CH 3CN) are compared with those for AAH +·(H 2O) and AAH +·(NH 3).

  4. Gas phase fractionation method using porous ceramic membrane

    DOEpatents

    Peterson, Reid A. (Madison, WI); Hill, Jr., Charles G. (Madison, WI); Anderson, Marc A. (Madison, WI)

    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.

  5. 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.

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

    PubMed

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

    2010-11-15

    Collision cross sections in both helium and nitrogen gases were measured directly using a drift cell with RF ion confinement inserted within a quadrupole/ion mobility/time-of-flight hybrid mass spectrometer (Waters Synapt HDMS, Manchester, U.K.). Collision cross sections for a large set of denatured peptide, denatured protein, native-like protein, and native-like protein complex ions are reported here, forming a database of collision cross sections that spans over 2 orders of magnitude. The average effective density of the native-like ions is 0.6 g cm(-3), which is significantly lower than that for the solvent-excluded regions of proteins and suggests that these ions can retain significant memory of their solution-phase structures rather than collapse to globular structures. Because the measurements are acquired using an instrument that mimics the geometry of the commercial Synapt HDMS instrument, this database enables the determination of highly accurate collision cross sections from traveling-wave ion mobility data through the use of calibration standards with similar masses and mobilities. Errors in traveling-wave collision cross sections determined for native-like protein complexes calibrated using other native-like protein complexes are significantly less than those calibrated using denatured proteins. This database indicates that collision cross sections in both helium and nitrogen gases can be well-correlated for larger biomolecular ions, but non-correlated differences for smaller ions can be more significant. These results enable the generation of more accurate three-dimensional models of protein and other biomolecular complexes using gas-phase structural biology techniques. PMID:20979392

  7. 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.

  8. 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

  9. Liquid-gas phase transition and Coulomb instability of asymmetric nuclear systems

    E-print Network

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

    2005-01-27

    We use a chiral SU(3) quark mean field model to study the properties of nuclear systems at finite temperature. The liquid-gas phase transition of symmetric and asymmetric nuclear matter is discussed. For two formulations of the model the critical temperature, $T_c$, for symmetric nuclear matter is found to be 15.8 MeV and 17.9 MeV. These values are consistent with those derived from recent experiments. The limiting temperatures for finite nuclei are in good agreement with the experimental points.

  10. A polysialic acid mimetic peptide promotes functional recovery in a mouse model of spinal cord injury.

    PubMed

    Marino, Philippe; Norreel, Jean-Chrétien; Schachner, Melitta; Rougon, Geneviève; Amoureux, Marie-Claude

    2009-09-01

    Contrary to lower species that recapitulate some of the developmental programs, in mammals, functional recovery after spinal cord injury is impaired by a non-permissive environment and the lack of plasticity of adult neurons. The developmental plasticity associated linear homopolymer of alpha 2,8-linked sialic acid (PolySialic Acid, PSA), represents a permissive determinant that could contribute to recovery. We previously showed that a PSA cyclic mimetic peptide (PR-21) displayed PSA-like biological functions (Torregrossa, P., Buhl, L., Bancila, M., Durbec, P., Schafer, C., Schachner, M., Rougon, G., 2004. Selection of poly-alpha 2,8-sialic acid mimotopes from a random phage peptide library and analysis of their bioactivity. J. Biol. Chem. 279, 30707-30714.). In the present study we investigated the therapeutic potential of PR-21 in young adult mice after dorsal hemisection at the T9 level. We show that PR-21 fulfills several criteria for an in vivo use as it is not toxic, not immunogenic and displays good stability in biological fluids or tissue. Delivery of PR-21 to the lesion site decreased the time of the animals' return to continence, and enhanced motor functions, sensorimotor control and coordination of hindlimbs with forelimbs when compared to a control peptide. At the cellular level, PR-21 increased serotonergic axon density at and caudal to the lesion site, and decreased reactive gliosis in vivo. In an in vitro model of reactive astrocytes, PR-21 increased NCAM expression in strongly GFAP positive cells. Our data point to the unique features of a carbohydrate mimicking peptide, and support the notion that PSA can be considered as an important factor in recovery from spinal cord injury. PMID:19445935

  11. A peptide dendrimer enzyme model with a single catalytic site at the core.

    PubMed

    Javor, Sacha; Delort, Estelle; Darbre, Tamis; Reymond, Jean-Louis

    2007-10-31

    Catalytic esterase peptide dendrimers with a core active site were discovered by functional screening of a 65,536-member combinatorial library of third-generation peptide dendrimers using fluorogenic 1-acyloxypyrene-3,6,8-trisulfonates as substrates. In the best catalyst, RMG3, ((AcTyrThr)(8)(DapTrpGly)(4)(DapArgSerGly)(2)DapHisSerNH2), ester hydrolysis is catalyzed by a single catalytic histidine residue at the dendrimer core. A pair of arginine residues in the first-generation branch assists substrate binding. The catalytic proficiency of dendrimer RMG3 (kcat/KM = 860 M(-1) min(-1) at pH 6.9) per catalytic site is comparable to that of the multivalent esterase dendrimer A3 ((AcHisSer)(8)(DapHisSer)(4)(DapHisSer)2DapHisSerNH2) which has fifteen histidines and five catalytic sites (Delort, E. et al. J. Am. Chem. Soc. 2004, 126, 15642-15643). Remarkably, catalysis in the single site dendrimer RMG3 is enhanced by the outer dendritic branches consisting of aromatic amino acids. These interactions take place in a relatively compact conformation similar to a molten globule protein as demonstrated by diffusion NMR. In another dendrimer, HG3 ((AcIlePro)(8)(DapIleThr)(4)(DapHisAla)(2)DapHisLeuNH2) by contrast, catalysis by a core of three histidine residues is unaffected by the outer dendritic layers. Dendrimer HG3 or its core HG1 exhibit comparable activity to the first-generation dendrimer A1 ((AcHisSer)(2)DapHisSerNH2). The compactness of dendrimer HG3 in solution is close to that a denatured peptide. These experiments document the first esterase peptide dendrimer enzyme models with a single catalytic site and suggest a possible relationship between packing and catalysis in these systems. PMID:17924626

  12. 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

  13. Gas phase hydroformylation of propylene and allyl alcohol with immobilized rhodium complexes

    SciTech Connect

    Munck, N.A.D.

    1980-01-01

    Contents: Introduction--(Carbon monoxide as a chemical feedstock, hydroformylation of alkenes, immobilization of homogeneous catalysts, synthesis of 1,4-butanediol, and scope of this thesis); Gas phase hydroformylation of propylene with porous resin anchored rhodium complexes--(Methods of catalyst preparation and characterization); Gas phase hydroformylation of propylene with porous resin anchored rhodium complexes--(The catalytic performance); Gas phase hydroformylation of propylene with immobilized rhodium complex monolayer catalysts; Gas phase hydroformylation of allyl alcohol with supported liquid phase catalysts.

  14. 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 ?-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

  15. An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS.

    PubMed

    Krokhin, O V; Craig, R; Spicer, V; Ens, W; Standing, K G; Beavis, R C; Wilkins, J A

    2004-09-01

    The proposed model is based on the measurement of the retention times of 346 tryptic peptides in the 560- to 4,000-Da mass range, derived from a mixture of 17 protein digests. These peptides were measured in HPLC-MALDI MS runs, with peptide identities confirmed by MS/MS. The model relies on summation of the retention coefficients of the individual amino acids, as in previous approaches, but additional terms are introduced that depend on the retention coefficients for amino acids at the N-terminal of the peptide. In the 17-protein mixture, optimization of two sets of coefficients, along with additional compensation for peptide length and hydrophobicity, yielded a linear dependence of retention time on hydrophobicity, with an R2 value about 0.94. The predictive capability of the model was used to distinguish peptides with close m/z values and for detailed peptide mapping of selected proteins. Its applicability was tested on columns of different sizes, from nano- to narrow-bore, and for direct sample injection, or injection via a pre-column. It can be used for accurate prediction of retention times for tryptic peptides on reversed-phase (300-A pore size) columns of different sizes with a linear water-ACN gradient and with TFA as the ion-pairing modifier. PMID:15238601

  16. Use of electrochemical oxidation and model peptides to study nucleophilic biological targets of reactive metabolites: the case of rimonabant.

    PubMed

    Thorsell, Annika; Isin, Emre M; Jurva, Ulrik

    2014-10-20

    Electrochemical oxidation of drug molecules is a useful tool to generate several different types of metabolites. In the present study we developed a model system involving electrochemical oxidation followed by characterization of the oxidation products and their propensity to modify peptides. The CB1 antagonist rimonabant was chosen as the model drug. Rimonabant has previously been shown to give high covalent binding to proteins in human liver microsomes and hepatocytes and the iminium ion and/or the corresponding aminoaldehyde formed via P450 mediated ?-carbon oxidation of rimonabant was proposed to be a likely contributor. This proposal was based on the observation that levels of covalent binding were significantly reduced when iminium species were trapped as cyanide adducts but also following addition of methoxylamine expected to trap aldehydes. Incubation of electrochemically oxidized rimonabant with peptides resulted in peptide adducts to the N-terminal amine with a mass increment of 64 Da. The adducts were shown to contain an addition of C5H4 originating from the aminopiperidine moiety of rimonabant. Formation of the peptide adducts required further oxidation of the iminium ion to short-lived intermediates, such as dihydropyridinium species. In addition, the metabolites and peptide adducts generated in human liver microsomes were compared with those generated by electrochemistry. Interestingly, the same peptide modification was found when rimonabant was coincubated with one of the model peptides in microsomes. This clearly indicated that reactive metabolite(s) of rimonabant identical to electrochemically generated species are also present in the microsomal incubations. In summary, electrochemical oxidation combined with peptide trapping of reactive metabolites identified a previously unobserved bioactivation pathway of rimonabant that was not captured by traditional trapping agents and that may contribute to the in vitro covalent binding. PMID:25210840

  17. Assembling gas-phase reaction mechanisms for high temperature inorganic systems based on quantum chemistry calculations

    E-print Network

    Swihart, Mark T.

    of atmospheric chemistry. The gas phase chemistry of many processes in high-temperature inorganic systems, from [1­6]. The gas phase chemistry of many processes in high- temperature inorganic systems, fromAssembling gas-phase reaction mechanisms for high temperature inorganic systems based on quantum

  18. Ion Trap Collisional Activation of c and z• Ions Formed via Gas-Phase Ion/Ion Electron Transfer Dissociation

    PubMed Central

    Han, Hongling; Xia, Yu; McLuckey, Scott A.

    2008-01-01

    A series of c- and z•-type product ions formed via gas-phase electron transfer ion/ion reactions between protonated polypeptides with azobenzene radical anions are subjected to ion trap collision activation in a linear ion trap. Fragment ions including a-, b-, y-type and ammonia-loss ions are typically observed in collision induced dissociation (CID) of c ions, showing almost identical CID patterns as those of the C-terminal amidated peptides consisting of the same sequences. Collisional activation of z• species mainly gives rise to side-chain losses and peptide backbone cleavages resulting in a-, b-, c-, x-, y-and z-type ions. Most of the fragmentation pathways of z• species upon ion trap CID can be accounted for by radical driven processes. The side-chain losses from z• species are different from the small losses observed from the charge-reduced peptide molecular species in electron transfer dissociation (ETD), which indicates rearrangement of the radical species. Characteristic side-chain losses are observed for several amino acid residues, which are useful to predict their presence in peptide/protein ions. Furthermore, the unique side-chain losses from leucine and isoleucine residues allow facile distinction of these two isomeric residues. PMID:17608403

  19. Thrombospondin peptide ABT-898 inhibits inflammation and angiogenesis in a colitis model

    PubMed Central

    Gutierrez, Linda S; Ling, Jun; Nye, Derek; Papathomas, Konstantina; Dickinson, Catherine

    2015-01-01

    AIM: To evaluate the efficacy of the improved thrombospondin mimetic peptide ABT-898 in a murine model of ulcerative colitis. METHODS: The dextran sodium sulfate (DSS) was used for the induction of colitis in both TSP-1 deficient (TSP-1-/-) and wild type (WT) mice during 7 d. While mice were receiving the DSS dissolved in the drinking water, the ABT-898 peptide was dissolved in sterile 5% glucose solution and delivered using mini pumps subcutaneously implanted. Plasma samples were analyzed for interleukin (IL)-6 by ELISA assay and colonic tissues were harvested, fixed and processed for histological evaluation. Immunohistochemistry using antibodies for the detection of CD31 and MECA in endothelial cells was performed. Inflammation was graded in colonic sections and the number of microvessels in each lesion was assessed. Activation of signal transducer and activator of transcription 3 (STAT3) in colonic samples was quantified by immunohistochemistry and Western blotting using antibodies against total STAT3 and phosphorylated STAT3 (pSTAT3) (Ser727). RESULTS: Treatment with ABT-898 considerably diminished the inflammatory response in WT and TSP-1-/- mice (P < 0.0001 in both groups vs control). Identification of blood vessels highlighted by CD31/MECA immunohistochemistry, showed significantly reduced vessel counts in colitic lesions of WT and TSP-1-/- mice treated with ABT898 (TSP-1-/- controls/TSP-1-/- treated, P = 0.0002; WT controls/WT treated, P = 0.0005). Consistently, IL-6 was significantly diminished in plasma samples of TSP-1-/- and WT treated with the peptide when compared to the control mice (P = 0.0002 and P = 0.0148, respectively). pSTAT3 positive cells were quantified in WT and TSP-1-/- treated with ABT-898. A significant decrease in positive cells for pSTAT3 was observed in treated mice (TSP-1-/- controls/TSP-1-/- treated, P = 0.0089; WT/WT treated, P = 0.0110). These results were confirmed by Western blotting analyses showing lower levels of pSTAT3 in colitic lesions from mice treated with the peptide ABT-898. CONCLUSION: These findings indicate that the new peptide ABT-898 ameliorates inflammation and angiogenesis and might be a therapeutic alternative in IBD and inflammatory diseases. PMID:26034351

  20. Biomimetic membranes of lipid-peptide model systems prepared on solid support

    E-print Network

    Chenghao Li; Doru Constantin; Tim Salditt

    2015-04-09

    The structure of membrane-active peptides and their interaction with lipid bilayers can be studied in oriented lipid membranes deposited on solid substrates. Such systems are desirable for a number of surface-sensitive techniques. Here we focus on structural characterization by x-ray and neutron reflectivity and give an account of recent progress in sample preparation and measurements. We show that the degree of mesoscopic disorder in the films can significantly influence the scattering curves. Static defects should be minimized by optimization of the preparation techniques and their presence must be taken into account in the modelling. Examples are given for alamethicin and magainin in bilayers of different phosphocholines.

  1. 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.

  2. An all gas-phase iodine laser based on amine chemistry

    NASA Astrophysics Data System (ADS)

    Masuda, Taizo; Nakamura, Tomonari; Endo, Masamori; Uchiyama, Taro

    2009-07-01

    Laser action has been demonstrated for the 2P1/2-2P3/2 transition of iodine atom pumped by energy transfer from NCl(a1?) produced by a set of amine-based, all gas-phase chemical reactions. Continuous-wave laser output of 50 mW with 40% duty factor is obtained from a stable optical resonator consisting of two 99.99% reflective mirrors. The observed laser characteristics are reasonably explained by numerical model calculations.

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

    E-print Network

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

    2008-01-29

    Critical temperature Tc for the nuclear liquid-gas phase transition is stimated both from the multifragmentation and fission data. In the first case,the critical temperature is obtained by analysis of the IMF yields in p(8.1 GeV)+Au collisions within the statistical model of multifragmentation (SMM). In the second case, the experimental fission probability for excited 188Os is compared with the calculated one with Tc as a free parameter. It is concluded for both cases that the critical temperature is higher than 16 MeV.

  4. 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.

  5. 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 ?Hads = -33 kJ mol(-1) and -36 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

  6. Modelling the electrophoretic migration behaviour of peptides and glycopeptides from glycoprotein digests in capillary electrophoresis-mass spectrometry.

    PubMed

    Barroso, Albert; Giménez, Estela; Benavente, Fernando; Barbosa, José; Sanz-Nebot, Victoria

    2015-01-01

    In this study, the classical semiempirical relationships between the electrophoretic mobility and the charge-to-mass ratio (me vs. q/M(?)) were used to model the migration behaviour of peptides and glycopeptides originated from the digestion of recombinant human erythropoietin (rhEPO), a biologically and therapeutically relevant glycoprotein. The Stoke's law (?=1/3), the classical polymer model (?=1/2) and the Offord's surface law (?=2/3) were evaluated to predict migration of peptides and glycopeptides, with and without sialic acids (SiA), in rhEPO digested with trypsin and trypsin-neuraminidase. The Stoke's law resulted in better correlations for the set of peptides used to evaluate the models, while glycopeptides fitted better with the classical polymer model. Once predicted migration times with both models, it was easy to simulate their separation electropherogram. Results were later validated predicting migration and simulating separation of a different set of rhEPO glycopeptides and also human transferrin (Tf) peptides and glycopeptides. The excellent agreement between the experimental and the simulated electropherograms with rhEPO and Tf digests confirmed the potential applicability of this simple strategy to predict, in general, the peptide-glycopeptide electrophoretic map of any digested glycoprotein. PMID:25479881

  7. 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.

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

    SciTech Connect

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

    1999-07-08

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

  9. 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.

  10. Antimicrobial Peptide, Lumbricusin, Ameliorates Motor Dysfunction and Dopaminergic Neurodegeneration in a Mouse Model of Parkinson's Disease.

    PubMed

    Kim, Dae Hong; Lee, Ik Hwan; Nam, Seung Taek; Hong, Ji; Zhang, Peng; Lu, Li Fang; Hwang, Jae Sam; Park, Ki Cheol; Kim, Ho

    2015-10-28

    We recently reported that the antimicrobial peptide Lumbricusin (NH2-RNRRWCIDQQA), isolated from the earthworm, increases cell proliferation in neuroblastoma SH-SY5Y cells. Here, we investigated whether Lumbricusin has neurotropic activity in mouse neural stem cells (MNSCs) and a protective effect in a mouse model of Parkinson's disease (PD). In MNSCs isolated from mouse brains, Lumbricusin treatment significantly increased cell proliferation (up to 12%) and reduced the protein expression of p27(Kip1) through proteasomal protein degradation but not transcriptional regulation. Lumbricusin inhibited the 6-OHDA-induced apoptosis of MNSCs, and also showed neuroprotective effects in a mouse PD model, ameliorating the motor impairments seen in the pole, elevated body swing, and rotation tests. These results suggest that the Lumbricusin-induced promotion of neural cell proliferation via p27(Kip1) degradation has a protective effect in an experimental PD model. Thus, the antimicrobial peptide Lumbricusin could possibly be developed as a potential therapeutic agent for the treatment of PD. PMID:26215270

  11. 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.

  12. The development of a model of Alpha helix formation for transmembrane peptides 

    E-print Network

    Funk, Geoffrey Alexander

    2013-02-22

    . Peptides, once synthesized, are characterized by MALDI mass spectrometry and HPLC and purified peptides are studied using circular dichroism (CD) spectroscopy to determine the a-helicity. Initial results suggest that the transmembrane environment...

  13. 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 Alzheimer’s 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 Alzheimer’s disease etiology. PMID:25014537

  14. A novel chemosynthetic peptide with ?-sheet motif efficiently kills Klebsiella pneumoniae in a mouse model

    PubMed Central

    Tan, Shirui; Gan, Changpei; Li, Rongpeng; Ye, Yan; Zhang, Shuang; Wu, Xu; Yang, Yi Yan; Fan, Weimin; Wu, Min

    2015-01-01

    Klebsiella pneumoniae (Kp) is one of the most common pathogens in nosocomial infections and is increasingly becoming multiple drug resistant. However, the molecular pathogenesis of Kp in causing tissue injury and dysregulated host defense remains elusive, further dampening the development of novel therapeutic measures. We have previously screened a series of synthetic antimicrobial beta-sheet forming peptides and identified a peptide (IRIKIRIK; ie, IK8L) with a broad range of bactericidal activity and low cytotoxicity in vitro. Here, employing an animal model, we investigated the antibacterial effects of IK8L in acute infection and demonstrated that peritoneal injection of IK8L to mice down-regulated inflammatory cytokines, alleviated lung injury, and importantly, decreased mortality compared to sham-injected controls. In addition, a math model was used to evaluate in vivo imaging data and predict infection progression in infected live animals. Mechanistically, IK8L can kill Kp by inhibiting biofilm formation and modulating production of inflammatory cytokines through the STAT3/JAK signaling both in vitro and in vivo. Collectively, these findings reveal that IK8L may have potential for preventing or treating Kp infection. PMID:25709431

  15. Antitumor Effects of EGFR Antisense Guanidine-Based Peptide Nucleic Acids in Cancer Models

    PubMed Central

    Thomas, Sufi M.; Sahu, Bichismita; Rapireddy, Srinivas; Bahal, Raman; Wheeler, Sarah E.; Procopio, Eva M.; Kim, Joseph; Joyce, Sonali C.; Contrucci, Sarah; Wang, Yun; Chiosea, Simion I.; Lathrop, Kira L.; Watkins, Simon; Grandis, Jennifer R.; Armitage, Bruce A.; Ly, Danith H.

    2013-01-01

    Peptide nucleic acids have emerged over the past two decades as a promising class of nucleic acid mimics because of their strong binding affinity and sequence selectivity toward DNA and RNA, and resistance to enzymatic degradation by proteases and nucleases. While they have been shown to be effective in regulation of gene expression in vitro, and to a small extent in vivo, their full potential for molecular therapy has not yet been fully realized due to poor cellular uptake. Herein, we report the development of cell-permeable, guanidine-based peptide nucleic acids targeting the epidermal growth factor receptor (EGFR) in preclinical models as therapeutic modality for head and neck squamous cell carcinoma (HNSCC) and nonsmall cell lung cancer (NSCLC). A GPNA oligomer, 16 nucleotides in length, designed to bind to EGFR gene transcript elicited potent antisense effects in HNSCC and NSCLC cells in preclinical models. When administered intraperitoneally in mice, EGFRAS-GPNA was taken-up by several tissues including the xenograft tumor. Systemic administration of EGFRAS-GPNA induced antitumor effects in HNSCC xenografts, with similar efficacies as the FDA-approved EGFR inhibitors: cetuximab and erlotinib. In addition to targeting wild-type EGFR, EGFRAS-GPNA is effective against the constitutively active EGFR vIII mutant implicated in cetuximab resistance. Our data reveals that GPNA is just as effective as a molecular platform for treating cetuximab resistant cells, demonstrating its utility in the treatment of cancer. PMID:23113581

  16. A novel chemosynthetic peptide with ?-sheet motif efficiently kills Klebsiella pneumoniae in a mouse model.

    PubMed

    Tan, Shirui; Gan, Changpei; Li, Rongpeng; Ye, Yan; Zhang, Shuang; Wu, Xu; Yang, Yi Yan; Fan, Weimin; Wu, Min

    2015-01-01

    Klebsiella pneumoniae (Kp) is one of the most common pathogens in nosocomial infections and is increasingly becoming multiple drug resistant. However, the molecular pathogenesis of Kp in causing tissue injury and dysregulated host defense remains elusive, further dampening the development of novel therapeutic measures. We have previously screened a series of synthetic antimicrobial beta-sheet forming peptides and identified a peptide (IRIKIRIK; ie, IK8L) with a broad range of bactericidal activity and low cytotoxicity in vitro. Here, employing an animal model, we investigated the antibacterial effects of IK8L in acute infection and demonstrated that peritoneal injection of IK8L to mice down-regulated inflammatory cytokines, alleviated lung injury, and importantly, decreased mortality compared to sham-injected controls. In addition, a math model was used to evaluate in vivo imaging data and predict infection progression in infected live animals. Mechanistically, IK8L can kill Kp by inhibiting biofilm formation and modulating production of inflammatory cytokines through the STAT3/JAK signaling both in vitro and in vivo. Collectively, these findings reveal that IK8L may have potential for preventing or treating Kp infection. PMID:25709431

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  18. 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.

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

    SciTech Connect

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

    1994-12-31

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

  20. 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.

  1. Analysis of gas-phase condensation of nickel nanoparticles

    SciTech Connect

    Gafner, S. L.; Gafner, Yu. Ya.

    2008-10-15

    Gas-phase condensation of 8000 nickel atoms is examined by molecular dynamics simulation with a tight-binding potential. A detailed study of the evolution of the system cooled at a constant rate from 1000 K to 77 K is presented. The results are used to identify four distinct stages of the evolution from a hot atomic gas to a few synthesized particles. An analysis of possible nanoparticle formation mechanisms suggests that cluster-cluster aggregation is the dominant one. The simulation shows that there two stages of cluster formation are of primary importance with regard to aggregation. At the first stage, spherical liquid clusters nucleate with uniform size distribution. The second stage is characterized by a distinct transition from uniform to bimodal size distribution due to aggregation of relatively large clusters. The particles obtained by gas-phase synthesis are analyzed by the CNA method [25]. It is found that most nanoparticles produced in the simulation have either icosahedral or mixed FCC/HCP structure.

  2. Gas-phase Dissociation of homo-DNA Oligonucleotides

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  3. DSMC Convergence for Microscale Gas-Phase Heat Conduction

    NASA Astrophysics Data System (ADS)

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

    2004-11-01

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

  4. 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

  5. Gas phase oxidation downstream of a catalytic combustor

    NASA Technical Reports Server (NTRS)

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

    1979-01-01

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

  6. 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.

  7. Solvent effects on the conformational transition of a model polyalanine peptide

    PubMed Central

    Nguyen, Hung D.; Marchut, Alexander J.; Hall, Carol K.

    2004-01-01

    We have investigated the folding of polyalanine by combining discontinuous molecular dynamics simulation with our newly developed off-lattice intermediate-resolution protein model. The thermodynamics of a system containing a single Ac-KA14K-NH2 molecule has been explored by using the replica exchange simulation method to map out the conformational transitions as a function of temperature. We have also explored the influence of solvent type on the folding process by varying the relative strength of the side-chain’s hydrophobic interactions and backbone hydrogen bonding interactions. The peptide in our simulations tends to mimic real polyalanine in that it can exist in three distinct structural states: ?-helix, ?-structures (including ?-hairpin and ?-sheet–like structures), and random coil, depending upon the solvent conditions. At low values of the hydrophobic interaction strength between nonpolar side-chains, the polyalanine peptide undergoes a relatively sharp transition between an ?-helical conformation at low temperatures and a random-coil conformation at high temperatures. As the hydrophobic interaction strength increases, this transition shifts to higher temperatures. Increasing the hydrophobic interaction strength even further induces a second transition to a ?-hairpin, resulting in an ?-helical conformation at low temperatures, a ?-hairpin at intermediate temperatures, and a random coil at high temperatures. At very high values of the hydrophobic interaction strength, polyalanines become ?-hairpins and ?-sheet–like structures at low temperatures and random coils at high temperatures. This study of the folding of a single polyalanine-based peptide sets the stage for a study of polyalanine aggregation in a forthcoming paper. PMID:15498937

  8. Peptides as Model Systems for the Unfolded State of Proteins Explored By Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Schweitzer-Stenner, Reinhard; Measey, Thomas; Hagarman, Andrew

    2008-11-01

    Unfolded proteins are generally thought to be structurally random with a minimum of non-local interactions. This concept implies that with the exception of glycine and proline the conformational propensities of amino acid residues in polypeptides should be comparable in that they all sample the statistically allowed region of the Ramachandran plot. However, over the last ten years experimental and computational evidence has emerged for the notion that the conformational space of residues might be more restricted than predicted by random or statistical coil models. We have developed several algorithms which can be used to simulate the amide I band profile of the IR, isotropic Raman, anisotropic Raman and Vibrational Circular Dichroism (VCD) spectra of polypeptides based on assumed ensembles of side chain conformations. The simulations are generally restricted by 3Jc?HNH coupling constants obtained from NMR spectroscopy. A comparison with experimental results reveals that e.g. alanine has a clear preference for the so called polyproline II (PPII) conformation in short peptides. The situation becomes more complex if longer polyalanines are doped with negatively charged residues. For the so-called XAO-peptide (X2A7O2, X: diaminobutyric acid, O;ornithine) we found a more compact structure owing to multiple turn conformations sampled by the X2A7 interfaces. For Salmon Calcitonin, a 32-residue hormone, we identified a mixture of PPII, ?-strand and helical conformations. Currently, we are in the process of investigating short GxG (x; different natural amino acid residues) peptides in terms of conformational distributions obtained from coil libraries. This will enable us obtain the conformational preferences of amino acid residues in the absence of nearest neighbor interactions.

  9. An isolated cryptic peptide influences osteogenesis and bone remodeling in an adult mammalian model of digit amputation.

    PubMed

    Agrawal, Vineet; Kelly, Jeremy; Tottey, Stephen; Daly, Kerry A; Johnson, Scott A; Siu, Bernard F; Reing, Janet; Badylak, Stephen F

    2011-12-01

    Biologic scaffolds composed of extracellular matrix (ECM) have been used successfully in preclinical models and humans for constructive remodeling of functional, site-appropriate tissue after injury. The mechanisms underlying ECM-mediated constructive remodeling are not completely understood, but scaffold degradation and site-directed recruitment of progenitor cells are thought to play critical roles. Previous studies have identified a cryptic peptide derived from the C-terminal telopeptide of collagen III? that has chemotactic activity for progenitor cells. The present study characterized the osteogenic activity of the same peptide in vitro and in vivo in an adult murine model of digit amputation. The present study showed that the cryptic peptide increased calcium deposition, alkaline phosphatase activity, and osteogenic gene expression in human perivascular stem cells in vitro. Treatment with the cryptic peptide in a murine model of mid-second phalanx digit amputation led to the formation of a bone nodule at the site of amputation. In addition to potential therapeutic implications for the treatment of bone injuries and facilitation of reconstructive surgical procedures, cryptic peptides with the ability to alter stem cell recruitment and differentiation at a site of injury may serve as powerful new tools for influencing stem cell fate in the local injury microenvironment. PMID:21740273

  10. An Isolated Cryptic Peptide Influences Osteogenesis and Bone Remodeling in an Adult Mammalian Model of Digit Amputation

    PubMed Central

    Agrawal, Vineet; Kelly, Jeremy; Tottey, Stephen; Daly, Kerry A.; Johnson, Scott A.; Siu, Bernard F.; Reing, Janet

    2011-01-01

    Biologic scaffolds composed of extracellular matrix (ECM) have been used successfully in preclinical models and humans for constructive remodeling of functional, site-appropriate tissue after injury. The mechanisms underlying ECM-mediated constructive remodeling are not completely understood, but scaffold degradation and site-directed recruitment of progenitor cells are thought to play critical roles. Previous studies have identified a cryptic peptide derived from the C-terminal telopeptide of collagen III? that has chemotactic activity for progenitor cells. The present study characterized the osteogenic activity of the same peptide in vitro and in vivo in an adult murine model of digit amputation. The present study showed that the cryptic peptide increased calcium deposition, alkaline phosphatase activity, and osteogenic gene expression in human perivascular stem cells in vitro. Treatment with the cryptic peptide in a murine model of mid-second phalanx digit amputation led to the formation of a bone nodule at the site of amputation. In addition to potential therapeutic implications for the treatment of bone injuries and facilitation of reconstructive surgical procedures, cryptic peptides with the ability to alter stem cell recruitment and differentiation at a site of injury may serve as powerful new tools for influencing stem cell fate in the local injury microenvironment. PMID:21740273

  11. 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.

  12. Peptide nanotubes.

    PubMed

    Hamley, Ian W

    2014-07-01

    The self-assembly of different classes of peptide, including cyclic peptides, amyloid peptides and surfactant-like peptides into nanotube structures is reviewed. The modes of self-assembly are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized. PMID:24920517

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

    PubMed Central

    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 ?M. 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

  14. 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.

  15. Delayed luminescence of indole derivatives in the gas phase

    NASA Astrophysics Data System (ADS)

    Sukhodola, A. A.

    2008-07-01

    Spectral and kinetic characteristics of delayed luminescence of indole derivatives in the gas phase have been studied. The mechanism for delayed luminescence has been shown to depend on the disposition of the two lowest excited singlet ??*-states, 1La and 1Lb. For vapors of 3-methyl-and 2,3-dimethylindole having a small 1La-2Lb energy gap ?E (?E < 500 cm-1), prolonged light emissions with maxima at 525 and 540 nm, respectively, have been observed and interpreted as luminescence of free radicals formed due to dissociation of an N-H bond. For vapors of 5-methoxyindole having ?E ? 3700 cm-1, annihilation of delayed luminescence has been observed. The lifetimes for triplet states of 3-methyl-, 2,3-dimethyl-, and 5-methoxyindole at T = 373 K equal to 30, 26, and 65 µsec, respectively, were calculated from the kinetics of the delayed luminescence.

  16. 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.

  17. 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

  18. Silicon nanowire-based devices for gas-phase sensing.

    PubMed

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

    2013-01-01

    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

  19. 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.

  20. Structures of platinum oxide clusters in the gas phase.

    PubMed

    Kerpal, Christian; Harding, Dan J; Hermes, Alexander C; Meijer, Gerard; Mackenzie, Stuart R; Fielicke, André

    2013-02-14

    The structures of small gas-phase Pt(n)O(2m)(+) (n = 1-6, m = 1, 2) cluster cations have been investigated in a combined infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) study. On the basis of the infrared spectra obtained, it is concluded that in most clusters oxygen is bound dissociatively, preferring 2-fold bridge binding motifs, sometimes combined with singly coordinated terminal binding. Comparison of the oxide cluster structures with those of bare cationic platinum clusters reported previously reveals major structural changes induced in the platinum core upon oxygen binding. For some cluster sizes the presence of the Ar messenger atom(s) is found to induce a significant change in the observed cluster structure. PMID:22894744

  1. Observation of small gas-phase metal oxygen dianions

    NASA Astrophysics Data System (ADS)

    Franzreb, Klaus; Williams, Peter

    2006-02-01

    Novel small metal-oxygen dianions have been produced in the gas phase by sputtering of metallic targets with simultaneous oxygen flooding. These exotic species were observed in a mass spectrometer for ion flight times of >10 ?s. Both Cs + bombardment of an elemental Be metal surface and of a copper-based Cu(Be) alloy foil, with exposure of these sputtered surfaces to O 2 gas, produced the novel dianions of BeOn2- with n = 4, 6. Be3O42- at m/ z 45.5 and 46.5 was unambiguously identified by its isotopic abundance. In addition, CuBe2O42- at m/ z 72.5 and 73.5 was detected for O 2 flooding of Cs + sputtered Cu(Be).

  2. 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.

  3. Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments.

    PubMed

    Searle, Brian C; Egertson, Jarrett D; Bollinger, James G; Stergachis, Andrew B; MacCoss, Michael J

    2015-09-01

    Targeted mass spectrometry is an essential tool for detecting quantitative changes in low abundant proteins throughout the proteome. Although selected reaction monitoring (SRM) is the preferred method for quantifying peptides in complex samples, the process of designing SRM assays is laborious. Peptides have widely varying signal responses dictated by sequence-specific physiochemical properties; one major challenge is in selecting representative peptides to target as a proxy for protein abundance. Here we present PREGO, a software tool that predicts high-responding peptides for SRM experiments. PREGO predicts peptide responses with an artificial neural network trained using 11 minimally redundant, maximally relevant properties. Crucial to its success, PREGO is trained using fragment ion intensities of equimolar synthetic peptides extracted from data independent acquisition experiments. Because of similarities in instrumentation and the nature of data collection, relative peptide responses from data independent acquisition experiments are a suitable substitute for SRM experiments because they both make quantitative measurements from integrated fragment ion chromatograms. Using an SRM experiment containing 12,973 peptides from 724 synthetic proteins, PREGO exhibits a 40-85% improvement over previously published approaches at selecting high-responding peptides. These results also represent a dramatic improvement over the rules-based peptide selection approaches commonly used in the literature. PMID:26100116

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

    NASA Astrophysics Data System (ADS)

    Hays, Gerry

    1997-10-01

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

  5. 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.

  6. Discovery of Interstellar Propylene (CH_2CHCH_3): Missing Links in Interstellar Gas-Phase Chemistry

    E-print Network

    N. Marcelino; J. Cernicharo; M. Agundez; E. Roueff; M. Gerin; J. Martin-Pintado; R. Mauersberger; C. Thum

    2007-07-09

    We report the discovery of propylene (also called propene, CH_2CHCH_3) with the IRAM 30-m radio telescope toward the dark cloud TMC-1. Propylene is the most saturated hydrocarbon ever detected in space through radio astronomical techniques. In spite of its weak dipole moment, 6 doublets (A and E species) plus another line from the A species have been observed with main beam temperatures above 20 mK. The derived total column density of propylene is 4 10^13 cm^-2, which corresponds to an abundance relative to H_2 of 4 10^-9, i.e., comparable to that of other well known and abundant hydrocarbons in this cloud, such as c-C_3H_2. Although this isomer of C_3H_6 could play an important role in interstellar chemistry, it has been ignored by previous chemical models of dark clouds as there seems to be no obvious formation pathway in gas phase. The discovery of this species in a dark cloud indicates that a thorough analysis of the completeness of gas phase chemistry has to be done.

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

    PubMed

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

    2014-03-27

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

  8. 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.

  9. Organophosphate vapor detection on gold electrodes using peptide nanotubes.

    PubMed

    Baker, Peter A; Goltz, Mark N; Schrand, Amanda M; Yoon, Do Young; Kim, Dong-Shik

    2014-11-15

    Peptide nanotubes (PNTs) encapsulating horseradish peroxidase and surface coated with acetylcholinesterase (AChE) were attached to gold screen printed electrodes to construct a novel gas phase organophosphate (OP) biosensor. When the sensor with the AChE enzyme is put in contact with acetylthiocholine (ATCh), the ATCh is hydrolyzed to produce thiocholine, which is then oxidized by horseradish peroxidase (HRP). Direct electron transfer between HRP and electrode is achieved through PNTs. The signal produced by the electron transfer is measured with cyclic voltammetry (CV). The presence of an OP compound inhibits this signal by binding with the AChE enzyme. In this study, gas phase malathion was used as a model OP due to the fact that it displays the identical binding mechanism with acetylcholinesterase (AChE) as its more potent counterparts such as sarin and VX, but has low toxicity, making it more practical and safer to handle. The CV signal was proportionally inhibited by malathion vapor concentrations as low as 12 ppbv. Depending on the method used in their preparation, the electrodes maintained their activity for up to 45 days. This research demonstrates the potential of applying nano-modified biosensors for the detection of low levels of OP vapor, an important development in countering weaponized organophosphate nerve agents and detecting commercially-used OP pesticides. PMID:24861572

  10. Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Kato, Koichiro; Fukuzawa, Kaori; Mochizuki, Yuji

    2015-06-01

    We have applied the four-body corrected fragment molecular orbital (FMO4) calculations to analyze the interaction between a designed peptide motif (Glu1-Ser2-Gln3-Glu4-Ser5) and the hydroxyapatite (HA) solid mimicked by a cluster model consisting of 1408 atoms. To incorporate statistical fluctuations, a total of 30 configurations were generated through classical molecular dynamics simulation with water molecules and were subjected to FMO4 calculations at the MP2 level. It was found that Ser5 plays a leading role in interacting with the phosphate moieties of HA via charge transfer and also that negatively charged Glu1 and Glu4 provide electrostatic stabilizations with the calcium ions.

  11. 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.

  12. 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 ...

  13. 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.

  14. 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…

  15. A semi-implicit solvent model for the simulation of peptides and proteins.

    PubMed

    Basdevant, Nathalie; Borgis, Daniel; Ha-Duong, Tap

    2004-06-01

    We present a new model of biomolecules hydration based on macroscopic electrostatic theory, that can both describe the microscopic details of solvent-solute interactions and allow for an efficient evaluation of the electrostatic hydration free energy. This semi-implicit model considers the solvent as an ensemble of polarizable pseudoparticles whose induced dipole describe both the electronic and orientational solvent polarization. In the presented version of the model, there is no mutual dipolar interaction between the particles, and they only interact through short-ranged Lennard-Jones interactions. The model has been integrated into a molecular dynamics code, and offers the possibility to simulate efficiently the conformational evolution of biomolecules. It is able to provide estimations of the electrostatic solvation free energy within short time windows during the simulation. It has been applied to the study of two small peptides, the octaalanine and the N-terminal helix of ribonuclease A, and two proteins, the bovine pancreatic trypsin inhibitor and the B1 immunoglobin-binding domain of streptococcal protein G. Molecular dynamics simulations of these biomolecules, using a slightly modified Amber force field, provide stable and meaningful trajectories in overall agreement with experiments and all-atom simulations. Correlations with respect to Poisson-Boltzmann electrostatic solvation free energies are also presented to discuss the parameterization of the model and its consequences. PMID:15067677

  16. Gaussian process: a promising approach for the modeling and prediction of Peptide binding affinity to MHC proteins.

    PubMed

    Ren, Yanrong; Chen, Xiaolin; Feng, Ming; Wang, Qiang; Zhou, Peng

    2011-07-01

    On the basis of Bayesian probabilistic inference, Gaussian process (GP) is a powerful machine learning method for nonlinear classification and regression, but has only very limited applications in the new areas of computational vaccinology and immunoinformatics. In the current work, we present a paradigmatic study of using GP regression technique to quantitatively model and predict the binding affinities of over 7000 immunodominant peptide epitopes to six types of human major histocompatibility complex (MHC) proteins. In this procedure, the sequence patterns of diverse peptides are characterized quantitatively and the resulting variables are then correlated with the experimentally measured affinities between different MHC and their peptide ligands, by using a linearity- and nonlinearity-hybrid GP approach. We also make systematical comparisons between the GP and two sophisticated modeling methods as partial least square (PLS) regression and support vector machine (SVM) with respect to their fitting ability, predictive power and generalization capability. The results suggest that GP could be a new and effective tool for the modeling and prediction of MHC-peptide interactions and would be promising in the field of computer-aided vaccine design (CAVD). PMID:21413918

  17. 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.

  18. Numerical simulation of an all gas-phase iodine laser based on NCl3 reaction system

    NASA Astrophysics Data System (ADS)

    Masuda, Taizo; Endo, Masamori; Uchiyama, Taro

    2008-03-01

    A numerical simulation code for an all gas-phase iodine laser based on the NCl3 reaction system is developed. The model is a one-dimensional, multiple-leaky-stream-tubes kinetics code combined with all the known rate equations to date. To confirm the validity of this simulation code, the calculated results are compared with the experimental results obtained in other laboratories. The results of computer calculations utilizing this model are in good agreement with those experimental results. This agreement shows that the code is capable of precisely predicting the small signal gain and laser output for a given set of flow conditions. Using this simulation code, we defined the flow rates and the nozzle configuration that should allow laser oscillation based on NCl3 reaction system to be achieved. The calculations suggest that a laser output power of 410 mW can be obtained under optimum conditions with facilities available in our laboratory.

  19. Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis

    PubMed Central

    Moser, Adam; Range, Kevin; York, Darrin M.

    2010-01-01

    Benchmark quantum calculations of proton affinities and gas phase basicities of molecules relevant to biochemical processes, particulsarly acid/base catalysis, are presented and compared for a variety of multi-level and density-functional quantum models. Included are nucleic acid bases in both keto and enol tautomeric forms, ribose in B-form and A-form sugar pucker conformations, amino acid side chains and backbone molecules, and various phosphates and phosphoranes including thio substitutions. This work presents a high-level thermodynamic characterization of biologically relevant protonation states, and provides a benchmark database for development of next-generation semiempirical and approximate density-functional quantum models, and parameterization of methods to predict pKa values and relative solvation energies. PMID:20942500

  20. Energetics of Selected Gas Phase Ion-Molecule Reactions

    NASA Astrophysics Data System (ADS)

    Paul, Gary John Charles

    1990-01-01

    The energetics of the gas phase negative ion-molecule association reactions M + X^{-} = McdotX^ {-}, where M are substituted benzenes, quinones and ethylenes and X^{-} are the halide ions (F^{-} , Cl^{-}, Br ^{-} and I^{ -}), were determined by equilibrium measurements with the pulsed electron high pressure mass spectrometer (PHPMS). Evaluation of the equilibrium constants for the halide association (XA) reactions leads directly to absolute bond free energy determinations, -DeltaG _sp{XA}{circ}, in McdotX^{- }. Under conditions where halide association equilibria could not be measured directly, relative bond free energies, -DeltaDeltaG _sp{XA}{circ}, were obtained by measurements of the transfer equilibria McdotX^{-} + M^' = M + cdotM^'cdot X^{-}. Combining -DeltaDeltaG_sp {XA}{circ} values with directly determined -DeltaG _sp{XA}{circ} values leads to further absolute bond free energy determinations. The hydrogen bond free energies in the singly substituted phenol complexes YPhOHcdotBr ^{-}, combined with previous data for X^{-} = Cl ^{-} and I^{ -} from this laboratory, are used to examine the substituent effects on hydrogen bonding. The dominant contribution to YPhOHcdotBr ^{-} stabilization, where the extent of proton transfer from YPhOH to Br^{ -} is small, is due to the field effects of the substituents with pi delocalization playing only a small part. Thus, the correlation with the acidity of YPhOH, where pi delocalization is important, is not very close. Substituent effect analysis of experimentally determined bond free energies and quantum mechanical calculations are used to gain structural information on the complexes McdotX^{-} where M does not possess substituents with protic hydrogens. The results indicate the complexes M cdotX^{-} have a variety of structures, depending on X^ {-} and the nature of the substituents. The temperature dependence of the equilibrium constants for the gas phase reactions HO^ - + HOH = HO^-cdotHOH and CH_3O^- + HOCH_3 = CH_3O ^-cdotHOCH_3 was measured with the PHPMS. The enthalpy and entropy changes were obtained from van't Hoff plots of the equilibrium constants. The enthalpy changes were found to be in good agreement with experimentally determined values reported by Meot-Ner and Sieck and recent theoretical results. The agreement for the entropy changes is found not to be as good. The electron affinities of 20 cyclic diones, mostly substituted maleic and phthalic anhydrides and maleimides and phthalimides, were determined with the PHPMS by measuring gas phase electron transfer equilibria A^ {-} + B = A + B^{ -} involving these compounds and reference compounds whose electron affinities were determined previously. The effects of substituents on electron affinities are similar to those observed previously for other groups of organic compounds.

  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. Energetics and Partition of Two Cecropin-Melittin Hybrid Peptides to Model Membranes of Different Composition

    E-print Network

    Pompeu Fabra, Universitat

    (21,22). One such hybrid peptide, CA(1­8)M(1­18), showed improved antimicrobial activity relative of antimicrobial activity (25­ 31), as well as on their membrane interaction properties (6 for new type of antibiotics (1­5). Among these, antimicrobial peptides (AMP) have been widely studied

  3. Proinsulin multi-peptide immunotherapy induces antigen-specific regulatory T cells and limits autoimmunity in a humanized model.

    PubMed

    Gibson, V B; Nikolic, T; Pearce, V Q; Demengeot, J; Roep, B O; Peakman, M

    2015-12-01

    Peptide immunotherapy (PIT) is a targeted therapeutic approach, involving administration of disease-associated peptides, with the aim of restoring antigen-specific immunological tolerance without generalized immunosuppression. In type 1 diabetes, proinsulin is a primary antigen targeted by the autoimmune response, and is therefore a strong candidate for exploitation via PIT in this setting. To elucidate the optimal conditions for proinsulin-based PIT and explore mechanisms of action, we developed a preclinical model of proinsulin autoimmunity in a humanized HLA-DRB1*0401 transgenic HLA-DR4 Tg mouse. Once proinsulin-specific tolerance is broken, HLA-DR4 Tg mice develop autoinflammatory responses, including proinsulin-specific T cell proliferation, interferon (IFN)-? and autoantibody production. These are preventable and quenchable by pre- and post-induction treatment, respectively, using intradermal proinsulin-PIT injections. Intradermal proinsulin-PIT enhances proliferation of regulatory [forkhead box protein 3 (FoxP3(+) )CD25(high) ] CD4 T cells, including those capable of proinsulin-specific regulation, suggesting this as its main mode of action. In contrast, peptide delivered intradermally on the surface of vitamin D3-modulated (tolerogenic) dendritic cells, controls autoimmunity in association with proinsulin-specific IL-10 production, but no change in regulatory CD4 T cells. These studies define a humanized, translational model for in vivo optimization of PIT to control autoimmunity in type 1 diabetes and indicate that dominant mechanisms of action differ according to mode of peptide delivery. PMID:26206289

  4. The Eco Logic gas-phase chemical reduction process

    SciTech Connect

    Hallett, D.J.; Campbell, K.R.

    1995-12-31

    The ECO LOGIC Process is a patented gas-phase chemical reduction process suitable for the destruction of highly hazardous organic chemicals. This is a commercial-scale mobile system for on-site treatment. With the ECO LOGIC technology any combination of organic contaminants at any concentration can be treated with proven destruction and removal efficiencies (DRES) of at least 99.9999%. Unlike typical incineration systems ECO LOGIC employs a closed-loop destruction process with no uncontrolled emissions and through the use of a reducing atmosphere there is no opportunity for the incidental formation of polychlorinated dibenzo-p-dioxins (dioxins) or dibenzofurans (furans). Organic contaminants are permanently destroyed, thus eliminating the need for off-site disposal of hazardous organic residuals. Outputs from the system can generally be recycled or reused on site. In the fall of 1992, ECO LOGIC completed a demonstration program in Bay City, Michigan, with the United States Environmental Protection Agency (USEPA) as part of the Superfund Innovative Technology Evaluation (SITE) Program. An organochlorine fluid containing 26% polychlorinated biphenyls (PCBs) as well as contaminated groundwater and soils were processed in separate streams. USEPA evaluation confirmed DREs of 99.9999%. Previously, in 1991, ECO LOGIC completed a field demonstration at Hamilton Harbour, Ontario, where audited results confirmed DREs of 99.9999% or better on polyaromatic hydrocarbon (PAH) coal tar contaminated sediments.

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

    PubMed

    Herceg, Zoran; Kova?evi?, Danijela Bursa?; Kljusuri?, Jasenka Gajdoš; Jambrak, Anet Režek; Zori?, Zoran; Dragovi?-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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Microwave spectrum and the gas phase structure of phthalimide

    NASA Astrophysics Data System (ADS)

    Pejlovas, Aaron M.; Lin, Wei; Oncer, Onur; Kukolich, Stephen G.

    2015-11-01

    The microwave spectrum of phthalimide (PhI) was measured in the 4.8-9.5 GHz range using a Flygare-Balle type, pulsed-beam Fourier transform microwave spectrometer. Rotational transitions were measured for the parent and all unique single 13C substituted isotopologues. The rotational (MHz), centrifugal distortion (kHz), and quadrupole coupling constants (MHz) were determined for the parent to be A = 1745.6655(10), B = 1199.3309(6), C = 711.0864(3), DJ = 0.012(7), DJK = -0.05(9), 1.5?aa = 2.719(11), and 0.25(?bb - ?cc) = 1.236(3). Using the measured rotational constants of the isotopologues, a nonlinear least squares fit was performed to obtain the best fit gas phase structure. The inertial defect is ? = -0.175 amu Å2, indicating a planar structure for PhI. Calculations using B3LYP/aug-cc-pVQZ provided rotational constants which are much closer to the experimental values compared to the MP2/6-311++G?? calculated values.

  11. 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...

  12. OXYGEN GAS-PHASE ABUNDANCE REVISITED M. K. Andre,1,2

    E-print Network

    Howk, Jay Christopher

    OXYGEN GAS-PHASE ABUNDANCE REVISITED M. K. Andre´,1,2 C. M. Oliveira,2 J. C. Howk,2 R. Ferlet,1 J gas-phase oxygen abundance along the sight lines toward 19 early-type Galactic stars at an average magÀ1 with a standard deviation of 15% is consistent with previous surveys. The mean oxygen abundance

  13. Infrared Spectroscopy of Cationized Arginine in the Gas Phase: Direct Evidence for the Transition from

    E-print Network

    Cohen, Ronald C.

    Infrared Spectroscopy of Cationized Arginine in the Gas Phase: Direct Evidence for the Transition@cchem.berkeley.edu Abstract: The gas-phase structures of protonated and alkali metal cationized arginine (Arg) and arginine spectra, measured in the hydrogen-stretch region, provide compelling evidence that arginine changes from

  14. 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 ...

  15. Protein Structure in Vacuo: Gas-Phase Conformations of BPTI and Cytochrome c

    E-print Network

    Clemmer, David E.

    Protein Structure in Vacuo: Gas-Phase Conformations of BPTI and Cytochrome c Konstantin B. Shelimov of Chemistry, Northwestern UniVersity, 2145 Sheridan Road, EVanston, Illinois 60208 ReceiVed June 6, 1996X. Furthermore, gas-phase BPTI retains its compact structure when collisionally heated. These results

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

    PubMed

    Sims, I R; Smith, I W

    1995-01-01

    Experimental studies of gas-phase chemical reactions and molecular energy transfer at very low temperatures and between electrically neutral species are reviewed. Although work of collisionally induced vibrational and rotational transfer is described, emphasis is placed on very recent results on the rates of free radical reactions obtained by applying the pulsed laser photolysis (PLP)-laser-induced fluorescence (LIF) technique in a CRESU (Cinétique de Réactions en Ecoulement Supersonique Uniforme) apparatus at temperatures as low as 13 K. These measurements demonstrate that quite a wide variety of reactions-including those between two radicals, those between radicals and unsaturated molecules, and even some of those between radicals and saturated molecules-remain rapid at very low temperatures. Theoretical efforts to explain some of these results are described, as is their impact on attempts to model the synthesis of molecules in interstellar clouds. PMID:24329120

  17. Cell Penetrating Peptides and Cationic Antibacterial Peptides

    PubMed Central

    Rodriguez Plaza, Jonathan G.; Morales-Nava, Rosmarbel; Diener, Christian; Schreiber, Gabriele; Gonzalez, Zyanya D.; Lara Ortiz, Maria Teresa; Ortega Blake, Ivan; Pantoja, Omar; Volkmer, Rudolf; Klipp, Edda; Herrmann, Andreas; Del Rio, Gabriel

    2014-01-01

    Cell penetrating peptides (CPP) and cationic antibacterial peptides (CAP) have similar physicochemical properties and yet it is not understood how such similar peptides display different activities. To address this question, we used Iztli peptide 1 (IP-1) because it has both CPP and CAP activities. Combining experimental and computational modeling of the internalization of IP-1, we show it is not internalized by receptor-mediated endocytosis, yet it permeates into many different cell types, including fungi and human cells. We also show that IP-1 makes pores in the presence of high electrical potential at the membrane, such as those found in bacteria and mitochondria. These results provide the basis to understand the functional redundancy of CPPs and CAPs. PMID:24706763

  18. 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.

  19. Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field

    PubMed Central

    Ryvkin, Faina; Greenaway, Frederick T.

    2010-01-01

    The utility of the extensible systematic force field (ESFF) was tested for copper(II) binding to a 34-amino-acid Cu(II) peptide, which includes five histidine residues and is the putative copper-binding site of lysyl oxidase. To improve computational efficiency, distance geometry calculations were used to constrain all combinations of three histidine ligands to be within bonding distance of the copper and the best results were utilized as starting structures for the ESFF computations. All likely copper geometries were modeled, but the results showed only a small dependence on the geometrical model in that all resulted in a distorted square pyramidal geometry about the copper, some of the imidazole rings were poorly oriented for ligation to the Cu(II), and the copper-nitrogen bond distances were too long. The results suggest that ESFF should be used with caution for Cu(II) complexes where the copper-ligand bonds have significant covalency and when the ligands are not geometrically constrained to be planar. PMID:20300581

  20. 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.

  1. A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Cannon, William R.; Oehmen, Christopher S.; Shah, Anuj R.; Gurumoorthi, Vidhya; Lipton, Mary S.; Waters, Katrina M.

    2008-07-01

    Motivation: The standard approach to identifying peptides based on accurate mass and elution time (AMT) compares these profiles obtained from a high resolution mass spectrometer to a database of peptides previously identified from tandem mass spectrometry (MS/MS) studies. It would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by MS (proteotypic). Results: We present a Support Vector Machine (SVM) model that uses a simple descriptor space based on 35 properties of amino acid content, charge, hydrophilicity, and polarity for the quantitative prediction of proteotypic peptides. Using three independently derived AMT databases (Shewanella oneidensis, Salmonella typhimurium, Yersinia pestis) for training and validation within and across species, the SVM resulted in an average accuracy measure of ~0.8 with a standard deviation of less than 0.025. Furthermore, we demonstrate that these results are achievable with a small set of 12 variables and can achieve high proteome coverage. Availability: http://omics.pnl.gov/software/STEPP.php

  2. Measurement of soil/dust arsenic by gas phase chemiluminescence.

    PubMed

    Sawalha, Maather F; Sengupta, Mrinal K; Ohira, Shin-Ichi; Idowu, Ademola D; Gill, Thomas E; Rojo, Lila; Barnes, Melanie; Dasgupta, Purnendu K

    2008-10-19

    A gas phase chemiluminescence (GPCL)-based method for trace measurement of arsenic has been recently described for the measurement of arsenic in water. The principle is based on the reduction of inorganic As to AsH(3) at a controlled pH (the choice of pH governs whether only As(III) or all inorganic As is converted) and the reaction of AsH(3) with O(3) to produce chemiluminescence (Idowu et al., Anal. Chem. 78 (2006) 7088-7097). The same general principle has also been used in postcolumn reaction detection of As, where As species are separated chromatographically, then converted into inorganic As by passing through a UV photochemical reactor followed by AsH(3) generation and CL reaction with ozone (Idowu and Dasgupta, Anal. Chem. 79 (2007) 9197-9204). In the present paper we describe the measurement of As in different soil and dust samples by serial extraction with water, citric acid, sulfuric acid and nitric acid. We also compare parallel measurements for total As by induction coupled plasma mass spectrometry (ICP-MS). As(V) was the only species found in our samples. Because of chloride interference of isobaric ArCl(+) ICP-MS analyses could only be carried out by standard addition; these results were highly correlated with direct GPCL and LC-GPCL results (r(2)=0.9935 and 1.0000, respectively). The limit of detection (LOD) in the extracts was 0.36 microg/L by direct GPCL compared to 0.1 microg/L by ICP-MS. In sulfuric acid-based extracts, the LC-GPCL method provided LODs inferior to those previously observed for water-based standards and were 2.6, 1.3, 6.7, and 6.4 microg/L for As(III), As(V), dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA), respectively. PMID:18804648

  3. Gas phase selective hydrogenation over oxide supported Ni-Au.

    PubMed

    Cárdenas-Lizana, Fernando; Keane, Mark A

    2015-11-14

    The chemoselective continuous gas phase (T = 573 K; P = 1 atm) hydrogenation of nitroarenes (p-chloronitrobenzene (p-CNB) and m-dinitrobenzene (m-DNB)) has been investigated over a series of oxide (Al2O3 and TiO2) supported Au and Ni-Au (1?:?10 mol ratio; 0.1-1 mol% Au) catalysts. Monometallic supported Au with mean particle size 3-9 nm promoted exclusive formation of p-chloroaniline (p-CAN) and m-nitroaniline (m-NAN). Selective hydrogenation rate was higher over smaller Au particles and can be attributed to increased surface hydrogen (from TPD measurements) at higher metal dispersion. (S)TEM analysis has confirmed an equivalent metal particle size for the supported bimetallics at the same Au loading where TPR indicates Ni-Au interaction and EDX surface mapping established Ni in close proximity to Au on isolated nanoparticles with a composition (Au/Ni) close to the bulk value (= 10). Increased spillover hydrogen due to the incorporation of Ni in the bimetallics resulted in elevated -NO2 group reduction rate. Full selectivity to p-CAN was maintained over all the bimetallic catalysts. Conversion of m-DNB over the lower loaded Ni-Au/Al2O3 generated m-NAN as sole product. An increase in Ni content (0.01 ? 0.1 mol%) or a switch from Al2O3 to TiO2 as support resulted in full -NO2 reduction (to m-phenylenediamine). Our results demonstrate the viability of Ni-promotion of Au in the continuous production of functionalised anilines. PMID:25752655

  4. 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.

  5. 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.

  6. 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.

  7. Molecular dynamics studies of peptide-membrane interactions: insights from coarse-grained models 

    E-print Network

    Gkeka, Paraskevi

    2010-01-01

    Peptide-membrane interactions play an important role in a number of biological processes, such as antimicrobial defence mechanisms, viral translocation, membrane fusion and functions ofmembrane proteins. In particular, ...

  8. Utilizing Antigenic Peptide and Adhesion Molecule Conjugates to Suppress Autoimmune Disease in Animal Models

    E-print Network

    Buyuktimkin, Barlas

    2011-12-31

    : ________________________________ Chairperson Teruna J. Siahaan ________________________________ Cory J. Berkland ________________________________ Jennifer S. Laurence ________________________________ David B. Volkin... ________________________________ Jennifer S. Laurence ________________________________ David B. Volkin ________________________________ Krzysztof Kuczera Date approved: October 7, 2011 iii Utilizing antigenic peptide and adhesion molecule conjugates to suppress...

  9. Rapid Selection of Cyclic Peptides that Reduce Alpha-Synuclein Toxicity in Yeast and Animal Models

    E-print Network

    Lindquist, Susan

    Phage display has demonstrated the utility of cyclic peptides as general protein ligands but cannot access proteins inside eukaryotic cells. Expanding a new chemical genetics tool, we describe the first expressed library ...

  10. Solid-Phase Synthesis, Characterization, and Cellular Activities of Collagen-Model Nanodiamond-Peptide Conjugates

    PubMed Central

    Knapinska, Anna M.; Tokmina-Roszyk, Dorota; Amar, Sabrina; Tokmina-Roszyk, Michal; Mochalin, Vadym N.; Gogotsi, Yury; Cosme, Patrick; Terentis, Andrew C.; Fields, Gregg B.

    2015-01-01

    Nanodiamonds (NDs) have received considerable attention as potential drug delivery vehicles. NDs are small (~5 nm diameter), can be surface modified in a controllable fashion with a variety of functional groups, and have little observed toxicity in vitro and in vivo. However, most biomedical applications of NDs utilize surface adsorption of biomolecules, as opposed to covalent attachment. Covalent modification provides reliable and reproducible ND–biomolecule ratios, and alleviates concerns over biomolecule desorption prior to delivery. The present study has outlined methods for the efficient solid-phase conjugation of ND to peptides and characterization of ND–peptide conjugates. Utilizing collagen-derived peptides, the ND was found to support or even enhance the cell adhesion and viability activities of the conjugated sequence. Thus, NDs can be incorporated into peptides and proteins in a selective manner, where the presence of the ND could potentially enhance the in vivo activities of the biomolecule it is attached to. PMID:25753561

  11. Machine Learning Approaches to Modeling the Physiochemical Properties of Small Peptides

    E-print Network

    Jensen, Kyle

    Peptide and protein sequences are most commonly represented as a strings: a series of letters selected from the twenty character alphabet of abbreviations for the naturally occurring amino acids. Here, we experiment with ...

  12. Modeling of the Ebola Virus Delta Peptide Reveals a Potential Lytic Sequence Motif

    PubMed Central

    Gallaher, William R.; Garry, Robert F.

    2015-01-01

    Filoviruses, such as Ebola and Marburg viruses, cause severe outbreaks of human infection, including the extensive epidemic of Ebola virus disease (EVD) in West Africa in 2014. In the course of examining mutations in the glycoprotein gene associated with 2014 Ebola virus (EBOV) sequences, a differential level of conservation was noted between the soluble form of glycoprotein (sGP) and the full length glycoprotein (GP), which are both encoded by the GP gene via RNA editing. In the region of the proteins encoded after the RNA editing site sGP was more conserved than the overlapping region of GP when compared to a distant outlier species, Tai Forest ebolavirus. Half of the amino acids comprising the “delta peptide”, a 40 amino acid carboxy-terminal fragment of sGP, were identical between otherwise widely divergent species. A lysine-rich amphipathic peptide motif was noted at the carboxyl terminus of delta peptide with high structural relatedness to the cytolytic peptide of the non-structural protein 4 (NSP4) of rotavirus. EBOV delta peptide is a candidate viroporin, a cationic pore-forming peptide, and may contribute to EBOV pathogenesis. PMID:25609303

  13. ?-sheet structures and dimer models of the two major tyrocidines, antimicrobial peptides from Bacillus aneurinolyticus.

    PubMed

    Munyuki, Gadzikano; Jackson, Graham E; Venter, Gerhard A; Kövér, Katalin E; Szilágyi, László; Rautenbach, Marina; Spathelf, Barbara M; Bhattacharya, Bhaswati; van der Spoel, David

    2013-11-01

    The structures of two major tyrocidines, antibiotic peptides from Bacillus aneurinolyticus, in an aqueous environment were studied using nuclear magnetic resonance spectroscopy, restrained molecular dynamics (MD), circular dichroism, and mass spectrometry. TrcA and TrcC formed ?-structures in an aqueous environment. Hydrophobic and hydrophilic residues were not totally separated into nonpolar and polar faces of the peptides, indicating that tyrocidines have low amphipathicity. In all the ?-structures, residues Trp(4)/Phe(4) and Orn(9) were on the same face. The ability of the peptides to form dimers in aqueous environment was studied by replica exchange MD simulations. Both peptides readily dimerize, and predominant complex structures were characterized through cluster analysis. The peptides formed dimers by either associating sideways or stacking on top of each other. Dimers formed through sideways association were mainly stabilized by hydrogen bonding, while the other dimers were stabilized by hydrophobic interactions. The ability of tyrocidine peptides to form different types of dimers with different orientations suggests that they can form larger aggregates, as well. PMID:24151934

  14. 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.

  15. Overexpressing Sonic Hedgehog Peptide Restores Periosteal Bone Formation in a Murine Bone Allograft Transplantation Model

    PubMed Central

    Huang, Chunlan; Tang, Minghui; Yehling, Eric; Zhang, Xinping

    2014-01-01

    Although activation of hedgehog (Hh) signaling has been shown to induce osteogenic differentiation in vitro and bone formation in vivo, the underlying mechanisms and the potential use of Hh-activated mesenchymal progenitors in bone defect repair remain elusive. In this study, we demonstrated that implantation of periosteal-derived mesenchymal progenitor cells (PDMPCs) that overexpressed an N-terminal sonic hedgehog peptide (ShhN) via an adenoviral vector (Ad-ShhN) restored periosteal bone collar formation in a 4-mm segmental bone allograft model in immunodeficient mice. Ad-ShhN enhanced donor cell survival and microvessel formation in collagen scaffold at 2 weeks after surgery and induced donor cell–dependent bone formation at 6 weeks after surgery. Fluorescence-activated cell sorting analysis further showed that Ad-ShhN-PDMPC–seeded scaffold contained a twofold more CD45?Sca-1+CD34+VEGFR2+ endothelial progenitors than Ad-LacZ-PDMPC–seeded scaffold at day 7 after surgery. Ad-ShhN–transduced PDMPCs induced a 1.8-fold more CD31+ microvessel formation than Ad-LacZ–transduced PDMPCs in a coculture of endothelial progenitors and PDMPCs. Taken together, our data show that overexpression of ShhN in mesenchymal progenitors improves bone defect reconstruction by enhancing donor progenitor cell survival, differentiation, and scaffold revascularization at the site of compromised periosteum. Hh agonist–based therapy, therefore, merits further investigation in tissue engineering–based applications aimed at enhancing bone defect repair and reconstruction. PMID:24089140

  16. Activity of potent and selective host defense peptide mimetics in mouse models of oral candidiasis.

    PubMed

    Ryan, Lisa K; Freeman, Katie B; Masso-Silva, Jorge A; Falkovsky, Klaudia; Aloyouny, Ashwag; Markowitz, Kenneth; Hise, Amy G; Fatahzadeh, Mahnaz; Scott, Richard W; Diamond, Gill

    2014-07-01

    There is a strong need for new broadly active antifungal agents for the treatment of oral candidiasis that not only are active against many species of Candida, including drug-resistant strains, but also evade microbial countermeasures which may lead to resistance. Host defense peptides (HDPs) can provide a foundation for the development of such agents. Toward this end, we have developed fully synthetic, small-molecule, nonpeptide mimetics of the HDPs that improve safety and other pharmaceutical properties. Here we describe the identification of several HDP mimetics that are broadly active against C. albicans and other species of Candida, rapidly fungicidal, and active against yeast and hyphal cultures and that exhibit low cytotoxicity for mammalian cells. Importantly, specificity for Candida over commensal bacteria was also evident, thereby minimizing potential damage to the endogenous microbiome which otherwise could favor fungal overgrowth. Three compounds were tested as topical agents in two different mouse models of oral candidiasis and were found to be highly active. Following single-dose administrations, total Candida burdens in tongues of infected animals were reduced up to three logs. These studies highlight the potential of HDP mimetics as a new tool in the antifungal arsenal for the treatment of oral candidiasis. PMID:24752272

  17. Ex Vivo Modeling of Multidomain Peptide Hydrogels with Intact Dental Pulp.

    PubMed

    Moore, A N; Perez, S C; Hartgerink, J D; D'Souza, R N; Colombo, J S

    2015-12-01

    Preservation of a vital dental pulp is a central goal of restorative dentistry. Currently, there is significant interest in the development of tissue engineering scaffolds that can serve as biocompatible and bioactive pulp-capping materials, driving dentin bridge formation without causing cytotoxic effects. Our earlier in vitro studies described the biocompatibility of multidomain peptide (MDP) hydrogel scaffolds with dental pulp-derived cells but were limited in their ability to model contact with intact 3-dimensional pulp tissues. Here, we utilize an established ex vivo mandible organ culture model to model these complex interactions. MDP hydrogel scaffolds were injected either at the interface of the odontoblasts and the dentin or into the pulp core of mandible slices and subsequently cultured for up to 10 d. Histology reveals minimal disruption of tissue architecture adjacent to MDP scaffolds injected into the pulp core or odontoblast space. Additionally, the odontoblast layer is structurally preserved in apposition to the MDP scaffold, despite being separated from the dentin. Alizarin red staining suggests mineralization at the periphery of MDP scaffolds injected into the odontoblast space. Immunohistochemistry reveals deposition of dentin sialophosphoprotein by odontoblasts into the adjacent MDP hydrogel, indicating continued functionality. In contrast, no mineralization or dentin sialophosphoprotein deposition is evident around MDP scaffolds injected into the pulp core. Collagen III expression is seen in apposition to gels at all experimental time points. Matrix metalloproteinase 2 expression is observed associated with centrally injected MDP scaffolds at early time points, indicating proteolytic digestion of scaffolds. Thus, MDP scaffolds delivered centrally and peripherally within whole dental pulp tissue are shown to be biocompatible, preserving local tissue architecture. Additionally, odontoblast function and pulp vitality are sustained when MDP scaffolds are intercalated between dentin and the odontoblast region, a finding that has significant implications when considering these materials as pulp-capping agents. PMID:26285809

  18. A DJ-1 Based Peptide Attenuates Dopaminergic Degeneration in Mice Models of Parkinson's Disease via Enhancing Nrf2

    PubMed Central

    Lev, Nirit; Barhum, Yael; Ben-Zur, Tali; Aharony, Israel; Trifonov, Lena; Regev, Noa; Melamed, Eldad; Gruzman, Arie; Offen, Daniel

    2015-01-01

    Drugs currently used for treating Parkinson's disease patients provide symptomatic relief without altering the neurodegenerative process. Our aim was to examine the possibility of using DJ-1 (PARK7), as a novel therapeutic target for Parkinson's disease. We designed a short peptide, named ND-13. This peptide consists of a 13 amino acids segment of the DJ-1-protein attached to 7 amino acids derived from TAT, a cell penetrating protein. We examined the effects of ND-13 using in vitro and in vivo experimental models of Parkinson's disease. We demonstrated that ND-13 protects cultured cells against oxidative and neurotoxic insults, reduced reactive oxygen species accumulation, activated the protective erythroid-2 related factor 2 system and increased cell survival. ND-13 robustly attenuated dopaminergic system dysfunction and in improved the behavioral outcome in the 6-hydroxydopamine mouse model of Parkinson's disease, both in wild type and in DJ-1 knockout mice. Moreover, ND-13 restored dopamine content in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine mouse model. These findings validate DJ-1 as a promising therapeutic target in Parkinson's disease and identify a novel peptide with clinical potential, which may be significant for a broader range of neurological diseases, possibly with an important impact for the neurosciences. PMID:26024237

  19. Branching Ratio and Pressure Dependent Rate Constants of Multichannel Unimolecular Decomposition of Gas-Phase r-HMX: An Ab Initio Dynamics Study

    E-print Network

    Truong, Thanh N.

    - 1,3,5,7-tetrazocine), RDX (1,3,5-trinitro- hexahydro-s-triazine), etc.) are very complicated of these reactions are important for modeling these complex processes in combustion and explosion. However, due. Experimental studies have shown that the initial decomposi- tion step of gas-phase HMX and RDX involves

  20. Unusual folding propensity of an unsubstituted ?,?-hybrid model peptide: importance of the C-H???O intramolecular hydrogen bond.

    PubMed

    Venugopalan, Paloth; Kishore, Raghuvansh

    2013-07-22

    The single-crystal X-ray diffraction analysis of a ?,?-hybrid model peptide Boc-?-Ala-?-Abu-NH2 revealed the existence of four crystallographically independent molecules (A, B, C and D conformers) in the asymmetric unit. The analysis revealed that unusual ?-turn-like folded structures predominate, wherein the conformational space of non-proteinogenic ?-Ala and ?-Abu residues are restricted to gauche-gauche-skew and skew-gauche-trans-skew orientations, respectively. Interestingly, the U-shaped conformers are seemingly stabilised by an effective unconventional C-H???O intramolecular hydrogen bond, encompassing a non-covalent 14-membered ring-motif. Taking into account the signs of torsion angles, these conformers could be grouped into two distinct categories, A/B and C/D, establishing the incidence of non-superimposable stereogeometrical features across a non-chiral one-component peptide model system, that is, "mirror-image-like" relationships. The natural occurrence of ?-Ala and ?-Abu entities in various pharmacologically important molecules, coupled with their biocompatibilities, highlight how the non-functionalised ?,?-hybrid segment may offer unique advantages for introducing and/or manipulating a wide spectrum of biologically relevant hydrogen bonded secondary structural mimics in short synthetic peptides. PMID:23775881

  1. Diagnostic model of saliva peptide finger print analysis of oral squamous cell carcinoma patients using weak cation exchange magnetic beads

    PubMed Central

    Jiang, Wei-Peng; Wang, Zhen; Xu, Li-Xin; Peng, Xin; Chen, Feng

    2015-01-01

    Saliva diagnostics utilizing nanotechnology and molecular technologies to detect oral squamous cell carcinoma (OSCC) has become an attractive field of study. However, no specific methods have been established. To refine the diagnostic power of saliva peptide fingerprints for the early detection of OSCC, we screened the expression spectrum of salivary peptides in 40 T1 stage OSCC patients (and healthy controls) using MALDI-TOF-MS combined with magnetic beads. Fifty proteins showed significantly different expression levels in the OSCC samples (P<0.05). Potential biomarkers were also predicted. The novel diagnostic proteomic model with m/z peaks of 1285.6 Da and 1432.2 Da are of certain value for early diagnosis of OSCC. PMID:26182373

  2. 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.

  3. Delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase, the multienzyme integrating the four primary reactions in beta-lactam biosynthesis, as a model peptide synthetase.

    PubMed

    Aharonowitz, Y; Bergmeyer, J; Cantoral, J M; Cohen, G; Demain, A L; Fink, U; Kinghorn, J; Kleinkauf, H; MacCabe, A; Palissa, H

    1993-07-01

    ACV synthetase forms the tripeptide precursor of penicillins and cephalosporins from alpha-aminoadipate, cysteine, and valine. Catalytic sites for substrate carboxyl activation as adenylates, peptide bond formations, epimerization and release of the tripeptide-thioester are integrated in multifunctional enzymes of 405 to 425 kD. These have been characterized from several pro- and eukaryotic beta-lactam producers. Implications of these results for the thio-template mechanism of peptide formation are discussed, as well as the use of this multienzyme as a model system for enzymatic peptide synthesis. PMID:7763859

  4. J. Chem. Soc., Perkin Trans. 2, 1999, 239248 239 Formation of secondary ozonides in the gas phase low-temperature

    E-print Network

    Haas, Yehuda

    J. Chem. Soc., Perkin Trans. 2, 1999, 239­248 239 Formation of secondary ozonides in the gas phase, Accepted 26th November 1998 The gas-phase ozonation of a series of alkenes RCH CH2 (R = Et, Hex), trans for the conversion of trans- RHC CHR (R = Me, Et, Pri ) to trans-secondary ozonides in the gas phase is similar

  5. Gas-Phase Molecular Halogen Formation from NaCl and NaBr Aerosols: When Are Interface Reactions Important?

    E-print Network

    Dabdub, Donald

    Gas-Phase Molecular Halogen Formation from NaCl and NaBr Aerosols: When Are Interface Reactions at the surface of sea-salt particles have been suggested as an important source of photolyzable gas-phase halogen the influence of interface reactions on gas-phase molecular halogen production from pure NaCl and NaBr aerosols

  6. 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 ?m 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.

  7. Molecular Descriptor Subset Selection in Theoretical Peptide Quantitative Structure-Retention Relationship Model Development Using Nature-Inspired Optimization Algorithms.

    PubMed

    Žuvela, Petar; Liu, J Jay; Macur, Katarzyna; B?czek, Tomasz

    2015-10-01

    In this work, performance of five nature-inspired optimization algorithms, genetic algorithm (GA), particle swarm optimization (PSO), artificial bee colony (ABC), firefly algorithm (FA), and flower pollination algorithm (FPA), was compared in molecular descriptor selection for development of quantitative structure-retention relationship (QSRR) models for 83 peptides that originate from eight model proteins. The matrix with 423 descriptors was used as input, and QSRR models based on selected descriptors were built using partial least squares (PLS), whereas root mean square error of prediction (RMSEP) was used as a fitness function for their selection. Three performance criteria, prediction accuracy, computational cost, and the number of selected descriptors, were used to evaluate the developed QSRR models. The results show that all five variable selection methods outperform interval PLS (iPLS), sparse PLS (sPLS), and the full PLS model, whereas GA is superior because of its lowest computational cost and higher accuracy (RMSEP of 5.534%) with a smaller number of variables (nine descriptors). The GA-QSRR model was validated initially through Y-randomization. In addition, it was successfully validated with an external testing set out of 102 peptides originating from Bacillus subtilis proteomes (RMSEP of 22.030%). Its applicability domain was defined, from which it was evident that the developed GA-QSRR exhibited strong robustness. All the sources of the model's error were identified, thus allowing for further application of the developed methodology in proteomics. PMID:26346190

  8. Lysylated phospholipids stabilize models of bacterial lipid bilayers and protect against antimicrobial peptides.

    PubMed

    Cox, Elizabeth; Michalak, Austen; Pagentine, Sarah; Seaton, Pamela; Pokorny, Antje

    2014-09-01

    Aminoacylated phosphatidylglycerols are common lipids in bacterial cytoplasmic membranes. Their presence in Staphylococcus aureus has been linked to increased resistance to a number of antibacterial agents, including antimicrobial peptides. Most commonly, the phosphatidylglycerol headgroup is esterified to lysine, which converts anionic phosphatidylglycerol into a cationic lipid with a considerably increased headgroup size. In the present work, we investigated the interactions of two well-studied antimicrobial peptides, cecropin A and mastoparan X, with lipid vesicles composed of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG), containing varying fractions of an aminoacylated phosphatidylethanolamine, a stable analog of the corresponding phosphatidylglycerol-derivative. To differentiate between the effects of headgroup size and charge on peptide-lipid interactions, we synthesized two different derivatives. In one, the headgroup was modified by the addition of lysine, and in the other, by glutamine. The modification by glutamine results in a phospholipid with a headgroup size comparable to that of the lysylated version. However, whereas lysyl-phosphatidylethanolamine (Lys-PE) is cationic, glutaminyl-phosphatidylethanolamine (Gln-PE) is zwitterionic. We found that binding of mastoparan X and cecropin A was not significantly altered if the content of aminoacylated phosphatidylethanolamines did not exceed 20mol.%, which is the concentration found in bacterial membranes. However, a lysyl-phosphatidylethanolamine content of 20mol% significantly inhibits dye release from lipid vesicles, to a degree that depends on the peptide. In the case of mastoparan X, dye release is essentially abolished at 20mol.% lysyl-phosphatidylethanolamine, whereas cecropin A is less sensitive to the presence of lysyl-phosphatidylethanolamine. These observations are understood through the complex interplay between peptide binding and membrane stabilization as a function of the aminoacylated lipid content. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. PMID:24780374

  9. Neuroprotective effect of physical exercise in a mouse model of Alzheimer's disease induced by ?-amyloid???? peptide.

    PubMed

    Souza, Leandro C; Filho, Carlos B; Goes, André T R; Fabbro, Lucian Del; de Gomes, Marcelo G; Savegnago, Lucielli; Oliveira, Mauro Schneider; Jesse, Cristiano R

    2013-08-01

    This study was designed to investigate the potential neuroprotective effect of exercise in a mouse model of Alzheimer's disease (AD) induced by intracerebroventricular (i.c.v.) injection of beta-amyloid???? (A?????) peptide. For this aim, male Swiss Albino mice were submitted to swimming training (ST) with progressive increase in intensity and duration for 8 weeks before A????? administration (400 pmol/animal; 3 ?l/site, i.c.v. route). The cognitive behavioral, oxidative stress, and neuroinflammatory markers in hippocampus and prefrontal cortex of mice were assessed 7 days after A????? administration. Our results demonstrated that ST was effective in preventing impairment in short- and long-term memories in the object recognition test. ST attenuated the increased levels of reactive species and decreased non-protein thiol levels in hippocampus and prefrontal cortex induced by A?????. Also, A????? inhibited superoxide dismutase activity and increased glutathione peroxidase, glutathione reductase, and glutathione S-transferase activities in hippocampus and prefrontal cortex-alterations that were mitigated by ST. In addition, ST was effective against the increase of tumor necrosis factor-alpha and interleukin-1 beta levels and the decrease of interleukin-10 levels in hippocampus and prefrontal cortex. This study confirmed the hypothesis that exercise is able to protect against some mechanisms of A?????-induced neurotoxicity. In conclusion, we suggest that exercise can prevent the cognitive decline, oxidative stress, and neuroinflammation induced by A????? in mice supporting the hypothesis that exercise can be used as a non-pharmacological tool to reduce the symptoms of AD. PMID:23307759

  10. 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 - ...

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

    PubMed Central

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

    2010-01-01

    In aqueous solution, aldehydes, and to a lesser extent ketones, hydrate to form geminal diols. We investigate the hydration of methylglyoxal (MG) in the gas phase, a process not previously considered to occur in water-restricted environments. In this study, we spectroscopically identified methylglyoxal diol (MGD) and obtained the gas-phase partial pressures of MG and MGD. These results, in conjunction with the relative humidity, were used to obtain the equilibrium constant, KP, for the water-mediated hydration of MG in the gas phase. The Gibbs free energy for this process, ?G°, obtained as a result, suggests a larger than expected gas-phase diol concentration. This may have significant implications for understanding the role of organics in atmospheric chemistry. PMID:20142510

  12. Gas-phase structures of molecules containing heavy p-block elements 

    E-print Network

    Wann, Derek A

    Gas-phase electron diffraction (GED) is the method of choice for determining the structures of molecules containing between two and 100 atoms, free from intermolecular interaction. However, for many molecules it becomes ...

  13. A PEPTIDE UNCOUPLING CRMP-2 FROM THE PRESYNAPTIC Ca(2+) CHANNEL COMPLEX DEMONSTRATES EFFICACY IN ANIMAL MODELS OF MIGRAINE AND AIDS THERAPY-INDUCED NEUROPATHY.

    PubMed

    Ripsch, Matthew S; Ballard, Carrie J; Khanna, May; Hurley, Joyce H; White, Fletcher A; Khanna, Rajesh

    2012-03-01

    Biological, genetic, and clinical data provide compelling proof for N-type voltage-gated calcium channels (CaV2.2) as therapeutic targets for chronic pain. While decreasing channel function is ultimately anti-nociceptive, directly targeting the channel can lead to multiple adverse effects. Targeting regulators of channel activity may facilitate improved analgesic properties associated with channel block and afford a broader therapeutic window. Towards this end, we recently identified a short peptide, designated CBD3, derived from collapsin response mediator protein 2 (CRMP-2) that suppressed inflammatory and neuropathic hypersensitivity by inhibiting CRMP-2 binding to CaV2.2 [Brittain et al., Nature Medicine 17:822-829 (2011)]. Rodents administered CBD3 intraperitoneally, fused to the HIV TAT protein cell penetrating domain, exhibited antinociception lasting ~4 hours highlighting potential instability, limited oral bioavailability, and/or rapid elimination of peptide. This report focuses on improving upon the parental CBD3 peptide. Using SPOTScan analysis of synthetic versions of the parental CBD3 peptide, we identified peptides harboring single amino acid mutations that bound with greater affinity to CaV2.2. One such peptide, harboring a phenylalanine instead of glycine (G14F), was tested in rodent models of migraine and neuropathic pain. In vivo laser Doppler blood flowmetry measure of capsaicin-induced meningeal vascular responses related to headache pain was almost completely suppressed by dural application of the G14F peptide. The G14F mutant peptide, administered intraperitoneally, also exhibited greater antinociception in Stavudine (2'-3'-didehydro-2'-3'-dideoxythymidine (d4T)/Zerit®) model of AIDS therapy-induced peripheral neuropathy compared to the parent CBD3 peptide. These results demonstrate the patent translational value of small biologic drugs targeting CaV2.2 for management of clinical pain. PMID:22662308

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation.

    PubMed Central

    Efremov, R G; Nolde, D E; Vergoten, G; Arseniev, A S

    1999-01-01

    We describe an efficient solvation model for proteins. In this model atomic solvation parameters imitating the hydrocarbon core of a membrane, water, and weak polar solvent (octanol) were developed. An optimal number of solvation parameters was chosen based on analysis of atomic hydrophobicities and fitting experimental free energies of gas-cyclohexane, gas-water, and octanol-water transfer for amino acids. The solvation energy term incorporated into the ECEPP/2 potential energy function was tested in Monte Carlo simulations of a number of small peptides with known energies of bilayer-water and octanol-water transfer. The calculated properties were shown to agree reasonably well with the experimental data. Furthermore, the solvation model was used to assess membrane-promoting alpha-helix formation. To accomplish this, all-atom models of 20-residue homopolypeptides-poly-Leu, poly-Val, poly-Ile, and poly-Gly in initial random coil conformation-were subjected to nonrestrained Monte Carlo conformational search in vacuo and with the solvation terms mimicking the water and hydrophobic parts of the bilayer. All the peptides demonstrated their largest helix-forming tendencies in a nonpolar environment, where the lowest-energy conformers of poly-Leu, Val, Ile revealed 100, 95, and 80% of alpha-helical content, respectively. Energetic and conformational properties of Gly in all environments were shown to be different from those observed for residues with hydrophobic side chains. Applications of the solvation model to simulations of peptides and proteins in the presence of membrane, along with limitations of the approach, are discussed. PMID:10233062

  19. Interaction study of three overlapping synthetic peptides belonging to E2 protein of GBV-C/HGV with liposomes as biomembrane models

    NASA Astrophysics Data System (ADS)

    Rojo, N.; Muñoz, M.; Pujol, M.; Alsina, M. A.; Haro, I.

    2004-12-01

    In this work we studied by DSC the interaction of three antigenic overlapping peptides belonging to the E2 envelope protein of Hepatitis G virus, namely E2(39-53), E2(32-53) and E2(26-53), with liposomes of different lipid composition (DPPC, DMPC and DMPG) as biomembrane models. The effect of the three selected peptides on the thermotropic behaviour of lipid bilayers has been evaluated.

  20. A dramatic change in the interaction of Cu(II) with bio-peptides promoted by SDS--a model for complex formation on a membrane surface.

    PubMed

    Bal, W; Kozlowski, H; Lisowski, M; Pettit, L; Robbins, R; Safavi, A

    1994-07-01

    The extent of complex formation between Cu(II) and many biologically active oligopeptides has been shown to change significantly in the presence of SDS micelles, a recognized model for cell lipid membranes. Protonation constants of peptides can be increased by up to 2 log unit, especially when they contain hydrophobic side chains. Metal complex formation is generally less extensive and the conformations of peptides can be altered dramatically when compared to those in simple aqueous solution. PMID:7519253

  1. 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.

  2. Uptake of gas phase nitrous acid onto boundary layer soil surfaces.

    PubMed

    Donaldson, Melissa A; Berke, Andrew E; Raff, Jonathan D

    2014-01-01

    Nitrous acid (HONO) is an important OH radical source that is formed on both ground and aerosol surfaces in the well-mixed boundary layer. Large uncertainties remain in quantifying HONO sinks and determining the mechanism of HONO uptake onto surfaces. We report here the first laboratory determination of HONO uptake coefficients onto actual soil under atmospheric conditions using a coated-wall flow tube coupled to a highly sensitive chemical ionization mass spectrometer (CIMS). Uptake coefficients for HONO decrease with increasing RH from (2.5 ± 0.4) × 10(-4) at 0% RH to (1.1 ± 0.4) × 10(-5) at 80% RH. A kinetics model of competitive adsorption of HONO and water onto the particle surfaces fits the dependence of the HONO uptake coefficients on the initial HONO concentration and relative humidity. However, a multiphase resistor model based on the physical and chemical processes affecting HONO uptake is more flexible as it accounts for the pH dependence of HONO uptake and bulk diffusion in the soil matrix. Fourier transform infrared (FTIR) spectrometry and cavity-enhanced absorption spectroscopy (CEAS) studies indicate that NO and N2O (16% and 13% yield, respectively) rather than NO2 are the predominant gas phase products, while NO2(-) and NO3(-) were detected on the surface post-exposure. Results are compared to uptake coefficients inferred from models and field measurements, and the atmospheric implications are discussed. PMID:24328088

  3. Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model

    E-print Network

    Pompeu Fabra, Universitat

    inspire the design of new peptide leads with enhanced activity. Here, we describe an artificial neural network approach, based on the AMP's physicochemical characteristics, that is able not only to identify, Charite´, Campus Benjamin Franklin, Germany Received December 14, 2010; Accepted January 19, 2011

  4. Penetration of Milk-Derived Antimicrobial Peptides into Phospholipid Monolayers as Model Biomembranes

    PubMed Central

    Rogalska, Ewa; Wi?c?aw-Czapla, Katarzyna

    2013-01-01

    Three antimicrobial peptides derived from bovine milk proteins were examined with regard to penetration into insoluble monolayers formed with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or 1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol) sodium salt (DPPG). Effects on surface pressure (?) and electric surface potential (?V) were measured, ? with a platinum Wilhelmy plate and ?V with a vibrating plate. The penetration measurements were performed under stationary diffusion conditions and upon the compression of the monolayers. The two type measurements showed greatly different effects of the peptide-lipid interactions. Results of the stationary penetration show that the peptide interactions with DPPC monolayer are weak, repulsive, and nonspecific while the interactions with DPPG monolayer are significant, attractive, and specific. These results are in accord with the fact that antimicrobial peptides disrupt bacteria membranes (negative) while no significant effect on the host membranes (neutral) is observed. No such discrimination was revealed from the compression isotherms. The latter indicate that squeezing the penetrant out of the monolayer upon compression does not allow for establishing the penetration equilibrium, so the monolayer remains supersaturated with the penetrant and shows an under-equilibrium orientation within the entire compression range, practically. PMID:24455264

  5. Solid-phase synthesis, characterization, and cellular activities of collagen-model Nanodiamond-peptide conjugates.

    PubMed

    Knapinska, Anna M; Tokmina-Roszyk, Dorota; Amar, Sabrina; Tokmina-Roszyk, Michal; Mochalin, Vadym N; Gogotsi, Yury; Cosme, Patrick; Terentis, Andrew C; Fields, Gregg B

    2015-05-01

    Nanodiamonds (NDs) have received considerable attention as potential drug delivery vehicles. NDs are small (?5 nm diameter), can be surface modified in a controllable fashion with a variety of functional groups, and have little observed toxicity in vitro and in vivo. However, most biomedical applications of NDs utilize surface adsorption of biomolecules, as opposed to covalent attachment. Covalent modification provides reliable and reproducible ND-biomolecule ratios, and alleviates concerns over biomolecule desorption prior to delivery. The present study has outlined methods for the efficient solid-phase conjugation of ND to peptides and characterization of ND-peptide conjugates. Utilizing collagen-derived peptides, the ND was found to support or even enhance the cell adhesion and viability activities of the conjugated sequence. Thus, NDs can be incorporated into peptides and proteins in a selective manner, where the presence of the ND could potentially enhance the in vivo activities of the biomolecule it is attached to. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 186-195, 2015. PMID:25753561

  6. The Transmembrane Domain of the Acetylcholine Receptor: Insights from Simulations on Synthetic Peptide Models

    E-print Network

    Saiz, Leonor

    and properties of a bundle of a-helical peptides embedded in a 1,2-dimyristoyl-3- phosphatidylcholine and the extracellular mouth of the channel blocked by the hydrocarbon chains of Arg1 residues. The arginine amino acids, 1993; Hille, 1992; Karlin and Akabas, 1995; Montal, 1995; Toyoshima and Unwin, 1988). At the chemical

  7. Redistribution of Cholesterol in Model Lipid Membranes in Response to the Membrane-Active Peptide Alamethicin

    NASA Astrophysics Data System (ADS)

    Heller, William; Qian, Shuo

    2013-03-01

    The cellular membrane is a heterogeneous, dynamic mixture of molecules and macromolecules that self-assemble into a tightly-regulated functional unit that provides a semipermeable barrier between the cell and its environment. Among the many compositional differences between mammalian and bacterial cell membranes that impact its physical properties, one key difference is cholesterol content, which is more prevalent in mammals. Cholesterol is an amphiphile that associates with membranes and serves to maintain its fluidity and permeability. Membrane-active peptides, such as the alpha-helical peptide alamethicin, interact with membranes in a concentration- and composition-dependent manner to form transmembrane pores that are responsible for the lytic action of the peptide. Through the use of small-angle neutron scattering and deuterium labeling, it was possible to observe a redistribution of the lipid and cholesterol in unilamellar vesicles in response to the presence of alamethicin at a peptide-to-lipid ratio of 1/200. The results demonstrate that the membrane remodeling powers of alamethicin reach beyond the membrane thinning effect to altering the localization of specific components in the bilayer, complementing the accepted two-state mechanism of pore formation. Research was supported by U. S. DOE-OBER (CSMB; FWP ERKP291) and the U. S. DOE-BES Scientific User Facilities Division (ORNL's SNS and HFIR).

  8. Mathematical Modeling of Interacting Glucose-Sensing Mechanisms and Electrical Activity Underlying Glucagon-Like Peptide 1 Secretion

    PubMed Central

    Riz, Michela; Pedersen, Morten Gram

    2015-01-01

    Intestinal L-cells sense glucose and other nutrients, and in response release glucagon-like peptide 1 (GLP-1), peptide YY and other hormones with anti-diabetic and weight-reducing effects. The stimulus-secretion pathway in L-cells is still poorly understood, although it is known that GLP-1 secreting cells use sodium-glucose co-transporters (SGLT) and ATP-sensitive K+-channels (K(ATP)-channels) to sense intestinal glucose levels. Electrical activity then transduces glucose sensing to Ca2+-stimulated exocytosis. This particular glucose-sensing arrangement with glucose triggering both a depolarizing SGLT current as well as leading to closure of the hyperpolarizing K(ATP) current is of more general interest for our understanding of glucose-sensing cells. To dissect the interactions of these two glucose-sensing mechanisms, we build a mathematical model of electrical activity underlying GLP-1 secretion. Two sets of model parameters are presented: one set represents primary mouse colonic L-cells; the other set is based on data from the GLP-1 secreting GLUTag cell line. The model is then used to obtain insight into the differences in glucose-sensing between primary L-cells and GLUTag cells. Our results illuminate how the two glucose-sensing mechanisms interact, and suggest that the depolarizing effect of SGLT currents is modulated by K(ATP)-channel activity. Based on our simulations, we propose that primary L-cells encode the glucose signal as changes in action potential amplitude, whereas GLUTag cells rely mainly on frequency modulation. The model should be useful for further basic, pharmacological and theoretical investigations of the cellular signals underlying endogenous GLP-1 and peptide YY release. PMID:26630068

  9. Lysylated Phospholipids Stabilize Models of Bacterial Lipid Bilayers and Protect Against Antimicrobial Peptides

    PubMed Central

    Cox, Elizabeth; Michalak, Austen; Pagentine, Sarah; Seaton, Pamela; Pokorny, Antje

    2014-01-01

    Aminoacylated phosphatidylglycerols are common lipids in bacterial cytoplasmic membranes. Their presence in S. aureus has been linked to increased resistance to a number of antibacterial agents, including antimicrobial peptides. Most commonly, the phosphatidylglycerol headgroup is esterified to lysine, which converts anionic phosphatidylglycerol into a cationic lipid with a considerably increased headgroup size. In the present work, we investigated the interactions of two well-studied antimicrobial peptides, cecropin A and mastoparan X, with lipid vesicles composed of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG), containing varying fractions of an aminoacylated phosphatidylethanolamine, a stable analog of the corresponding phosphatidylglycerol-derivative. To differentiate between the effects of headgroup size and charge on peptide-lipid interactions, we synthesized two different derivatives. In one, the headgroup was modified by the addition of lysine, and in the other, by glutamine. The modification by glutamine results in a phospholipid with a headgroup size comparable to that of the lysylated version. However, whereas lysylphosphatidylethanolamine (Lys-PE) is cationic, glutaminylphosphatidylethanolamine (Gln-PE) is zwitterionic. We found that binding of mastoparan X and cecropin A was not significantly altered if the content of aminoacylated phosphatidylethanolamines did not exceed 20 mol%, which is the concentration found in bacterial membranes. However, a lysylphosphatidylethanolamine content of 20 mol% significantly inhibits dye release from lipid vesicles, to a degree that depends on the peptide. In the case of mastoparan X, dye release is essentially abolished at 20 mol% lysylphosphatidylethanolamine, whereas cecropin A is less sensitive to the presence of lysylphosphatidylethanolamine. These observations are understood through the complex interplay between peptide binding and membrane stabilization as a function of the aminoacylated lipid content. PMID:24780374

  10. Revealing charge-transfer effects in gas-phase water chemistry.

    PubMed

    Cappelletti, David; Ronca, Enrico; Belpassi, Leonardo; Tarantelli, Francesco; Pirani, Fernando

    2012-09-18

    An understanding of the interactions involving water and other small hydrogenated molecules such as H(2)S and NH(3) at the molecular level is an important and elusive scientific goal with potential implications for fields ranging from biochemistry to astrochemistry. One longstanding question about water's intermolecular interactions, and notably hydrogen bonding, is the extent and importance of charge transfer (CT) , which can have important implications for the development of reliable model potentials for water chemistry, among other applications. The weakly bound adducts, commonly regarded as pure van der Waals systems, formed by H(2)O, H(2)S, and NH(3) with noble gases or simple molecules such as H(2), provide an interesting case study for these interactions. Their binding energies are approximately 1 or 2 kJ/mol at most, and CT effects in these systems are thought to be negligible. Our laboratory has performed high-resolution molecular-beam scattering experiments that probe the (absolute scale) intermolecular potential of various types of these gas-phase binary complexes with extreme sensitivity. These experiments have yielded surprising and intriguing quantitative results. The key experimental measurable is the "glory" quantum interference shift that shows a systematic, anomalous energy stabilization for the water complexes and clearly points to a significant role for CT effects. To investigate these findings, we have performed very accurate theoretical calculations and devised a simple approach to study the electron displacement that accompanies gas-phase binary intermolecular interactions in extreme detail. These calculations are based on a partial progressive integration of the electron density changes. The results unambiguously show that water's intermolecular interactions are not typical van der Waals complexes. Instead, these interactions possess a definite, strongly stereospecific CT component, even when very weak, where a water molecule may act as electron donor or acceptor depending on its orientation. CT is mediated by an asymmetric role played by the two hydrogen atoms, which causes strong orientation effects. The careful comparison of these calculations with the experimental results shows that the stabilization energy associated to CT is approximately 2-3 eV per electron transferred and may make up for a large portion of the total interaction energy. A simple electron delocalization model helps to validate and explain these findings. PMID:22775359

  11. 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.

  12. Cold, Gas-Phase UV and IR Spectroscopy of Protonated Leucine Enkephalin and its Analogues

    NASA Astrophysics Data System (ADS)

    Burke, Nicole L.; Redwine, James; Dean, Jacob C.; McLuckey, Scott A.; Zwier, Timothy S.

    2014-06-01

    The conformational preferences of peptide backbones and the resulting hydrogen bonding patterns provide critical biochemical information regarding the structure-function relationship of peptides and proteins. The spectroscopic study of cryogenically-cooled peptide ions in a mass spectrometer probes these H-bonding arrangements and provides information regarding the influence of a charge site. Leucine enkephalin, a biologically active endogenous opiod peptide, has been extensively studied as a model peptide in mass spectrometry. This talk will present a study of the UV and IR spectroscopy of protonated leucine enkephalin [YGGFL+H]+ and two of its analogues: the sodiated [YGGFL+Na]+ and C-terminally methyl esterified [YGGFL-OMe+H]+ forms. All experiments were performed in a recently completed multi-stage mass spectrometer outfitted with a cryocooled ion trap. Ions are generated via nano-electrospray ionization and the analyte of interest is isolated in a linear ion trap. The analyte ions are trapped in a 22-pole ion trap held at 5 K by a closed cycle helium cryostat and interrogated via UV and IR lasers. Photofragments are trapped and isolated in a second LIT and mass analyzed. Double-resonance UV and IR methods were used to assign the conformation of [YGGFL+H]+, using the NH/OH stretch, Amide I, and Amide II regions of the infrared spectrum. The assigned structure contains a single backbone conformation at vibrational/rotational temperatures of 10 K held together with multiple H-bonds that self-solvate the NH3+ site. A "proton wire" between the N and C termini reinforces the H-bonding activity of the COO-H group to the F-L peptide bond, whose cleavage results in formation of the b4 ion, which is a prevalent, low-energy fragmentation pathway for [YGGFL+H]+. The reinforced H-bonding network in conjunction with the mobile proton theory may help explain the prevalence of the b4 pathway. In order to elucidate structural changes caused by modifying this H-bonding activity, structural analogues were investigated. Determining the [YGGFL+Na]+ structure will lend insight as to the impact of the ammonium group and methyl esterification of the C-terminus eliminates the carboxy proton. The talk will also report on high resolution, cold UV spectra, non-conformation specific IR gain spectra and conformation specific IR dip spectra for the analogues.

  13. 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

  14. Formation of phenoxy and cyclopentadienyl radicals from the gas-phase pyrolysis of phenol.

    PubMed

    Khachatryan, Lavrent; Adounkpe, Julien; Dellinger, Barry

    2008-01-24

    The formation of radicals from the gas-phase pyrolysis of phenol over a temperature range of 400-1000 degrees C was studied using the technique of low temperature matrix isolation electron paramagnetic resonance (LTMI EPR). Cooling the reactor effluent in a CO2 carrier gas to 77 K produces a cryogenic matrix that exhibits complex EPR spectra. However, annealing by slowly raising the matrix temperature yielded well-resolved, identifiable spectra. All annealed spectra over the temperature range of 700-1000 degrees C resulted in the generation of EPR spectra with six lines, hyperfine splitting constant approximately 6.0 G, g = 2.00430, and peak-to-peak width approximately 3 G that was readily assignable, based on comparison with the literature and theoretical calculations, as that of cyclopentadienyl radical. Annihilation procedures along with microwave power saturation experiments helped to clearly identify phenoxy radicals in the same temperature region. Conclusive identifications of cyclopentadienyl and phenoxy radicals were based on pure spectra of these radicals under the same experimental conditions generated from suitable precursors. Cyclopentadienyl is clearly the dominant radical at temperatures above 700 degrees C and is observed at temperatures as low as 400 degrees C. The low-temperature formation is attributed to heterogeneous initiation of phenol decomposition under very low pressure conditions. The high cyclopentadienyl to phenoxy ratio was consistent with the results of reaction kinetic modeling calculations using the CHEMKIN kinetic package and a phenol pyrolysis model adapted from the literature. PMID:18154322

  15. Review: Formation of Peptide Radical Ions Through Dissociative Electron Transfer in Ternary Metal-Ligand-Peptide Complexes

    SciTech Connect

    Chu, Ivan K.; Laskin, Julia

    2011-12-31

    The formation and fragmentation of odd-electron ions of peptides and proteins is of interest to applications in biological mass spectrometry. Gas-phase redox chemistry occurring during collision-induced dissociation of ternary metal-ligand-peptide complexes enables the formation of a variety of peptide radicals including the canonical radical cations, M{sup +{sm_bullet}}, radical dications, [M{sup +}H]{sup 2+{sm_bullet}}, radical anions, [M-2H]{sup -{sm_bullet}}. In addition, odd-electron peptide ions with well-defined initial location of the radical site are produced through side chain losses from the radical ions. Subsequent fragmentation of these species provides information on the role of charge and the location of the radical site on the competition between radical-induced and proton-driven fragmentation of odd-electron peptide ions. This account summarizes current understanding of the factors that control the efficiency of the intramolecular electron transfer (ET) in ternary metal-ligand-peptide complexes resulting in formation of odd-electron peptide ions. Specifically, we discuss the effect of the metal center, the ligand and the peptide structure on the competition between the ET, proton transfer (PT), and loss of neutral peptide and neutral peptide fragments from the complex. Fundamental studies of the structures, stabilities, and the energetics and dynamics of fragmentation of such complexes are also important for detailed molecular-level understanding of photosynthesis and respiration in biological systems.

  16. A nerve growth factor peptide retards seizure development and inhibits neuronal sprouting in a rat model of epilepsy.

    PubMed Central

    Rashid, K; Van der Zee, C E; Ross, G M; Chapman, C A; Stanisz, J; Riopelle, R J; Racine, R J; Fahnestock, M

    1995-01-01

    Kindling, an animal model of epilepsy wherein seizures are induced by subcortical electrical stimulation, results in the upregulation of neurotrophin mRNA and protein in the adult rat forebrain and causes mossy fiber sprouting in the hippocampus. Intraventricular infusion of a synthetic peptide mimic of a nerve growth factor domain that interferes with the binding of neurotrophins to their receptors resulted in significant retardation of kindling and inhibition of mossy fiber sprouting. These findings suggest a critical role for neurotrophins in both kindling and kindling-induced synaptic reorganization. Images Fig. 2 PMID:7568161

  17. Dinosaur peptides suggest mechanisms of protein survival

    E-print Network

    San Antonio, James D.

    Eleven collagen peptide sequences recovered from chemical extracts of dinosaur bones were mapped onto molecular models of the vertebrate collagen fibril derived from extant taxa. The dinosaur peptides localized to fibril ...

  18. MEPE-Derived ASARM Peptide Inhibits Odontogenic Differentiation of Dental Pulp Stem Cells and Impairs Mineralization in Tooth Models of X-Linked Hypophosphatemia

    PubMed Central

    Khaddam, Mayssam; Naji, Jiar; Coyac, Benjamin R.; Baroukh, Brigitte; Letourneur, Franck; Lesieur, Julie; Decup, Franck; Le Denmat, Dominique; Nicoletti, Antonino; Poliard, Anne; Rowe, Peter S.; Huet, Eric; Vital, Sibylle Opsahl; Linglart, Agnès; McKee, Marc D.; Chaussain, Catherine

    2013-01-01

    Mutations in PHEX (phosphate-regulating gene with homologies to endopeptidases on the X-chromosome) cause X-linked familial hypophosphatemic rickets (XLH), a disorder having severe bone and tooth dentin mineralization defects. The absence of functional PHEX leads to abnormal accumulation of ASARM (acidic serine- and aspartate-rich motif) peptide ? a substrate for PHEX and a strong inhibitor of mineralization ? derived from MEPE (matrix extracellular phosphoglycoprotein) and other matrix proteins. MEPE-derived ASARM peptide accumulates in tooth dentin of XLH patients where it may impair dentinogenesis. Here, we investigated the effects of ASARM peptides in vitro and in vivo on odontoblast differentiation and matrix mineralization. Dental pulp stem cells from human exfoliated deciduous teeth (SHEDs) were seeded into a 3D collagen scaffold, and induced towards odontogenic differentiation. Cultures were treated with synthetic ASARM peptides (phosphorylated and nonphosphorylated) derived from the human MEPE sequence. Phosphorylated ASARM peptide inhibited SHED differentiation in vitro, with no mineralized nodule formation, decreased odontoblast marker expression, and upregulated MEPE expression. Phosphorylated ASARM peptide implanted in a rat molar pulp injury model impaired reparative dentin formation and mineralization, with increased MEPE immunohistochemical staining. In conclusion, using complementary models to study tooth dentin defects observed in XLH, we demonstrate that the MEPE-derived ASARM peptide inhibits both odontogenic differentiation and matrix mineralization, while increasing MEPE expression. These results contribute to a partial mechanistic explanation of XLH pathogenesis: direct inhibition of mineralization by ASARM peptide leads to the mineralization defects in XLH teeth. This process appears to be positively reinforced by the increased MEPE expression induced by ASARM. The MEPE-ASARM system can therefore be considered as a potential therapeutic target. PMID:23451077

  19. TOPICAL REVIEW: The behaviour of nanostructured magnetic materials produced by depositing gas-phase nanoparticles

    NASA Astrophysics Data System (ADS)

    Binns, C.; Trohidou, K. N.; Bansmann, J.; Baker, S. H.; Blackman, J. A.; Bucher, J.-P.; Kechrakos, D.; Kleibert, A.; Louch, S.; Meiwes-Broer, K.-H.; Pastor, G. M.; Perez, A.; Xie, Y.

    2005-11-01

    Depositing pre-formed gas-phase nanoparticles, whose properties can be widely varied, onto surfaces enables the production of films with designed properties. The films can be nanoporous or, if co-deposited with an atomic vapour, granular, allowing independent control over the size and volume fraction of the grains. This high degree of control over the nanostructure of the film enables the production of thin films with a wide variety of behaviour, and the technique is destined to make a significant contribution to the production of high-performance magnetic materials. Here we review the behaviour of magnetic nanoparticle assemblies on surfaces and in non-magnetic and magnetic matrices deposited from the gas phase at densities from the dilute limit to pure nanoparticle films with no matrix. At sufficiently low volume fractions (~1%), and temperatures well above their blocking temperature, nanoparticle assemblies in non-magnetic matrices show ideal superparamagnetism. At temperatures below the blocking temperature, the magnetization behaviour of both Fe and Co particles is consistent with a uniaxial intra-particle magnetic anisotropy and an anisotropy constant several times higher than the bulk magnetocrystalline value. At relatively low volume fractions (>=5%) the effect of inter-particle interactions becomes evident, and the magnetization behaviour becomes characteristic of agglomerates of nanoparticles exchange coupled to form magnetic grains larger than a single particle that interact with each other via dipolar forces. The evolution of the magnetic behaviour with volume fraction is predicted by a Monte-Carlo model that includes exchange and dipolar couplings. Above the percolation threshold the films become magnetically softer, and films of pure clusters have a magnetic ground state that obeys the predicted magnetization behaviour of a correlated super-spin glass characteristic of random anisotropy materials. Magnetic nanoparticles in non-magnetic matrices show giant magnetoresistance behaviour, and the magnetotransport in deposited nanoparticle films is reviewed. Assembling Fe nanoparticles in Co matrices and vice versa is a promising technique for producing magnetic materials with a saturation magnetization that exceeds the Slater-Pauling limit. Structural studies reveal that the particles' atomic structure is dependent on the matrix material, and it is possible to prepare Fe nanoparticles with an fcc structure and, unusually, Co particles with a bcc structure. We also look to the future and discuss applications for materials made from more complex bi-metallic and core-shell nanoparticles.

  20. 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}(?P{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, ? (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)

  1. Chloroquine and chloroquinoline derivatives as models for the design of modulators of amyloid Peptide precursor metabolism.

    PubMed

    Melnyk, Patricia; Vingtdeux, Valérie; Burlet, Stéphane; Eddarkaoui, Sabiha; Grosjean, Marie-Eve; Larchanché, Paul-Emmanuel; Hochart, Guillaume; Sergheraert, Christian; Estrella, Cecilia; Barrier, Mathieu; Poix, Virginie; Plancq, Pauline; Lannoo, Cécile; Hamdane, Malika; Delacourte, André; Verwaerde, Philippe; Buée, Luc; Sergeant, Nicolas

    2015-04-15

    The amyloid precursor protein (APP) plays a central role in Alzheimer's disease (AD). Preventing deregulated APP processing by inhibiting amyloidogenic processing of carboxy-terminal fragments (APP-CTFs), and reducing the toxic effect of amyloid beta (A?) peptides remain an effective therapeutic strategy. We report the design of piperazine-containing compounds derived from chloroquine structure and evaluation of their effects on APP metabolism and ability to modulate the processing of APP-CTF and the production of A? peptide. Compounds which retained alkaline properties and high affinity for acidic cell compartments were the most effective. The present study demonstrates that (1) the amino side chain of chloroquine can be efficiently substituted by a bis(alkylamino)piperazine chain, (2) the quinoline nucleus can be replaced by a benzyl or a benzimidazole moiety, and (3) pharmacomodulation of the chemical structure allows the redirection of APP metabolism toward a decrease of A? peptide release, and increased stability of APP-CTFs and amyloid intracellular fragment. Moreover, the benzimidazole compound 29 increases APP-CTFs in vivo and shows promising activity by the oral route. Together, this family of compounds retains a lysosomotropic activity which inhibits lysosome-related A? production, and is likely to be beneficial for therapeutic applications in AD. PMID:25611616

  2. Evolution of Homochirality by Epimerization of Random Peptide Chains. A Stochastic Model

    NASA Astrophysics Data System (ADS)

    Schmidt, Peter

    2006-08-01

    A cyclic process is described which is constituted of polymerization, epimerization, and hydrolysis steps. During the first cycle peptides with random sequences are formed from racemic amino acids. A small portion of these peptides have substructures with a terminal residue linked to a homochiral sequence of optical antipodes. In such a substructure the terminal residue is assumed to invert into its mirror image so that a thermodynamically favourable epimeric stucture with continuous homochirality is formed. In the hydrolysis step the peptides are split back to monomeric units with retention of configuration. Due to stochastic differences between L- and D-substructures a net excess of one of the enantiomers results. This excess enhances the probability of the formation of substructures having the dominant configuration in the next cycle. It is shown by probabilistic considerations and computer simulations that this mechanism generates an autocatalytic growth of one of the enantiomers which finally results in homochiral populations of amino acids. The number of cycles necessary to attain homochirality depends on the number of residues of the substructure, on the chain length distribution of the polymers and on the total number of amino acid units.

  3. Model membrane interaction and DNA-binding of antimicrobial peptide Lasioglossin II derived from bee venom.

    PubMed

    Bandyopadhyay, Susmita; Lee, Meryl; Sivaraman, J; Chatterjee, Chiradip

    2013-01-01

    Lasioglossins, a new family of antimicrobial peptide, have been shown to have strong antimicrobial activity with low haemo-lytic and mast cell degranulation activity, and exhibit cytotoxic activity against various cancer cells in vitro. In order to understand the active conformation of these pentadecapeptides in membranes, we have studied the interaction of Lasioglossin II (LL-II), one of the members of Lasioglossins family with membrane mimetic micelle Dodecylphosphocholine (DPC) by fluorescence, Circular Dichroism (CD) and two dimensional (2D) (1)H NMR spectroscopy. Fluorescence experiments provide evidence of interaction of the N-terminal tryptophan residue of LL-II with the hydrophobic core of DPC micelle. CD results show an extended chain conformation of LL-II in water which is converted to a partial helical conformation in the presence of DPC micelle. Moreover we have determined the first three-dimensional NMR structure of LL-II bound to DPC micelle with rmsd of 0.36Å. The solution structure of LL-II shows hydrophobic and hydrophilic core formation in peptide pointing towards different direction in the presence of DPC. This amphipathic structure may allow this peptide to penetrate deeply into the interfacial region of negatively charged membranes and leading to local membrane destabilization. Further we have elucidated the DNA binding ability of LL-II by agarose gel retardation and fluorescence quenching experiments. PMID:23159628

  4. 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.

  5. 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

  6. Toward industrial scale synthesis of ultrapure singlet nanoparticles with controllable sizes in a continuous gas-phase process.

    PubMed

    Feng, Jicheng; Biskos, George; Schmidt-Ott, Andreas

    2015-01-01

    Continuous gas-phase synthesis of nanoparticles is associated with rapid agglomeration, which can be a limiting factor for numerous applications. In this report, we challenge this paradigm by providing experimental evidence to support that gas-phase methods can be used to produce ultrapure non-agglomerated "singlet" nanoparticles having tunable sizes at room temperature. By controlling the temperature in the particle growth zone to guarantee complete coalescence of colliding entities, the size of singlets in principle can be regulated from that of single atoms to any desired value. We assess our results in the context of a simple analytical model to explore the dependence of singlet size on the operating conditions. Agreement of the model with experimental measurements shows that these methods can be effectively used for producing singlets that can be processed further by many alternative approaches. Combined with the capabilities of up-scaling and unlimited mixing that spark ablation enables, this study provides an easy-to-use concept for producing the key building blocks for low-cost industrial-scale nanofabrication of advanced materials. PMID:26511290

  7. Conformation-dependent reaction thermochemistry: study of lactones and lactone enolates in the gas phase.

    PubMed

    Karty, Joel M; Janaway, Gordon A; Brauman, John I

    2002-05-01

    Gas-phase acidities (Delta H degrees (acid)) of lactones with ring sizes from four to seven have been measured on a Fourier transform ion cyclotron resonance mass spectrometer. Electron affinities (EAs) of the corresponding lactone enolate radicals were measured on a continuous-wave ion cyclotron resonance mass spectrometer, and the bond dissociation energies (BDEs) of the alpha C-H bonds were derived. In order of increasing ring size, Delta H degrees (acid) = 368.7 +/- 2., 369.4 +/- 2.2, 367.3 +/- 2.2, and 368.3 +/- 2.2 kcal/mol and BDE = 99.4 +/- 2.3, 94.8 +/- 2.3, 89.2 +/- 2.3, and 92.8 +/- 2.4 kcal/mol for beta-propiolactone, gamma-butyrolactone, delta-valerolactone, and epsilon-caprolactone, respectively. For their corresponding enolate radicals, EA = 44.1 +/- 0.3, 38.8 +/- 0.3, 35.3 +/- 0.3, and 37.9 +/- 0.6 kcal/mol. All of these lactones are considerably more acidic than methyl acetate, consistent with a dipole repulsion model. Both BDEs and EAs show a strong dependence on ring size, whereas Delta H degrees (acid) does not. These findings are discussed, taking into account differential electronic effects and differential strain between the reactant and product species in each reaction. PMID:11982386

  8. 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.

  9. 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 ?-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

  10. Output power enhancement of all gas-phase iodine laser by addition of hydrocarbon gases

    NASA Astrophysics Data System (ADS)

    Masuda, T.; Nakamura, T.; Endo, M.

    2011-06-01

    In this work, we studied the output power enhancement of an all gas-phase iodine laser (AGIL) by the addition of hydrocarbon gases. Enhancement is expected because hydrocarbon gases might scavenge Cl atoms, which are strong quenchers of the upper state of the laser medium, I(2 P 1/2). In AGILs, suppression of the Cl atom concentration is the key to improving the efficiency of the operation of the laser because Cl atoms are inherently generated by the self-annihilation of the energy donor, NCl(a1 ?). We found that the addition of CH4 gave the best results, because of its high scavenging rate constant and inertness to I(2 P 1/2). An enhancement of 10% was observed in the output power when CH4 was added at a flow rate twice that of NCl3. On the other hand, when C2H4 or C2H2 were added at the same flow rate as that of CH4, the output power reduced despite their fast removal rate of Cl atoms. The reason for the reduced output power was that the unsaturated bonds scavenged not only the Cl atoms but also the H atoms, resulting in a low density of H atoms, and this decelerated the production of NCl(a1 ?). The observed laser characteristics could reasonably be explained by numerical model calculations. To our knowledge, this is the first report of successful output power enhancement of an AGIL using a chemical agent.

  11. 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, ? = -2.1 and ? = 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.

  12. 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 4min 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

  13. Perspectives and Peptides of the Next Generation

    NASA Astrophysics Data System (ADS)

    Brogden, Kim A.

    Shortly after their discovery, antimicrobial peptides from prokaryotes and eukaryotes were recognized as the next potential generation of pharmaceuticals to treat antibiotic-resistant bacterial infections and septic shock, to preserve food, or to sanitize surfaces. Initial research focused on identifying the spectrum of antimicrobial agents, determining the range of antimicrobial activities against bacterial, fungal, and viral pathogens, and assessing the antimicrobial activity of synthetic peptides versus their natural counterparts. Subsequent research then focused on the mechanisms of antimicrobial peptide activity in model membrane systems not only to identify the mechanisms of antimicrobial peptide activity in microorganisms but also to discern differences in cytotoxicity for prokaryotic and eukaryotic cells. Recent, contemporary work now focuses on current and future efforts to construct hybrid peptides, peptide congeners, stabilized peptides, peptide conjugates, and immobilized peptides for unique and specific applications to control the growth of microorganisms in vitro and in vivo.

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

    PubMed

    Voronina, Liudmila; Rizzo, Thomas R

    2015-09-30

    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

  15. An in silico model to predict the potential of dietary proteins as sources of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides.

    PubMed

    Nongonierma, Alice B; FitzGerald, Richard J

    2014-12-15

    An in silico approach was developed to predict the potential of 72 dietary proteins to act as a source of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides. The model takes 68 DPP-IV inhibitory peptides (having an IC50 value <2000 ?M) and the specific contribution of their amino acids into account. Bovine ?-lactalbumin (?-La) and ?-casein (CN) displayed the highest protein coverage (PC, 43.9%) and potency index (PI, 17.9 10(-6) ?M(-1)g(-1)), respectively for DPP-IV inhibitory peptides. Sequence alignment of 39 DPP-IV inhibitory peptides having IC50's<200 ?M revealed the frequent occurrence of Trp at the N-terminus and Pro at position 2. Canola, chicken egg, oat and wheat were identified as potential sources of DPP-IV inhibitory peptides. In silico approaches may assist in the selection of food proteins for the enzymatic release of DPP-IV inhibitory peptides. The results are relevant to the generation of biofunctional ingredients for glycaemic management. PMID:25038703

  16. A Spectroscopic Study of the Aggregation State of the Human Antimicrobial Peptide LL-37 in Bacterial versus Host Cell Model Membranes.

    PubMed

    Bonucci, Alessio; Caldaroni, Elena; Balducci, Enrico; Pogni, Rebecca

    2015-11-17

    The LL-37 antimicrobial peptide is the only cathelicidin peptide found in humans that has antimicrobial and immunomodulatory properties. Because it exerts also chemotactic and angiogenetic activity, LL-37 is involved in promoting wound healing, reducing inflammation, and strengthening the host immune response. The key to the effectiveness of antimicrobial peptides (AMPs) lies in the different compositions of bacterial versus host cell membranes. In this context, antimicrobial peptide LL-37 and two variants were studied in the presence of model membranes with different lipid compositions and charges. The investigation was performed using an experimental strategy that combines the site-directed spin labeling-electron paramagnetic resonance technique with circular dichroism and fluorescence emission spectroscopies. LL-37 interacts with negatively charged membranes forming a stable aggregate, which can likely produce toroidal pores until the amount of bound peptide exceeds a critical concentration. At the same time, we have clearly detected an aggregate with a higher oligomeric degree for interaction of LL-37 with neutral membranes. These data confirm the absence of cell selectivity of the peptide and a more complex role in stimulating host cells. PMID:26502164

  17. Estimation of electrokinetic and hydrodynamic global properties of relevant amyloid-beta peptides through the modeling of their effective electrophoretic mobilities and analysis of their propensities to aggregation.

    PubMed

    Deiber, Julio A; Piaggio, Maria V; Peirotti, Marta B

    2014-09-01

    Neuronal activity loss may be due to toxicity caused by amyloid-beta peptides forming soluble oligomers. Here amyloid-beta peptides (1-42, 1-40, 1-39, 1-38, and 1-37) are characterized through the modeling of their experimental effective electrophoretic mobilities determined by a capillary zone electrophoresis method as reported in the literature. The resulting electrokinetic and hydrodynamic global properties are used to evaluate amyloid-beta peptide propensities to aggregation through pair particles interaction potentials and Brownian aggregation kinetic theories. Two background electrolytes are considered at 25°C, one for pH 9 and ionic strength I = 40 mM (aggregation is inhibited through NH4OH) the other for pH 10 and I = 100 mM (without NH4OH). Physical explanations of peptide oligomerization mechanisms are provided. The effect of hydration, electrostatic, and dispersion forces in the amyloidogenic process of amyloid-beta peptides (1-40 and 1-42) are quantitatively presented. The interplay among effective charge number, hydration, and conformation of chains is described. It is shown that amyloid-beta peptides (1-40 and 1-42) at pH 10, I = 100 mM and 25°C, may form soluble oligomers, mainly of order 2 and 4, after an incubation of 48 h, which at higher times evolve and end up in complex structures (protofibrils and fibrils) found in plaques associated with Alzheimer's disease. PMID:24975363

  18. Resolving Isomeric Peptide Mixtures: A Combined HPLC/Ion Mobility-TOFMS Analysis of a

    E-print Network

    Clemmer, David E.

    Resolving Isomeric Peptide Mixtures: A Combined HPLC/Ion Mobility-TOFMS Analysis of a 4000 chromatogra- phy (HPLC) separation approach has been combined with ion mobility/time-of-flight (TOF) mass, Leu, Lys, Phe, Ser, and Val). Addition of the gas-phase mobility separation between the HPLC

  19. Quantitative Analysis and Parametric Imaging of 18F-Labeled Monomeric and Dimeric RGD Peptides Using Compartment Model

    PubMed Central

    Guo, Ning; Lang, Lixin; Gao, Haokao; Niu, Gang; Kiesewetter, Dale O.; Xie, Qingguo; Chen, Xiaoyuan

    2012-01-01

    Purpose Non-invasive PET imaging with radiolabeled RGD peptides for ?v?3 integrin targeting has become an important tool for tumor diagnosis and treatment monitoring in both pre-clinical and clinical studies. To better understand the molecular process and tracer pharmacokinetics, we introduced kinetic modeling in the investigation of 18F-labeled RGD peptide monomer 18F-FP-c(RGDyK) (denoted as 18F-FPRGD) and dimer 18F-FP-PEG3-E[c(RGDyK)]2 (denoted as 18F-FPPRGD2). Procedures MDA-MB-435 tumor-bearing mice underwent 60 min dynamic PET scans following the injection of either 18F-FPRGD or 18F-FPPRGD2. Blocking studies with pre-injection of a blocking mass dose were performed for both monomeric and dimeric RGD groups. 18F-FPRAD (RAD) was used as a negative control. Kinetic parameters (K1, k2, k3, k4) of a three-compartment model were fitted to the dynamic data to allow quantitative comparisons between the monomeric and dimeric RGD peptides. Results Dimeric RGD peptide tracer showed significantly higher binding potential (BpND = k3/k4, 5.87 ± 0.31) than that of the monomeric analog (2.75 ± 0.48, p = 0.0022, n = 4/group). The BpND values showed a significantly greater ratio (dimer/monomer ~2.1) than the difference in %ID/g uptake measured from static images (dimer/monomer ~1.5, p = 0.0045). Significant decrease in BpND was found in the blocked groups compared with the unblocked ones (dimer p = 0.00024, monomer p = 0.005, n = 4/group). Similarly, the RAD control group showed the lowest BpND value among all the test groups, as the RAD peptide does not bind to integrin ?v?3. Volume of distribution (VT = K1/k2(1+k3/k4)) could be separated into non-specific (VND = K1/k2) and specific (VS = K1k3/(k2k4)) components. Specific distribution volume (VS) was the dominant component of VT in the unblocked groups and decreased in the blocked groups. Unblocked RGD dimer also showed higher VS than that of the monomer (dimer VS = 2.38 ± 0.15, monomer VS = 0.90 ± 0.17, p = 0.0013, n = 4/group), well correlated with BpND calculations. Little difference in VND was found among all groups. Moreover, parametric maps allowed quantitative analysis at voxel level and provided higher tumor-to-background contrast for BpND maps than the static images. Tumor heterogeneity in kinetic parameters was found in parametric images, which couldn’t be clearly identified in static intensity images. Conclusions The pharmacokinetics of both monomeric and dimeric RGD peptide tracers was compared, and the RGD dimers showed significantly higher binding affinity than the monomeric analogs. Kinetic parameters were demonstrated to be valuable for separating specific and non-specific binding and may allow more sensitive and detailed quantification than simple standard uptake value (SUV) analysis. PMID:22437879

  20. Recruitment of progenitor cells by an extracellular matrix cryptic peptide in a mouse model of digit amputation.

    PubMed

    Agrawal, Vineet; Tottey, Stephen; Johnson, Scott A; Freund, John M; Siu, Bernard F; Badylak, Stephen F

    2011-10-01

    Biologic scaffolds composed of extracellular matrix (ECM) have been used successfully in preclinical models and humans for constructive remodeling of functional, site-appropriate tissue after injury. The mechanisms underlying ECM-mediated constructive remodeling are not completely understood, but scaffold degradation and site-directed recruitment of both differentiated and progenitor cells are thought to play critical roles. Previous studies have shown that degradation products of ECM scaffolds can recruit a population of progenitor cells both in vitro and in vivo. The present study identified a single cryptic peptide derived from the ? subunit of the collagen III molecule that is chemotactic for a well-characterized perivascular stem cell in vitro and causes the site-directed accumulation of progenitor cells in vivo. The oligopeptide was additionally chemotactic for human cortical neural stem cells, rat adipocyte stem cells, C2C12 myoblast cells, and rat Schwann cells in vitro. In an adult murine model of digit amputation, treatment with this peptide after mid-second phalanx amputation resulted in a greater number of Sox2+ and Sca1+,Lin- cells at the site of injury compared to controls. Since progenitor cell activation and recruitment are key prerequisites for epimorphic regeneration in adult mammalian tissues, endogenous site-directed recruitment of such cells has the potential to alter the default wound healing response from scar tissue toward regeneration. PMID:21563860

  1. Device for two-dimensional gas-phase separation and characterization of ion mixtures

    DOEpatents

    Tang, Keqi (Richland, WA); Shvartsburg, Alexandre A. (Richland, WA); Smith, Richard D. (Richland, WA)

    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.

  2. 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.

  3. Gas phase diffusion coefficients of reactive trace gases in the atmosphere

    NASA Astrophysics Data System (ADS)

    Tang, Mingjin; Shiraiwa, Manabu; Cox, Tony; Pöschl, Ulrich; Kalberer, Markus

    2015-04-01

    Diffusion of gas molecules to the surface is the first step for all gas-surface reactions. Gas phase diffusion can influence and sometimes even limit the overall rates of these reactions. However, there is no database of the gas phase diffusion coefficients of atmospheric reactive trace gases. We have compiled and evaluated, for the first time, the diffusivities (pressure independent diffusion coefficients) of atmospheric inorganic (Tang et al., 2014) and organic reactive trace gases reported in the literature. The measured diffusivities are then compared with estimated values using a semi-empirical method developed by Fuller et al. (1966). The diffusivities estimated using Fuller's method are typically found to be in good agreement with the measured values within ±30%, and therefore Fuller's method can be used to estimate the diffusivities of trace gases for which experimental data are not available. The two experimental methods used in the atmospheric chemistry community to measure the gas phase diffusion coefficients are also discussed.

  4. Real-Time Optical Monitoring of Flow Kinetics and Gas Phase Reactions Under High-Pressure OMCVD Conditions

    NASA Technical Reports Server (NTRS)

    Dietz, N.; McCall, S.; Bachmann, K. J.

    2001-01-01

    This contribution addresses the real-time optical characterization of gas flow and gas phase reactions as they play a crucial role for chemical vapor phase depositions utilizing elevated and high pressure chemical vapor deposition (HPCVD) conditions. The objectives of these experiments are to validate on the basis of results on real-time optical diagnostics process models simulation codes, and provide input parameter sets needed for analysis and control of chemical vapor deposition at elevated pressures. Access to microgravity is required to retain high pressure conditions of laminar flow, which is essential for successful acquisition and interpretation of the optical data. In this contribution, we describe the design and construction of the HPCVD system, which include access ports for various optical methods of real-time process monitoring and to analyze the initial stages of heteroepitaxy and steady-state growth in the different pressure ranges. To analyze the onset of turbulence, provisions are made for implementation of experimental methods for in-situ characterization of the nature of flow. This knowledge will be the basis for the design definition of experiments under microgravity, where gas flow conditions, gas phase and surface chemistry, might be analyzed by remote controlled real-time diagnostics tools, developed in this research project.

  5. Laser-induced carbon plasma emission spectroscopic measurements on solid targets and in gas-phase optical breakdown

    SciTech Connect

    Nemes, Laszlo; Keszler, Anna M.; Hornkohl, James O.; Parigger, Christian

    2005-06-20

    We report measurements of time- and spatially averaged spontaneous-emission spectra following laser-induced breakdown on a solid graphite/ambient gas interface and on solid graphite in vacuum, and also emission spectra from gas-phase optical breakdown in allene C3H4 and helium, and in CO2 and helium mixtures. These emission spectra were dominated by CII (singly ionized carbon), CIII (doubly ionized carbon), hydrogen Balmer beta (H{sub b}eta), and Swan C2 band features. Using the local thermodynamic equilibrium and thin plasma assumptions, we derived electron number density and electron temperature estimates. The former was in the 1016 cm{sup -3} range, while the latter was found to be near 20000 K. In addition, the vibration-rotation temperature of the Swan bands of the C2 radical was determined to be between 4500 and 7000 K, using an exact theoretical model for simulating diatomic emission spectra. This temperature range is probably caused by the spatial inhomogeneity of the laser-induced plasma plume. Differences are pointed out in the role of ambient CO2 in a solid graphite target and in gas-phase breakdown plasma.

  6. Continuous stirred-tank-reactor investigation of the gas-phase reaction of hydroxyl radicals and toluene

    SciTech Connect

    Gery, M.W.; Fox, D.L.; Jeffries, H.E.; Stockburger, L.; Weathers, W.S.

    1985-01-01

    A continuous stirred-tank reactor (CSTR) was used to study the gas-phase reaction between HO and toluene. HO was generated by the in situ photolysis of nitrous acid. Flow-reactor operation at steady-state conditions with a residence time of 20 minutes allowed investigation of primary and very rapid secondary reactions. CSTR and batch-reactor experiments were also performed with selected products. Both gas-phase and aerosol products were identified by chromatography and mass spectroscopy, with total product yields between 55 and 75% of reacted carbon. Toluene reaction products included cresols, nitrocresols, nitrotoluenes, 3,5-dinitrotoluene, benzaldehyde, benzyl nitrate, nitrophenols, methyl-p-benzoquinone, methylglyoxal, glyoxal, formaldehyde, methyl nitrate, PAN, and CO. The fraction of HO methyl hydrogen abstraction was calculated to be 0.13 + or - 0.04. The ratio of reaction rate constants for nitrotoluene versus cresol formation from the HO adduct was calculated to be about 3.3 x 10,000. Also, the ratio of cresol formation versus O2 addition to the HO adduct was estimated to be > or = 0.55. Comparisons of these measurements with previous values and the implications with respect to photochemical kinetics modeling of the atmosphere are discussed.

  7. Effects of isospin and momentum dependent interactions on liquid-gas phase transition in hot asymmetric nuclear matter

    E-print Network

    Jun Xu; Lie-Wen Chen; Bao-An Li; Hong-Ru Ma

    2007-05-29

    The liquid-gas phase transition in hot neutron-rich nuclear matter is investigated within a self-consistent thermal model using an isospin and momentum dependent interaction (MDI) constrained by the isospin diffusion data in heavy-ion collisions, a momentum-independent interaction (MID), and an isoscalar momentum-dependent interaction (eMDYI). The boundary of the phase-coexistence region is shown to be sensitive to the density dependence of the nuclear symmetry energy with a softer symmetry energy giving a higher critical pressure and a larger area of phase-coexistence region. Compared with the momentum-independent MID interaction, the isospin and momentum-dependent MDI interaction is found to increase the critical pressure and enlarge the area of phase-coexistence region. For the isoscalar momentum-dependent eMDYI interaction, a limiting pressure above which the liquid-gas phase transition cannot take place has been found and it is shown to be sensitive to the stiffness of the symmetry energy.

  8. Conformational Ordering of Biomolecules in the Gas Phase: Nitrogen Collision Cross Sections Measured on a Prototype High Resolution Drift Tube Ion Mobility-Mass Spectrometer

    PubMed Central

    2014-01-01

    Ion mobility-mass spectrometry measurements which describe the gas-phase scaling of molecular size and mass are of both fundamental and pragmatic utility. Fundamentally, such measurements expand our understanding of intrinsic intramolecular folding forces in the absence of solvent. Practically, reproducible transport properties, such as gas-phase collision cross-section (CCS), are analytically useful metrics for identification and characterization purposes. Here, we report 594 CCS values obtained in nitrogen drift gas on an electrostatic drift tube ion mobility-mass spectrometry (IM-MS) instrument. The instrument platform is a newly developed prototype incorporating a uniform-field drift tube bracketed by electrodynamic ion funnels and coupled to a high resolution quadrupole time-of-flight mass spectrometer. The CCS values reported here are of high experimental precision (±0.5% or better) and represent four chemically distinct classes of molecules (quaternary ammonium salts, lipids, peptides, and carbohydrates), which enables structural comparisons to be made between molecules of different chemical compositions for the rapid “omni-omic” characterization of complex biological samples. Comparisons made between helium and nitrogen-derived CCS measurements demonstrate that nitrogen CCS values are systematically larger than helium values; however, general separation trends between chemical classes are retained regardless of the drift gas. These results underscore that, for the highest CCS accuracy, care must be exercised when utilizing helium-derived CCS values to calibrate measurements obtained in nitrogen, as is the common practice in the field. PMID:24446877

  9. Modeling deamidation in sheep ?-keratin peptides and application to archeological wool textiles.

    PubMed

    Solazzo, Caroline; Wilson, Julie; Dyer, Jolon M; Clerens, Stefan; Plowman, Jeffrey E; von Holstein, Isabella; Walton Rogers, Penelope; Peacock, Elizabeth E; Collins, Matthew J

    2014-01-01

    Deamidation of glutamine (Q) and asparagine (N) has been recognized as a marker of degradation and aging in ancient proteins. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to study deamidation in wool textiles, we identified eight peptides from ?-keratin proteins in sheep wool that could potentially be used to assess the level of degradation. For each chosen peptide, the extent of deamidation was determined by comparing the calculated theoretical distribution with the measured distribution using a genetic algorithm that gives the best fit to the measured distribution. Variations in the levels of deamidation were observed between peptides and in modern wool samples buried for up to 8 years in which deamidation levels were relatively low under short-term burial. In contrast, deamidation was higher in archeological textile fragments from medieval sites ranging from the 9th to 13th century in York (United Kingdom) and Newcastle (United Kingdom) and from the 13th to 16th century in Reykholt (Iceland). Major differences were observed between the British and the Icelandic samples, showing a negative correlation between age of samples and levels of deamidation, but highlighting the effect of local environment. In addition, nanoscale liquid chromatography-electrospray ionization tandem mass spectrometry (nanoLC-ESI-MS/MS) data indicated that deamidation in wool's ?-keratin was influenced by primary and higher-order structures. Predominance of deamidation on glutamine rather than asparagine in the archeological samples was attributed to a higher abundance of Q in the ?-helical core domain of keratins, neighboring residues and steric hindrance preventing deamidation of N. PMID:24299235

  10. Real-Time Gas-Phase Imaging over a Pd(110) Catalyst during CO Oxidation by Means of Planar Laser-Induced Fluorescence

    PubMed Central

    2015-01-01

    The gas composition surrounding a catalytic sample has direct impact on its surface structure, which is essential when in situ investigations of model catalysts are performed. Herein a study of the gas phase close to a Pd(110) surface during CO oxidation under semirealistic conditions is presented. Images of the gas phase, provided by planar laser-induced fluorescence, clearly visualize the formation of a boundary layer with a significantly lower CO partial pressure close to the catalytically active surface, in comparison to the overall concentration as detected by mass spectrometry. The CO partial pressure variation within the boundary layer will have a profound effect on the catalysts’ surface structure and function and needs to be taken into consideration for in situ model catalysis studies. PMID:25893136

  11. A new tandem mass spectrometer for photofragment spectroscopy of cold, gas-phase molecular ions

    SciTech Connect

    Svendsen, Annette; Lorenz, Ulrich J.; Boyarkin, Oleg V.; Rizzo, Thomas R.

    2010-07-15

    We present here the design of a new tandem mass spectrometer that combines an electrospray ion source with a cryogenically cooled ion trap for spectroscopic studies of cold, gas-phase ions. The ability to generate large ions in the gas phase without fragmentation, cool them to {approx}10 K in an ion trap, and perform photofragment spectroscopy opens up new possibilities for spectroscopic characterization of large biomolecular ions. The incorporation of an ion funnel, together with a number of small enhancements, significantly improves the sensitivity, signal stability, and ease of use compared with the previous instrument built in our laboratory.

  12. Pair Formation of Free Nucleobases and Mononucleosides in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Dey, Michael; Grotemeyer, Jürgen; Schlag, Edward W.

    1994-08-01

    The formation of neutral bimolecular clusters of unsubstituted nucleobases and mononucleosides in the gas phase has been studied by IR laser desorption of the neutral molecules into a supersonic beam expansion. The complementary nucleobase pairs adenine-thymine and cytosine-guanine of D N A have been found to be formed in preference to non complementary base pairs. Association constants for the formation of the dimers of free nucleobases and nucleosides in the gas phase are calculated from the experimental results. A strong influence due to side groups affecting the dimer formation of the nucleobases is shown.

  13. Gas Phase Spectra and Structural Determination of Glucose 6 Phosphate Using Cryogenic Ion Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kregel, Steven J.; Voss, Jonathan; Marsh, Brett; Garand, Etienne

    2014-06-01

    Glucose-6-Phosphate (G6P) is one member of a class of simple phosphorylated sugars that are relevant in biological processes. We have acquired a gas phase infrared spectrum of G6P- using cryogenic ion vibrational spectroscopy (CIVS) in a home-built spectrometer. The experimental spectrum was compared with calculated vibrational spectra from a systematic conformer search. For both of the ? and ? anomers, results show that only the lowest energy conformers are present in the gas phase. If spectral signatures for similar sugars could be cataloged, it would allow for conformer-specific determination of mixture composition, for example, for glycolyzation processes.

  14. Gas-phase formation of silicon carbides, oxides, and sulphides from atomic silicon ions

    NASA Technical Reports Server (NTRS)

    Bohme, Diethard K.; Wlodek, Stanislaw; Fox, Arnold

    1989-01-01

    A systematic experimental study of the kinetics and mechanisms of the chemical reactions in the gas phase between ground-state Si(+)2p and a variety of astrophysical molecules. The aim of this study is to identify the reactions which trigger the formation of chemical bonds between silicon and carbon, oxygen and sulphur, and the chemical pathways which lead to further molecular growth. Such knowledge is valuable in the identification of new extraterrestrial silicon-bearing molecules and for an assessment of the gas-phase transition from atomic silicon to silicon carbide and silicate grain particles in carbon-rich and oxygen-rich astrophysical environments.

  15. Study of Hind Limb Tissue Gas Phase Formation in Response to Suspended Adynamia and Hypokinesia

    NASA Technical Reports Server (NTRS)

    Butler, Bruce D.

    1996-01-01

    The purpose of this study was to investigate the hypothesis that reduced joint/muscle activity (hypo kinesia) as well as reduced or null loading of limbs (adynamia) in gravity would result in reduced decompression-induced gas phase and symptoms of decompression sickness (DCS). Finding a correlation between the two phenomena would correspond to the proposed reduction in tissue gas phase formation in astronauts undergoing decompression during extravehicular activity (EVA) in microgravity. The observation may further explain the reported low incidence of DCS in space.

  16. Combining UV photodissociation with electron transfer for peptide structure analysis.

    PubMed

    Shaffer, Christopher J; Marek, Ales; Pepin, Robert; Slovakova, Kristina; Turecek, Frantisek

    2015-03-01

    The combination of near-UV photodissociation with electron transfer and collisional activation provides a new tool for structure investigation of isolated peptide ions and reactive intermediates. Two new types of pulse experiments are reported. In the first one called UV/Vis photodissociation-electron transfer dissociation (UVPD-ETD), diazirine-labeled peptide ions are shown to undergo photodissociation in the gas phase to form new covalent bonds, guided by the ion conformation, and the products are analyzed by electron transfer dissociation. In the second experiment, called ETD-UVPD wherein synthetic labels are not necessary, electron transfer forms new cation-peptide radical chromophores that absorb at 355?nm and undergo specific backbone photodissociation reactions. The new method is applied to distinguish isomeric ions produced by ETD of arginine containing peptides. PMID:25800183

  17. Model peptides to study the effects of P2 and P3 substitutions in statine-containing HIV proteinase inhibitors.

    PubMed

    Hui, K Y; Hermann, R B; Manetta, J V; Gygi, T; Angleton, E L

    1993-08-01

    Through a series of synthetic model peptides, we have examined the structural requirements of the P2 and P3 residues in statine-based HIV protease (PR) inhibitors. Results agree with the general observations that, the more bulky the P3 aromatic hydrophobic side chain, the more potent is the inhibitor. At P2, an isopropyl side chain is critical in maintaining potency. Three-dimensional modeling demonstrates that the steric bulk of a leucyl residue or the unfavorable energy transfer, from water to enzyme, for a basic amino acid residue at P2 markedly compromises activity. A naphthylalaninyl-valyl P3-P2 substituted analogue inhibits PR with an IC50 value of 6 nM, and was also effective as an antiviral agent. PMID:8348964

  18. TRAM-Derived Decoy Peptides inhibits the inflammatory response in mouse mammary epithelial cells and a mastitis model in mice.

    PubMed

    Hu, Xiaoyu; Tian, Yuan; Wang, Tiancheng; Zhang, Wenlong; Wang, Wei; Gao, Xuejiao; Qu, Shihui; Cao, Yongguo; Zhang, Naisheng

    2015-10-01

    It has been proved that TRAM-Derived Decoy peptides have anti-inflammatory properties. In this study, we synthesized a TRAM-Derived decoy peptide (TM6), belongs to TRAM TIR domain, of which sequence is "N"-RQIKIWFQNRRMKWK, KENFLRDTWCNFQFY-"C" and evaluated the effects of TM6 on lipopolysaccharide-induced mastitis in mice. In vivo, LPS-induced mice mastitis model was established by injection of LPS through the duct of mammary gland. TM6 was injected 1h before or after LPS treatment. In vitro, primary mouse mammary epithelial cells were used to investigate the effects of TM6 on LPS-induced inflammatory responses. The results showed that TM6 inhibited LPS-induced mammary gland histopathologic changes, MPO activity, and TNF-?, IL-1? and IL-6 production in mice. In vitro, TM6 significantly inhibited LPS-induced TNF-? and IL-6 production, as well as NF-?B and MAPKs activation. In conclusion, this study demonstrated that TM6 had protective effects on LPS-mastitis and may be a promising therapeutic reagent for mastitis treatment. PMID:26101068

  19. Intrathecal application of the antimicrobial peptide CRAMP reduced mortality and neuroinflammation in an experimental model of pneumococcal meningitis.

    PubMed

    Dörr, Arndt; Kress, Eugenia; Podschun, Rainer; Pufe, Thomas; Tauber, Simone C; Brandenburg, Lars-Ove

    2015-08-01

    Antimicrobial peptides (AP) are important components of the innate immune system. Our previous work revealed a higher mortality rate and up-regulation of proinflammatory gene expression as well as glial cell activation in cathelicidin-related antimicrobial peptide (CRAMP)-deficient mice after bacterial meningitis. However, the influence of CRAMP application on the progression of inflammation and its impact on mortality after bacterial meningitis remains unknown. To assess the effects of continuous CRAMP exposure in the brain, C57BL/6 wildtype mice were given intracerebroventricular infusion of CRAMP to investigate the effects on mortality, glial cell activation and inflammation in a mouse model of pneumococcal meningitis using immunohistochemistry and realtime RT-PCR. Our results revealed a decrease of mortality after CRAMP infusion. The intrathecal CRAMP infusion after pneumococcal meningitis resulted in a decreased mRNA expression of pro-inflammatory cytokines, whereas the immune responses including the expression of pattern recognition receptors and chemokines were increased in bacterial meningitis. Taken together, the results support the important role of CRAMP as part of the innate immune response against pathogens in bacterial CNS infections. The APs may be a promising approach for the development of an adjuvant therapy for bacterial meningitis. PMID:25896094

  20. Development of Ion Mobility-mass Spectrometry Instrumentation to Probe the Conformations and Capture the Solution to Gas Phase Transition of Electrosprayed Biomolecules 

    E-print Network

    Silveira, Joshua A

    2013-11-22

    evaporation model IIMS inverse ion mobility spectrometry IM ion mobility IM-MS ion mobility-mass spectrometry IMS ion mobility spectrometry MS mass spectrometry FAIMS high-field asymmetric waveform ion mobility spectrometry (also termed... IMS (PF IMS), high-field asymmetric IMS (FAIMS), overtone mobility spectrometry (OMS), trapped IMS (TIMS), inverse IMS (IIMS), and the gas-phase electrophoretic mobility molecular analyzer (GEMMA)—all of which have been coupled to MS. Together...

  1. Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide.

    PubMed

    Fu, Iwen; Case, David A; Baum, Jean

    2015-10-01

    In the canonical (G-X-Y)n sequence of the fibrillar collagen triple helix, stabilizing direct interchain hydrogen bonding connects neighboring chains. Mutations of G can disrupt these interactions and are linked to connective tissue diseases. Here we integrate computational approaches with nuclear magnetic resonance (NMR) to obtain a dynamic view of hydrogen bonding distributions in the (POG)4-(POA)-(POG)5 peptide, showing that the solution conformation, dynamics, and hydrogen bonding deviate from the reported X-ray crystal structure in many aspects. The simulations and NMR data provide clear evidence of inequivalent environments in the three chains. Molecular dynamics (MD) simulations indicate direct interchain hydrogen bonds in the leading chain, water bridges in the middle chain, and nonbridging waters in the trailing chain at the G ? A substitution site. Theoretical calculations of NMR chemical shifts using a quantum fragmentation procedure can account for the unusual downfield NMR chemical shifts at the substitution sites and are used to assign the resonances to the individual chains. The NMR and MD data highlight the sensitivity of amide shifts to changes in the acceptor group from peptide carbonyls to water. The results are used to interpret solution NMR data for a variety of glycine substitutions and other sequence triplet interruptions to provide new connections between collagen sequences, their associated structures, dynamical behavior, and their ability to recognize collagen receptors. PMID:26339765

  2. Liquid-gas phase transition in nuclear multifragmentation

    E-print Network

    Das-Gupta, S; Tsang, M B

    2000-01-01

    The equation of state of nuclear matter suggests that at suitable beam energies the disassembling hot system formed in heavy ion collisions will pass through a liquid-gas coexistence region. Searching for the signatures of the phase transition has been a very important focal point of experimental endeavours in heavy ion collisions, in the last fifteen years. Simultaneously theoretical models have been developed to provide information about the equation of state and reaction mechanisms consistent with the experimental observables. This article is a review of this endeavour.

  3. Liquid-gas phase transition in nuclear multifragmentation

    E-print Network

    S. Das Gupta; A. Z. Mekjian; M. B. Tsang

    2000-10-23

    The equation of state of nuclear matter suggests that at suitable beam energies the disassembling hot system formed in heavy ion collisions will pass through a liquid-gas coexistence region. Searching for the signatures of the phase transition has been a very important focal point of experimental endeavours in heavy ion collisions, in the last fifteen years. Simultaneously theoretical models have been developed to provide information about the equation of state and reaction mechanisms consistent with the experimental observables. This article is a review of this endeavour.

  4. Gas-phase chemical mechanism compression strategies: Treatment of reactants

    NASA Astrophysics Data System (ADS)

    Makar, P. A.; Stockwell, W. R.; Li, S. M.

    A new technique for condensing detailed organic reactions into more compact forms is introduced, and compared to methods which have been used in the ADOM and RADM air quality models. The previous methods made use of integrated reactivity weighting, designed to predict the correct product concentrations on time scales of one to two days or longer. The latter methods are shown to be subject to high errors in the prediction of initial hydrocarbon product concentrations. These errors occur when the hydrocarbon chemistry is the most reactive. The new method is a hybrid scheme which uses the reaction rates at the initial time as a further constraint on the lumping. This results in improved prediction of product concentrations on shorter time scales while retaining the long-term accuracy of the earlier techniques. The hybrid reactivity weighting technique is shown to have higher accuracy than the earlier ADOM or RADM techniques in the regions of the most reactive chemistry, and is therefore very relevant to regional oxidant models.

  5. A reference trajectory approach to Langevin equations in gas phase collision dynamics

    NASA Astrophysics Data System (ADS)

    Schatz, George C.; Moser, Mark D.

    1980-09-01

    In this paper, a new approach to the development of Langevin-like equations for studying gas phase collisional energy tranfer and other dynamical problems is introduced based on the use of reference trajectories to describe memory effects and nonlinear interactions. In this development, the exact equations of motion are first expressed in terms of the deviations of the coordinates and momenta from some reference trajectory values and then linearized about those values. A partitioning between fast and slow variables is then assumed, and those members of the above mentioned linearized equations which refer to the fast variables are re-expressed as integral equations. A ''local Brownian-like'' approximation is then made in the memory kernel appearing in the integral equations to reduce them to algebraic equations, and upon substitution of these into the slow variable equations of motion, we obtain Langevin-like equations for the slow variables. In these equations the interaction between slow and fast variables appears as frictionlike and random forcelike terms, and in these terms, information about nonlinear interactions and correlated motions (including recurrences) is evaluated using the reference trajectory. In order to keep the deviations from the reference trajectory small during each collision, this trajectory is best chosen as the ensemble averaged trajectory, and we find that a good approximation to this for many problems is provided by a trajectory in which all initial vibrational energies are set equal to zero. Applications of this Langevin-like approach to several models of gas phase VT collisional energy transfer show that it is capable of quantitative predictions (errors typically<20%) of the first and second (classical) moments of the final translational distributions, provided that the initial translational energy is low enough to make the collision duration long compared with typical vibrational periods, and that the initial vibrational energy is low enough to make the deviations about the reference trajectory small. Often these restrictions are not particularly severe. For example, in a collinear Kr+CO2(000) model, the average energy transfer is accurate to 5% for initial translational energies as high as 10 eV, while for a collinear He+H2 model, energy transfers accurate to 30% or better are obtained with five quanta of initial vibrational excitation in the H2. In addition, accurate results are obtained even when the average energy transfer is of different sign than that of the reference, and in spite of the fact that the width of the translational distribution is a factor of 10 or more larger than its first moment. We also demonstrate that the Langevin equation works well when the average energy transfer becomes comparable to a quantum of vibrational energy (i.e., in the nonperturbative regime) provided that the necessary time scale separations for invoking the Langevin treatment exist.

  6. Irreducible mass-transport limitations during a heterogeneously catalyzed gas-phase chain reaction: Oxidative coupling of methane

    SciTech Connect

    Couwenberg, P.M.; Chen, Q.; Marin, G.B.

    1996-02-01

    A heterogeneous reactor model was developed describing kinetic experiments on the heterogeneously catalyzed oxidative coupling of methane in a laboratory fixed-bed reactor. The catalyst produces radicals which react further through gas-phase reactions in the pores of the catalyst and in the interstitial phase. The reactor model accounts for the irreducible mass-transport limitations for the reactive radicals, which occur even at conditions where no mass-transport limitations occur for the molecules, both reactants and reaction products. The effects of these irreducible mass-transport limitations on the conversion and selectivity of the process were investigated and were found to be essential for an adequate description of experimental data.

  7. Peptide dimethylation: fragmentation control via distancing the dimethylamino group.

    PubMed

    McShane, Adam J; Shen, Yuanyuan; Castillo, Mary Joan; Yao, Xudong

    2014-10-01

    Direct reductive methylation of peptides is a common method for quantitative proteomics. It is an active derivatization technique; with participation of the dimethylamino group, the derivatized peptides preferentially release intense a1 ions. The advantageous generation of a1 ions for quantitative proteomic profiling, however, is not desirable for targeted proteomic quantitation using multiple reaction monitoring mass spectrometry; this mass spectrometric method prefers the derivatizing group to stay with the intact peptide ions and multiple fragments as passive mass tags. This work investigated collisional fragmentation of peptides whose amine groups were derivatized with five linear ?-dimethylamino acids, from 2-(dimethylamino)-acetic acid to 6-(dimethylamino)-hexanoic acid. Tandem mass spectra of the derivatized tryptic peptides revealed different preferential breakdown pathways. Together with energy resolved mass spectrometry, it was found that shutting down the active participation of the terminal dimethylamino group in fragmentation of derivatized peptides is possible. However, it took a separation of five methylene groups between the terminal dimethylamino group and the amide formed upon peptide derivatization. For the first time, the gas-phase fragmentation of peptides derivatized with linear ?-dimethylamino acids of systematically increasing alkyl chain lengths is reported. PMID:25091822

  8. Peptide Dimethylation: Fragmentation Control via Distancing the Dimethylamino Group

    NASA Astrophysics Data System (ADS)

    McShane, Adam J.; Shen, Yuanyuan; Castillo, Mary Joan; Yao, Xudong

    2014-10-01

    Direct reductive methylation of peptides is a common method for quantitative proteomics. It is an active derivatization technique; with participation of the dimethylamino group, the derivatized peptides preferentially release intense a1 ions. The advantageous generation of a1 ions for quantitative proteomic profiling, however, is not desirable for targeted proteomic quantitation using multiple reaction monitoring mass spectrometry; this mass spectrometric method prefers the derivatizing group to stay with the intact peptide ions and multiple fragments as passive mass tags. This work investigated collisional fragmentation of peptides whose amine groups were derivatized with five linear ?-dimethylamino acids, from 2-(dimethylamino)-acetic acid to 6-(dimethylamino)-hexanoic acid. Tandem mass spectra of the derivatized tryptic peptides revealed different preferential breakdown pathways. Together with energy resolved mass spectrometry, it was found that shutting down the active participation of the terminal dimethylamino group in fragmentation of derivatized peptides is possible. However, it took a separation of five methylene groups between the terminal dimethylamino group and the amide formed upon peptide derivatization. For the first time, the gas-phase fragmentation of peptides derivatized with linear ?-dimethylamino acids of systematically increasing alkyl chain lengths is reported.

  9. Chemical reactions between cold trapped Ba+ ions and neutral molecules in the gas phase

    E-print Network

    Schiller, Stephan

    Chemical reactions between cold trapped Ba+ ions and neutral molecules in the gas phase B. Roth, D-cooled ion trapping apparatus, we have investigated laser-induced chemical reactions between cold trapped Ba is to investigate chemical reactions between cold atomic and molecular ions trapped in radio-frequency traps

  10. Molecular orbital studies of titanium nitride chemical vapor deposition: gas phase b-elimination

    E-print Network

    Schlegel, H. Bernhard

    Molecular orbital studies of titanium nitride chemical vapor deposition: gas phase b) of titanium nitride can be carried out using TiNR24 and NH3 (R Me or Et). Imido compounds are thought. Ó 2001 Pub- lished by Elsevier Science B.V. 1. Introduction It is well known that titanium nitride

  11. Molecular Orbital Studies of Titanium Nitride Chemical Vapor Deposition: Gas Phase Complex Formation,

    E-print Network

    Schlegel, H. Bernhard

    Molecular Orbital Studies of Titanium Nitride Chemical Vapor Deposition: Gas Phase Complex Received June 6, 2000 The chemical vapor deposition (CVD) of titanium nitride can be carried out with TiCl4 Titanium nitride thin films have a variety of proper- ties, such as extreme hardness, high chemical

  12. Universal correlations of onedimensional interacting electrons in the gas phase F. Gohmann and V. E. Korepin

    E-print Network

    representation for the dynamical two­point Green functions was obtained in [5], and, subsequently Brook, NY 11794­3840, USA We consider dynamical correlation functions of short range interactingUniversal correlations of one­dimensional interacting electrons in the gas phase F. G¨ohmann and V

  13. ECO LOGIC INTERNATIONAL GAS-PHASE CHEMICAL REDUCTION PROCESS - THE THERMAL DESORPTION UNIT - APPLICATIONS ANALYSIS REPORT

    EPA Science Inventory

    ELI ECO Logic International, Inc.'s Thermal Desorption Unit (TDU) is specifically designed for use with Eco Logic's Gas Phase Chemical Reduction Process. The technology uses an externally heated bath of molten tin in a hydrogen atmosphere to desorb hazardous organic compounds fro...

  14. ADVANCED OXIDATION AND REDUCTION PROCESSES IN THE GAS PHASE USING NON-THERMAL PLASMAS

    EPA Science Inventory

    In the past several years interest in gas-phase pollution control has increased, arising from a larger body of regulations and greater respect for the environment. Advanced oxidation technologies (AOTs), historically used to treat recalcitrant water pollutants via hydroxyl-radica...

  15. SPECIATION OF GAS-PHASE AND FINE PARTICLE EMISSIONS FROM BURNING OF FOLIAR FUELS

    EPA Science Inventory

    Particle size distributions (10-1000 nm aerodynamic diameter), physical and chemical properties of fine particle matter (PM2.5) with aerodynamic diameter <2.5 micrometers, and gas-phase emissions from controlled open burning of assorted taxa were measured. Chemical speciation of ...

  16. SPECIATION OF GAS-PHASE AND FINE PARTICLE EMISSIONS FROM BURNING OF FOLIAR FUELS: JOURNAL ARTICLE

    EPA Science Inventory

    NRMRL-RTP-P- 620 Hays**, M.D., Geron*, C.D., Linna**, K.J., Smith*, N.D., and Schauer, J.J. Speciation of Gas-Phase and Fine Particle Emissions from Burning of Foliar Fuels. Submitted to: Environmental Science & Technology EPA/600/J-02/234, http://pubs.acs.org/journals/esthag/...

  17. DEMONSTRATION BULLETIN: GAS-PHASE CHEMICAL REDUCTION - ECO LOGIC INTERNATIONAL, INC.

    EPA Science Inventory

    The patented Eco Logic Process employs a gas-phase reduction reaction of hydrogen with organic and chlorinated organic compounds at elevated temperatures to convert aqueous and oily hazardous contaminants into a hydrocarbon-rich gas product. After passing through a scrubber, the ...

  18. Conformational effects in sugar ions: spectroscopic investigations in the gas phase and in solution

    E-print Network

    Davis, Ben G.

    Conformational effects in sugar ions: spectroscopic investigations in the gas phase and in solution of sugars with a positively charged substituent at their anomeric centre, C-1, which display in solution in an ionic sugar, per-acetylated a-D-glucopyranosyl pyridinium, which reversed the axial (and equatorial

  19. Bond-Specific Dissociation Following Excitation Energy Transfer for Distance Constraint Determination in the Gas Phase

    PubMed Central

    2015-01-01

    Herein, we report chemistry that enables excitation energy transfer (EET) to be accurately measured via action spectroscopy on gaseous ions in an ion trap. It is demonstrated that EET between tryptophan or tyrosine and a disulfide bond leads to excited state, homolytic fragmentation of the disulfide bond. This phenomenon exhibits a tight distance dependence, which is consistent with Dexter exchange transfer. The extent of fragmentation of the disulfide bond can be used to determine the distance between the chromophore and disulfide bond. The chemistry is well suited for the examination of protein structure in the gas phase because native amino acids can serve as the donor/acceptor moieties. Furthermore, both tyrosine and tryptophan exhibit unique action spectra, meaning that the identity of the donating chromophore can be easily determined in addition to the distance between donor/acceptor. Application of the method to the Trpcage miniprotein reveals distance constraints that are consistent with a native-like fold for the +2 charge state in the gas phase. This structure is stabilized by several salt bridges, which have also been observed to be important previously in proteins that retain native-like structures in the gas phase. The ability of this method to measure specific distance constraints, potentially at numerous positions if combined with site-directed mutagenesis, significantly enhances our ability to examine protein structure in the gas phase. PMID:25174489

  20. TECHNOLOGY EVALUATION REPORT: ECO LOGIC INTERNATIONAL GAS-PHASE CHEMICAL REDUCTION PROCESS - BAY CITY, MICHIGAN - APPENDICES

    EPA Science Inventory

    This document reviews the results of a 28 day demonstration program conducted by the Superfund Innovative Technology Evaluation (SITE) Program. co Logic International owners and operators of the process, provided their Gas-Phase Chemical Reduction Reactor and a companion Thermal ...

  1. TECHNOLOGY EVALUATION REPORT: ECO LOGIC INTERNATIONAL GAS-PHASE CHEMICAL REDUCTION PROCESS - BAY CITY, MICHIGAN

    EPA Science Inventory

    This document reviews the results of a 28 day demonstration program conducted by the Superfund Innovative Technology Evaluation (SITE) Program. co Logic International owners and operators of the process, provided their Gas-Phase Chemical Reduction Reactor and a companion Thermal ...

  2. GAS-PHASE OXIDATION PRODUCTS OF BIPHENYL AND POLYCHLORINATED BIPHENYLS (R825377)

    EPA Science Inventory

    Our laboratory recently measured the gas-phase reaction rate constants of
    polychlorinated biphenyls (PCBs) with the hydroxyl radical (OH) and concluded
    that OH reactions are the primary removal pathway of PCBs from the atmosphere.
    With the reaction system previousl...

  3. Field ionization kinetic and electron impact studies of gas phase transition states - The cyclic bromonium ion

    NASA Technical Reports Server (NTRS)

    Green, M. M.; Giguere, R. J.; Falick, A. M.; Aberth, W.; Burlingame, A. L.

    1978-01-01

    Cis- and trans-isomers of 4-t-butylcyclohexyl bromide were studied to determine the mechanism of cyclic bromonium ion formation. The field ionization kinetic and electron impact data indicate that the formation of the cyclic structure occurs simultaneously with loss of the neutral fragment. The data also show that little or no gas-phase cis-trans isomerization occurs.

  4. Journal of Power Sources 160 (2006) 10171025 Gas-phase particle image velocimetry (PIV) for application

    E-print Network

    Mench, Matthew M.

    2006-01-01

    Journal of Power Sources 160 (2006) 1017­1025 Gas-phase particle image velocimetry (PIV fields have been measured using particle image velocimetry (PIV) in representative geometries, including in operational cells. © 2006 Elsevier B.V. All rights reserved. Keywords: Particle image velocimetry; PIV; Flow

  5. Gas-phase products and secondary aerosol yields from the photooxidation of 16 different terpenes

    E-print Network

    Goldstein, Allen

    Gas-phase products and secondary aerosol yields from the photooxidation of 16 different terpenes products using PTR-MS. Several oxidation products were calibrated in the PTR-MS, including formaldehyde products were inferred from known fragmentation patterns, such as pinonaldehyde; and other products were

  6. Gas phase electronic spectrum of the nitrogen terminated nanowire NC16N

    E-print Network

    Maier, John Paul

    Gas phase electronic spectrum of the nitrogen terminated nanowire NC16N H. Ding, A.E. Boguslavskiy imply that a long carbon nanowire terminated with nitrogen will be semiconducting due to p of, for example, a 1D nanowire, may differ significantly from that of 3D materials and show strong

  7. Gas-phase synthesis and characterization of heteroleptic divalent germanium compounds by FVT/UV-PES

    E-print Network

    Leigh, William J.

    Gas-phase synthesis and characterization of heteroleptic divalent germanium compounds by FVT-coordinated germanium compounds UV photoelectron spectroscopy Ionization energies Quantum mechanical calculation Flash-amino, and thio-amino substitu- tion at germanium. The three compounds (4b, 5b and 6b) were prepared from

  8. Gas-phase products and secondary aerosol yields from the ozonolysis of ten different terpenes

    E-print Network

    Goldstein, Allen

    Gas-phase products and secondary aerosol yields from the ozonolysis of ten different terpenes Anita-caryophyllene), and two oxygenated terpenes (methyl chavicol and linalool) were conducted individually in Teflon chambers with the PTR-MS, varied significantly between the different parent terpene compounds. The sum of measured

  9. Regular arrangement of nanoparticles from the gas phase on bacterial surface-protein layers

    NASA Astrophysics Data System (ADS)

    Queitsch, Ute; Mohn, Elias; Schäffel, Franziska; Schultz, Ludwig; Rellinghaus, Bernd; Blüher, Anja; Mertig, Michael

    2007-03-01

    FePt nanoparticles from the gas phase are deposited onto the two-dimensional crystalline surface layer protein from the bacterium Bacillus sphaericus NCTC 9602. The potential of this protein layer to facilitate the ordered spatial arrangement of the otherwise statistically distributed nanoparticles on the substrate is studied. Transmission electron microscopy reveals the particles positions to be directed by the regular protein template.

  10. CONTINUOUS STIRRED TANK REACTOR INVESTIGATION OF THE GAS-PHASE REACTION OF HYDROXYL RADICALS AND TOLUENE

    EPA Science Inventory

    A continuous stirred tank reactor (CSTR) was used to study the gas phase reaction between HO and toluene. HO was generated by the in situ photolysis of nitrous acid. Flow reactor operation at steady state conditions with a residence time of 20 minutes allowed investigation of pri...

  11. Design of a Supercritical Fluid Expansion Source for Gas-Phase Spectroscopy of Fullerenes

    E-print Network

    McCall, Benjamin J.

    Design of a Supercritical Fluid Expansion Source for Gas-Phase Spectroscopy of Fullerenes of Illinois Bradley M. Gibson 20 February 2013 271 RAL 2:00 PM #12;I. Introduction The fullerenes, including C-poor and also presented data showing fullerene and PAH emission features together in other planetary nebulae

  12. Chemical reaction of metal-fullerene in gas phase (2) >Masamichi Konoa

    E-print Network

    Maruyama, Shigeo

    f18-068 Chemical reaction of metal-fullerene in gas phase (2) ·>Masamichi Konoa , Syuhei Inoueb.of Tokyo Since the discovery of macroscopic generation and purification procedure of fullerenes and endohedral fullerenes, the geometric structure and the formation mechanism of them has been one of the most

  13. Chemical reaction of metal-fullerene in gas phase ^

    E-print Network

    Maruyama, Shigeo

    Chemical reaction of metal-fullerene in gas phase ·^Masamichi Kohno1 , Shuhei·" `··ZZOE±·S ,Q·D"OEfullerenes-ray diffraction study has proven (1) that some metal-fullerenes such as Sc@C82 and Sc2@C84 that were prepared

  14. Molecular Orbital Studies of Zinc Oxide Chemical Vapor Deposition: Gas-Phase Hydrolysis of Diethyl Zinc,

    E-print Network

    Schlegel, H. Bernhard

    Molecular Orbital Studies of Zinc Oxide Chemical Vapor Deposition: Gas-Phase Hydrolysis of Diethyl Zinc, Elimination Reactions, and Formation of Dimers and Tetramers Stanley M. Smith and H. Bernhard deposition of zinc oxide thin films can be carried out with diethyl zinc and water vapor. The present study

  15. # Title Authors Release of gas phase species from the photolysis of thin

    E-print Network

    Nizkorodov, Sergey

    Poster # Title Authors 1 Release of gas phase species from the photolysis of thin water films.A., Greaves J., Finlayson-Pitts B.J. 11 WRF/CHEM simulation of ozone and precursors in the LA basin during.M., Paulson S.E. 13 Oxygen isotopic anomaly in secondary carbonates: evidence of anthropogenic pollution Chong

  16. Methylation of 2-Naphthol Using Dimethyl Carbonate under Continuous-Flow Gas-Phase Conditions

    ERIC Educational Resources Information Center

    Tundo, Pietro; Rosamilia, Anthony E.; Arico, Fabio

    2010-01-01

    This experiment investigates the methylation of 2-naphthol with dimethyl carbonate. The volatility of the substrates, products, and co-products allows the reaction to be performed using a continuous-flow gas-phase setup at ambient pressure. The reaction uses catalytic quantities of base, achieves high conversion, produces little waste, and…

  17. OH REACTION KINETICS OF GAS-PHASE A- AND G-HEXACHLOROCYCLOHEXANE AND HEXACHLOROBENZENE. (R825377)

    EPA Science Inventory

    Rate constants for the gas-phase reactions of the hydroxyl
    radical (OH) with - and -hexachlorocyclohexane (-
    and ANALYSIS OF A GAS-PHASE PARTITIONING TRACER TEST CONDUCTED THROUGH FRACTURED MEDIA

    EPA Science Inventory

    The gas-phase partitioning tracer method was used to estimate non-aqueous phase liquid (NAPL), water, and air saturations in the vadose zone at a chlorinated-solvent contaminated field site in Tucson, AZ. The tracer test was conducted in a fractured clay system that is the confin...

  18. Intramolecular vibrational energy redistribution and intermolecular energy transfer of benzene in supercritical CO 2: measurements from the gas phase up to liquid densities

    NASA Astrophysics Data System (ADS)

    von Benten, R.; Charvat, A.; Link, O.; Abel, B.; Schwarzer, D.

    2004-03-01

    Femtosecond pump probe spectroscopy was employed to measure intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) of benzene in the gas phase and in supercritical (sc) CO 2. We observe two IVR time scales the faster of which proceeds within ? IVR(1)<0.5 ps. The slower IVR component has a time constant of ? IVR(2)=(48±5) ps in the gas phase and in scCO 2 is accelerated by interactions with the solvent. At the highest CO 2 density it is reduced to ? IVR(2)=(6±1) ps. The corresponding IVR rate constants show a similar density dependence as the VET rate constants. Model calculations suggest that both quantities correlate with the local CO 2 density in the immediate surrounding of the benzene molecule.

  19. Effects of atrial natriuretic peptide on the unicellular Tetrahymena pyriformis model.

    PubMed

    Köhidai, L; Csaba, G; Karsa, J

    1995-01-01

    The vertebral hormone, atrial natriuretic peptide (ANP) has characteristic effects in Tetrahymena cells. ANP is able to induce the release of sodium ions, probably via the membrane rather than the contractile vacuole. The hormone is a potent inhibitor of Chinese ink-phagocytosis. A 10(-12) M concentration of ANP has the maximum positive effect on the division of cells but long-term treatments indicate the presence of a down-regulation-like mechanism. ANP has a strong chemoattractant characteristic between 10(-13) and 10(-11) M concentrations. Significant concentration dependent FITC-ANP binding at pretreatments of 10(-12) M suggest the presence of special receptor-dependent mechanisms which are responsible for the development of hormonal imprinting. The similarities between the most effective concentrations (10(-13) - 10(-12) M) and the human serum level of ANP shows that the effects of ANP have a more evolutionary background than previously considered. PMID:7791630

  1. A gas-phase amplified quartz crystal microbalance immunosensor based on catalase modified immunoparticles.

    PubMed

    Liu, Wei; Huang, Renliang; Qi, Wei; Wang, Mengfan; Su, Rongxin; He, Zhimin

    2015-02-21

    A novel signal amplification strategy for quartz crystal microbalance (QCM) based on catalytic gas generation was developed to construct an ultrasensitive immunosensor for the detection of proteins (immunoglobulin G, IgG, used as a model). A catalase modified immunoparticle was prepared to form a sandwich-type immunocomplex with the IgG and anti-IgG antibodies that were immobilized on the QCM sensor. The amount of immunoparticles on the sensor surface was thus controlled by the IgG concentration. Then H2O2 was added and catalyzed by catalase for oxygen generation. The generated oxygen replaced some of the liquid on the sensor surface, leading to the change in the shear modulus of the immunocomplex layer and the apparent viscosity and density of the liquid layer. Due to the ultrasensitive response of QCM to these changes, a significant frequency shift related to the IgG concentration was achieved. Different parameters, including the flow cell structure, operation temperature, immunoparticle concentration, and H2O2 concentration were optimized to achieve steady and efficient frequency shifts. Under the optimal conditions, the proposed gas-phase amplified QCM sensor could achieve up to 72 times improvement of detection sensitivity compared to the label-free sensor as a control, in the concentration range of 0.1-3.0 ?g mL(-1). The detection limit was also reduced from 236 ng mL(-1) to 51.0 ng mL(-1) at the 3Sblank level. PMID:25519742

  2. Condensed-phase versus gas-phase ozonolysis of catechol: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Barnum, Timothy J.; Medeiros, Nicholas; Hinrichs, Ryan Z.

    2012-08-01

    Anthropogenic emissions of volatile aromatic compounds contribute to the formation of secondary organic aerosols (SOA), especially in urban environments. Aromatic SOA precursors typically require oxidation by hydroxyl radicals, although recent work suggests that ozonolysis of 1,2-benzenediols produces SOA in high yields. We employed attenuated total reflectance and transmission infrared spectroscopy to investigate the heterogeneous ozonolysis of catechol thin films. Formation of the dominant condensed-phase product muconic acid was highly dependent on relative humidity (RH) with few products detected below 40% RH and a maximum reactive uptake coefficient of ? = (5.6 ± 0.5) × 10-5 measured at 81.2% RH. We also performed quantum chemical calculations mapping out several reaction pathways for the homogeneous ozonolysis of gaseous catechol. 1,3-cycloaddition transition states were rate limiting with the most favorable activation energies at 45.4 and 47.1 kJ mol-1 [CCSD(T)/6-311++G(d,p)] corresponding to addition across and adjacent to the diol Cdbnd C, respectively. Gas-phase rate constants, calculated using transition state theory, were six orders of magnitude slower than experimental values. In contrast, a calculated activation energy was lower for the ozonolysis of a catechol•H2O complex, which serves as a first-approximation for modeling the ozonolysis of condensed-phase catechol. These combined results suggests that homogeneous ozonolysis of catechol may not be important for the formation of secondary organic aerosols but that ozonolysis of surface-adsorbed catechol may contribute to SOA growth.

  3. Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

    NASA Astrophysics Data System (ADS)

    Mawhorter, Richard J., Jr.

    A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

  4. Gas-phase ion-mobility characterization of SAM-functionalized Au nanoparticles.

    PubMed

    Tsai, D-H; Zangmeister, R A; Pease, L F; Tarlov, M J; Zachariah, M R

    2008-08-19

    We present results of a systematic examination of functionalized gold nanoparticles (Au-NPs) by electrospray-differential mobility analysis (ES-DMA). Commercially available, citrate-stabilized Au colloid solutions (10-60 nm) were sized using ES-DMA, from which changes in particle size of less than 0.3 nm were readily discerned. It was found that the formation of salt particles and the coating of Au-NPs by salt during the electrospray process can interfere with the mobility analysis, which required the development of sample preparation and data correction protocols to extract correct values for the Au-NP size. Formation of self-assembled monolayers (SAMs) of alkanethiol molecules on the Au-NP surface was detected from a change in particle mobility, which could be modeled to extract the surface packing density of SAMs. A gas-phase temperature-programmed desorption (TPD) kinetic study of SAMs on Au-NPs found the data to be consistent with a second-order Arrhenius-based rate law, yielding an Arrhenius factor of 1.0 x 10 (11) s (-1) and an activation energy approximately 105 kJ/mol. For the size range of SAM-modified Au-NP we considered, the effect of surface curvature on the energetics of binding of carboxylic acid terminated SAMs is evidently negligible, with binding energies determined by TPD agreeing with those reported for the same SAMs on planar surfaces. This study suggests that the ES-DMA can be added to the tool set of characterization methods used to study the structure and properties of coated nanoparticles. PMID:18661963

  5. Hybrid femtosecond/picosecond coherent anti-Stokes Raman scattering for gas-phase temperature measurements

    NASA Astrophysics Data System (ADS)

    Miller, Joseph Daniel

    Hybrid femtosecond/picosecond coherent anti-Stokes Raman scattering (fs/ps CARS) is employed for quantitative gas-phase temperature measurements in combustion processes and heated flows. In this approach, ultrafast 100-fs laser pulses are used to induce vibrational and rotational transitions in N2 and O2, while a third spectrally narrowed picosecond pulse is used to probe the molecular response. Temporal suppression of the nonresonant contribution and elimination of collisional effects are achieved by delay of the probe pulse, while sufficient spectral resolution is maintained for frequency-domain detection and thermometry. A theoretical framework is developed to model experimental spectra by phenomenologically describing the temporal evolution of the vibrational and rotational wavepackets as a function of temperature and pressure. Interference-free, single-shot vibrational fs/ps CARS thermometry is demonstrated at 1-kHz from 1400-2400 K in a H2-air flame, with accuracy better than 3%. A time-asymmetric exponential pulse shape is introduced to optimize nonresonant suppression with a 103 reduction at a probe delay of 0.31 ps. Low-temperature single-shot thermometry (300-700 K) with better than 1.5% accuracy is demonstrated using a fully degenerate rotational fs/ps CARS scheme, and the influence of collision energy transfer on thermometry error is quantified at atmospheric pressure. Interference-free thermometry, without nonresonant contributions and collision-induced error, is demonstrated for the first time using rotational fs/ps CARS at room temperature and pressures from 1-15 atm. Finally, the temporal and spectral resolution of fs/ps CARS is exploited for transition-resolved time-domain measurements of N2 and O2 self-broadened S-branch Raman linewidths at pressures of 1-20 atm.

  6. CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine

    NASA Astrophysics Data System (ADS)

    Montero-Cabrera, Luis Alberto; Röhrig, Ute; Padrón-Garcia, Juan A.; Crespo-Otero, Rachel; Montero-Alejo, Ana L.; Garcia de la Vega, José M.; Chergui, Majed; Rothlisberger, Ursula

    2007-10-01

    Very large molecular systems can be calculated with the so called CNDOL approximate Hamiltonians that have been developed by avoiding oversimplifications and only using a priori parameters and formulas from the simpler NDO methods. A new diagonal monoelectronic term named CNDOL/21 shows great consistency and easier SCF convergence when used together with an appropriate function for charge repulsion energies that is derived from traditional formulas. It is possible to obtain a priori molecular orbitals and electron excitation properties after the configuration interaction of single excited determinants with reliability, maintaining interpretative possibilities even being a simplified Hamiltonian. Tests with some unequivocal gas phase maxima of simple molecules (benzene, furfural, acetaldehyde, hexyl alcohol, methyl amine, 2,5 dimethyl 2,4 hexadiene, and ethyl sulfide) ratify the general quality of this approach in comparison with other methods. The calculation of large systems as porphine in gas phase and a model of the complete retinal binding pocket in rhodopsin with 622 basis functions on 280 atoms at the quantum mechanical level show reliability leading to a resulting first allowed transition in 483nm, very similar to the known experimental value of 500nm of "dark state." In this very important case, our model gives a central role in this excitation to a charge transfer from the neighboring Glu- counterion to the retinaldehyde polyene chain. Tests with gas phase maxima of some important molecules corroborate the reliability of CNDOL/2 Hamiltonians.

  7. The role of Staphylococcal carotenogenesis in resistance to host defense peptides and in vivo virulence in experimental endocarditis model.

    PubMed

    Xiong, Yan Q; Yang, Soo-Jin; Tong, Steven Y C; Alvarez, Danya N; Mishra, Nagendra N

    2015-10-01

    The defining hallmark of the newly described species, Staphylococcus argenteus, in comparison to its sister species, S. aureus and S. schweitzeri, is the absence of production of the carotenoid pigment, staphyloxanthin. Staphylococcus argenteus lacks the responsible genetic locus crtOPQMN. We examined the impact of carotenoid synthesis in two non-pigmented S. argenteus strains, MSHR1132 and SCC1165. Following complementation with a plasmid containing the carotenoid operon (pTX-crtOPQMN), compared to wild type, both complemented strains showed substantial carotenoid production, with a resultant increase in cell membrane rigidity. Surprisingly, both crtOPQMN-complemented strains exhibited increased susceptibility to the host defense peptides, LL-37 and hNP-1 in vitro, and reduced virulence in an experimental rabbit endocarditis model. PMID:26242278

  8. Gas-phase and Solution-phase Peptide Conformations Studied by Ion Mobility-mass Spectrometry and Molecular Dynamics Simulations 

    E-print Network

    Chen, Liuxi

    2012-10-19

    tryptophan zipper 1 (trpzip1) ions and its six derivatives (ii) alkali metal ion (Na, K and Cs) adducts of gramicidin A (GA). The structural distributions obtained from ITS-MDS are compared well with results obtained from matrix-assisted laser desorption...

  9. COLLISON-ACTIVATED CLEAVAGE OF A PEPTIDE/ANTIOBIOTIC LINKAGE: EVIDENCE FOR GAS-PHASE INTRAMOLECULAR DISULFIDE EXCHANGE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ceftiofur is a third generation beta-lactam antibiotic widely used in livestock for treatment of infections. Upon administration, ceftiofur is rapidly metabolized to desfuroylceftiofur, an antimicrobially active metabolite that has a free thiol functional group. Previous experiments using electron...

  10. Micelle Bound Structure and Model Membrane Interaction Studies of the Peptide Hylin a1 from the Arboreal South American Frog Hypsiboas albopunctatus.

    PubMed

    Alves, Eliane S F; Junior, Edson C; Cilli, Eduardo M; Castro, Mariana S; Fontes, Wagner; de Magalhães, Mariana T Q; Lião, Luciano M; de Oliveira, Aline L

    2015-01-01

    Antimicrobial peptides (AMPs) appear as a promising therapeutic candidate against multiresistant pathogens, because they are able to kill microorganisms and have low toxicity of resistance cells. Hylin a1 (Hy-a1, IFGAILPLALGALKNLIK-NH2) is a peptide extracted from the skin secretion of the frog Hypsiboas albopunctatus, which displays antimicrobial and hemolytic activities. We report here structural studies of Hy-a1 using different techniques such as fluorescence, CD and NMR. Our data showed that Hy-a1 acquires a well defined amphipathic ?-helix when interacting with a membrane-like environment. Furthermore, Hy-a1 presented different affinity when compared to membranes of zwitterionic or anionic lipid composition. Finally, we proposed a molecular interaction model of this peptide with micelles. PMID:26059694

  11. Imidate-Based Cross-Linkers for Structural Proteomics: Increased Charge of Protein and Peptide Ions and CID and ECD Fragmentation Studies

    NASA Astrophysics Data System (ADS)

    Koolen, Hector H. F.; Gomes, Alexandre F.; Schwab, Nicolas V.; Eberlin, Marcos N.; Gozzo, Fabio C.

    2014-07-01

    Chemical cross-linking is an attractive low-resolution technique for structural studies of protein complexes. Distance constraints obtained from cross-linked peptides identified by mass spectrometry (MS) are used to construct and validate protein models. Amidinating cross-linkers such as diethyl suberthioimidate (DEST) have been used successfully in chemical cross-linking experiments. In this work, the application of a commercial diimidate cross-linking reagent, dimethyl suberimidate (DMS), was evaluated with model peptides and proteins. The peptides were designed with acetylated N-termini followed by random sequences containing two Lys residues separated by an Arg residue. After cross-linking reactions, intra- and intermolecular cross-linked species were submitted to CID and ECD dissociations to study their fragmentation features in the gas phase. Fragmentation of intramolecular peptides by collision induced dissociation (CID) demonstrates a unique two-step fragmentation pathway involving formation of a ketimine as intermediate. Electron capture and electron transfer dissociation (ECD and ETD) experiments demonstrated that the cyclic moiety is not dissociated. Intermolecular species demonstrated previously described fragmentation behavior in both CID and ECD experiments. The charge state distributions (CSD) obtained after reaction with DMS were compared with those obtained with disuccinimidyl suberate (DSS). CSDs for peptides and proteins were increased after their reaction with DMS, owing to the higher basicity of DMS modified species. These features were also observed in LC-MS experiments with bovine carbonic anhydrase II (BCA) after cross-linking with DMS and tryptic proteolysis. Cross-linked peptides derived from this protein were identified at high confidence and those species were in agreement with the crystal structure of BCA.

  12. Gas-phase study of the reactivity of optical coating materials with hydrocarbons by use of a

    E-print Network

    Rocca, Jorge J.

    Gas-phase study of the reactivity of optical coating materials with hydrocarbons by use with hydrocarbons is studied in the gas phase by use of mass spectroscopy of metal-oxide clusters. We report-layer materials with hydrocarbons. An increased understanding of these reactions could lead to the development

  13. Free-standing AlxGa1-xAs heterostructures by gas-phase etching of germanium

    E-print Network

    Free-standing AlxGa1-xAs heterostructures by gas-phase etching of germanium Garrett D. Cole,1,a Yu and selectively remove a sacrificial germanium Ge underlayer in a room temperature gas-phase etching procedure. We

  14. The role of gas phase reactions in the deflagration-to-detonation transition of high energy propellants

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

    The inadequacies of the two commonly used assumptions are shown, along with the need for considering gas phase reactions. Kinetic parameters that describe the gas phase reactions for several ingredients are provided, and the first steps in convective combustion leading to deflagration to detonation transition are described.

  15. Acid-Base Electronic Properties in the Gas Phase: Permanent Electric Dipole Moments of a Photoacidic Substrate.

    NASA Astrophysics Data System (ADS)

    Fleisher, Adam J.; Morgan, Philip J.; Pratt, David W.

    2009-06-01

    The permanent electric dipole moments of two conformers of 2-naphthol (2HN) in their ground and electronically excited states have been experimentally determined by Stark-effect measurements in a molecular beam. When in solution, 2HN is a weak base in the S{_0} state and a strong acid in the S{_1} state. Using sequential solvation of the cis-2HN photoacid with the base ammonia, we have begun to approach condensed phase acid-base interactions with gas phase rotational resolution. Our study, void of bulk solvent perturbations, is of importance to the larger community currently describing aromatic biomolecule and "super" photoacid behavior via theoretical modeling and condensed phase solvatochromism. [2] A. Weller. Prog. React. Kinet. 5, 273 (1970). [3] D. F. Plusquellic, X. -Q. Tan, and D. W. Pratt. J. Chem. Phys. 96, 8026 (1992).

  16. Gas-phase Oxygen Abundances and Radial Metallicity Gradients in the Two nearby Spiral Galaxies NGC 7793 and NGC 4945

    NASA Astrophysics Data System (ADS)

    Stanghellini, Letizia; Magrini, Laura; Casasola, Viviana

    2015-10-01

    Gas-phase abundances in H ii regions of two spiral galaxies, NGC 7793 and NGC 4945, have been studied to determine their radial metallicity gradients. We used the strong-line method to derive oxygen abundances from spectra acquired with GMOS-S, the multi-object spectrograph on the 8 m Gemini South telescope. We found that NGC 7793 has a well-defined gas-phase radial oxygen gradient of -0.321 ± 0.112 dex {R}25-1 (or -0.054 ± 0.019 dex kpc-1) in the galactocentric range 0.17 < RG/R25 < 0.82, not dissimilar from gradients calculated with direct abundance methods in galaxies of similar mass and morphology. We also determined a shallow radial oxygen gradient in NGC 4945, -0.253 ± 0.149 dex {R}25-1 (or -0.019 ± 0.011 dex kpc-1) for 0.04 < RG/R25 < 0.51, where the larger relative uncertainty derives mostly from the larger inclination of this galaxy. NGC 7793 and NGC 4945 have been selected for this study because they are similar, in mass and morphology, to M33 and the Milky Way, respectively. Since at zeroth order we expect the radial metallicity gradients to depend on mass and galaxy type, we compared our galaxies in the framework of radial metallicity models best suited for M33 and the Galaxy. We found a good agreement between M33 and NGC 7793, pointing toward similar evolution for the two galaxies. We notice instead differences between NGC 4945 and the radial metallicity gradient model that best fits the Milky Way. We found that these differences are likely related to the presence of an active galactic nucleus combined with a bar in the central regions of NGC 4945, and to its interacting environment.

  17. Design and characterization of a smog chamber for studying gas-phase chemical mechanisms and aerosol formation

    NASA Astrophysics Data System (ADS)

    Wang, X.; Liu, T.; Bernard, F.; Ding, X.; Wen, S.; Zhang, Y.; Zhang, Z.; He, Q.; Lü, S.; Chen, J.; Saunders, S.; Yu, J.

    2014-01-01

    We describe here characterization of a new state-of-the-art smog chamber facility for studying atmospheric gas-phase and aerosol chemistry. The chamber consists of a 30 m3 fluorinated ethylene propylene (FEP) Teflon film reactor housed in a temperature-controlled enclosure equipped with black lamps as the light source. Temperature can be set in the range from -10 to 40 °C at accuracy of ±1 °C as measured by eight temperature sensors inside the enclosure and one just inside the reactor. Matrix air can be purified with non-methane hydrocarbons (NMHCs) < 0.5 ppb, NOx/O3/carbonyls < 1 ppb and particles < 1 cm-3. The photolysis rate of NO2 is adjustable between 0 and 0.49 min-1. At 298 K under dry conditions, the average wall loss rates of NO, NO2 and O3 were measured to be 1.41 × 10-4 min-1, 1.39 × 10-4 min-1 and 1.31 × 10-4 min-1, respectively, and the particle number wall loss rate was measured to be 0.17 h-1. Auxiliary mechanisms of this chamber are determined and included in the Master Chemical Mechanism to evaluate and model propene-NOx-air irradiation experiments. The results indicate that this new smog chamber can provide high-quality data for mechanism evaluation. Results of ?-pinene dark ozonolysis experiments revealed secondary organic aerosol (SOA) yields comparable to those from other chamber studies, and the two-product model gives a good fit for the yield data obtained in this work. Characterization experiments demonstrate that our Guangzhou Institute of Geochemistry, Chinese Academy Sciences (GIG-CAS), smog chamber facility can be used to provide valuable data for gas-phase chemistry and secondary aerosol formation.

  18. Gas-phase saturation and evaporative cooling effects during wet compression of a fuel aerosol under RCM conditions

    SciTech Connect

    Goldsborough, S.S.; Johnson, M.V.; Zhu, G.S.; Aggarwal, S.K.

    2011-01-15

    Wet compression of a fuel aerosol has been proposed as a means of creating gas-phase mixtures of involatile diesel-representative fuels and oxidizer + diluent gases for rapid compression machine (RCM) experiments. The use of high concentration aerosols (e.g., {proportional_to}0.1 mL{sub fuel}/L{sub gas}, {proportional_to}1 x 10{sup 9} droplets/L{sub gas} for stoichiometric fuel loading at ambient conditions) can result in droplet-droplet interactions which lead to significant gas-phase fuel saturation and evaporative cooling during the volumetric compression process. In addition, localized stratification (i.e., on the droplet scale) of the fuel vapor and of temperature can lead to non-homogeneous reaction and heat release processes - features which could prevent adequate segregation of the underlying chemical kinetic rates from rates of physical transport. These characteristics are dependent on many factors including physical parameters such as overall fuel loading and initial droplet size relative to the compression rate, as well as fuel and diluent properties such as the boiling curve, vaporization enthalpy, heat capacity, and mass and thermal diffusivities. This study investigates the physical issues, especially fuel saturation and evaporative cooling effects, using a spherically-symmetric, single-droplet wet compression model. n-Dodecane is used as the fuel with the gas containing 21% O{sub 2} and 79% N{sub 2}. An overall compression time and compression ratio of 15.3 ms and 13.4 are used, respectively. It is found that smaller droplets (d{sub 0}{proportional_to} 2-3 {mu}m) are more affected by 'far-field' saturation and cooling effects, while larger droplets (d{sub 0}{proportional_to} 14 {mu}m) result in greater localized stratification of the gas-phase due to the larger diffusion distances for heat and mass transport. Vaporization of larger droplets is more affected by the volumetric compression process since evaporation requires more time to be completed even at the same overall fuel loading. All of the cases explored here yield greater compositional stratification than thermal stratification due to the high Lewis numbers of the fuel-air mixtures (Le{sub g} {proportional_to} 3.8). (author)

  19. Lysosomal dysfunction in a mouse model of Sandhoff disease leads to accumulation of ganglioside-bound amyloid-? peptide.

    PubMed

    Keilani, Serene; Lun, Yi; Stevens, Anthony C; Williams, Hadis N; Sjoberg, Eric R; Khanna, Richie; Valenzano, Kenneth J; Checler, Frederic; Buxbaum, Joseph D; Yanagisawa, Katsuhiko; Lockhart, David J; Wustman, Brandon A; Gandy, Sam

    2012-04-11

    Alterations in the lipid composition of endosomal-lysosomal membranes may constitute an early event in Alzheimer's disease (AD) pathogenesis. In this study, we investigated the possibility that GM2 ganglioside accumulation in a mouse model of Sandhoff disease might be associated with the accumulation of intraneuronal and extracellular proteins commonly observed in AD. Our results show intraneuronal accumulation of amyloid-? peptide (A?)-like, ?-synuclein-like, and phospho-tau-like immunoreactivity in the brains of ?-hexosaminidase knock-out (HEXB KO) mice. Biochemical and immunohistochemical analyses confirmed that at least some of the intraneuronal A?-like immunoreactivity (iA?-LIR) represents amyloid precursor protein C-terminal fragments (APP-CTFs) and/or A?. In addition, we observed increased levels of A?40 and A?42 peptides in the lipid-associated fraction of HEXB KO mouse brains, and intraneuronal accumulation of ganglioside-bound A? (GA?) immunoreactivity in a brain region-specific manner. Furthermore, ?-synuclein and APP-CTFs and/or A? were found to accumulate in different regions of the substantia nigra, indicating different mechanisms of accumulation or turnover pathways. Based on the localization of the accumulated iA?-LIR to endosomes, lysosomes, and autophagosomes, we conclude that a significant accumulation of iA?-LIR may be associated with the lysosomal-autophagic turnover of A? and fragments of APP-containing A? epitopes. Importantly, intraneuronal GA? immunoreactivity, a proposed prefibrillar aggregate found in AD, was found to accumulate throughout the frontal cortices of postmortem human GM1 gangliosidosis, Sandhoff disease, and Tay-Sachs disease brains. Together, these results establish an association between the accumulation of gangliosides, autophagic vacuoles, and the intraneuronal accumulation of proteins associated with AD. PMID:22496568

  20. Determination of gas phase protein ion densities via ion mobility analysis with charge reduction.

    PubMed

    Maisser, Anne; Premnath, Vinay; Ghosh, Abhimanyu; Nguyen, Tuan Anh; Attoui, Michel; Hogan, Christopher J

    2011-12-28

    We use a charge reduction electrospray (ESI) source and subsequent ion mobility analysis with a differential mobility analyzer (DMA, with detection via both a Faraday cage electrometer and a condensation particle counter) to infer the densities of single and multiprotein ions of cytochrome C, lysozyme, myoglobin, ovalbumin, and bovine serum albumin produced from non-denaturing (20 mM aqueous ammonium acetate) and denaturing (1?:?49.5?:?49.5, formic acid?:?methanol?:?water) ESI. Charge reduction is achieved through use of a Po-210 radioactive source, which generates roughly equal concentrations of positive and negative ions. Ions produced by the source collide with and reduce the charge on ESI generated drops, preventing Coulombic fissions, and unlike typical protein ESI, leading to gas-phase protein ions with +1 to +3 excess charges. Therefore, charge reduction serves to effectively mitigate any role that Coulombic stretching may play on the structure of the gas phase ions. Density inference is made via determination of the mobility diameter, and correspondingly the spherical equivalent protein volume. Through this approach it is found that for both non-denaturing and denaturing ESI-generated ions, gas-phase protein ions are relatively compact, with average densities of 0.97 g cm(-3) and 0.86 g cm(-3), respectively. Ions from non-denaturing ESI are found to be slightly more compact than predicted from the protein crystal structures, suggesting that low charge state protein ions in the gas phase are slightly denser than their solution conformations. While a slight difference is detected between the ions produced with non-denaturing and denaturing ESI, the denatured ions are found to be much more dense than those examined previously by drift tube mobility analysis, in which charge reduction was not employed. This indicates that Coulombic stretching is typically what leads to non-compact ions in the gas-phase, and suggests that for gas phase measurements to be correlated to biomolecular structures in solution, low charge state ions should be analyzed. Further, to determine if different solution conditions give rise to ions of different structure, ions of similar charge state should be compared. Non-denatured protein ion densities are found to be in excellent agreement with non-denatured protein ion densities inferred from prior DMA and drift tube measurements made without charge reduction (all ions with densities in the 0.85-1.10 g cm(-3) range), showing that these ions are not strongly influenced by Coulombic stretching nor by analysis method. PMID:22073403

  1. Antimicrobial Peptides

    PubMed Central

    Bahar, Ali Adem; Ren, Dacheng

    2013-01-01

    The rapid increase in drug-resistant infections has presented a serious challenge to antimicrobial therapies. The failure of the most potent antibiotics to kill “superbugs” emphasizes the urgent need to develop other control agents. Here we review the history and new development of antimicrobial peptides (AMPs), a growing class of natural and synthetic peptides with a wide spectrum of targets including viruses, bacteria, fungi, and parasites. We summarize the major types of AMPs, their modes of action, and the common mechanisms of AMP resistance. In addition, we discuss the principles for designing effective AMPs and the potential of using AMPs to control biofilms (multicellular structures of bacteria embedded in extracellular matrixes) and persister cells (dormant phenotypic variants of bacterial cells that are highly tolerant to antibiotics). PMID:24287494

  2. Probability-Based Pattern Recognition and Statistical Framework for Randomization: Modeling Tandem Mass Spectrum/Peptide Sequence False Match Frequencies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Estimating and controlling the frequency of false matches between a peptide tandem mass spectrum and candidate peptide sequences is an issue pervading proteomics research. To solve this problem, we designed an unsupervised pattern recognition algorithm for detecting patterns with various lengths fr...

  3. Vibrational signatures of sodiated oligopeptides (GG-Na+, GGG-Na+, AA-Na+ and AAA-Na+) in the gas phase

    NASA Astrophysics Data System (ADS)

    Balaj, O. P.; Kapota, C.; Lemaire, J.; Ohanessian, G.

    2008-02-01

    The structures of the sodium complexes of oligoglycines (GG-Na+, GGG-Na+) and oligoalanines (AA-Na+, AAA-Na+) have been studied by infrared spectroscopy in the gas phase. Two different experimental set-ups have been used to generate, trap and analyze the ions. In the first, the complexes were generated by MALDI and analyzed in the cell of a home built FT-ICR mass spectrometer. In the second an external electrospray source was coupled to a Paul type ion trap. Following their trapping, the ions are irradiated in both cases with intense, tunable infrared light in the 1000-2000 cm-1 range, leading to sodium ion detachment and ion fragmentation via the absorption of multiple photons. The resulting experimental spectra are compared to theoretical linear absorption spectra to assign structures. In agreement with calculations, peptide attachment to Na+ is found to have a strong structuring effect: the lowest energy structures involve binding of all carbonyl oxygens to the cation. Detailed comparison of experimental and computed spectra shows that the IRMPD spectroscopy of such gaseous ions allows the differentiation between structures which do not have the same number of carbonyl oxygens bound to Na+, and structures in which the peptide is either wrapped around the ion or capped by it.

  4. Copper(II)-bis-histidine coordination structure in a fibrillar amyloid ?-peptide fragment and model complexes revealed by electron spin echo envelope modulation spectroscopy.

    PubMed

    Hernández-Guzmán, Jessica; Sun, Li; Mehta, Anil K; Dong, Jijun; Lynn, David G; Warncke, Kurt

    2013-09-23

    Truncated and mutated amyloid-? (A?) peptides are models for systematic study-in homogeneous preparations-of the molecular origins of metal ion effects on A? aggregation rates, types of aggregate structures formed, and cytotoxicity. The 3D geometry of bis-histidine imidazole coordination of Cu(II) in fibrils of the nonapetide acetyl-A?(13-21)H14A has been determined by powder (14) N electron spin echo envelope modulation (ESEEM) spectroscopy. The method of simulation of the anisotropic combination modulation is described and benchmarked for a Cu(II) -bis-cis-imidazole complex of known structure. The revealed bis-cis coordination mode, and the mutual orientation of the imidazole rings, for Cu(II) in Ac-A?(13-21)H14A fibrils are consistent with the proposed ?-sheet structural model and pairwise peptide interaction with Cu(II) , with an alternating [-metal-vacancy-]n pattern, along the N-terminal edge. Metal coordination does not significantly distort the intra-?-strand peptide interactions, which provides a possible explanation for the acceleration of Ac-A?(13-21)H14A fibrillization by Cu(II) , through stabilization of the associated state and low-reorganization integration of ?-strand peptide pair precursors. PMID:24014287

  5. Intraperitoneal Administration of a Novel TAT-BDNF Peptide Ameliorates Cognitive Impairments via Modulating Multiple Pathways in Two Alzheimer’s Rodent Models

    PubMed Central

    Wu, Yuanyuan; Luo, Xiaobin; Liu, Xinhua; Liu, Deyi; Wang, Xiong; Guo, Ziyuan; Zhu, Lingqiang; Tian, Qing; Yang, Xifei; Wang, Jian-Zhi

    2015-01-01

    Although Alzheimer’s disease (AD) has been reported for more than 100 years, there is still a lack of effective cures for this devastating disorder. Among the various obstacles that hold back drug development, the blood-brain barrier (BBB) is one of them. Here, we constructed a novel fusion peptide by linking the active domain of brain-derived neurotrophic factor (BDNF) with an HIV-encoded transactivator of transcription (TAT) that has a strong membrane-penetrating property. After intraperitoneal injection, the eGFP-TAT could be robustly detected in different brain regions. By using scopolamine-induced rats and APPswe mice representing AD-like cholinergic deficits and amyloidosis, respectively, we found that intraperitoneal administration of the peptide significantly improved spatial memory with activation of the TrkB/ERK1/2/Akt pathway and restoration of several memory-associated proteins in both models. Administration of the peptide also modulated ?-amyloid and tau pathologies in APPswe mice, and it increased the amount of M receptor with modulation of acetylcholinesterase in scopolamine-induced rats. We conclude that intraperitoneal administration of our TAT-BDNF peptide could efficiently target multiple molecular pathways in the brain and improve the cognitive functions in AD-like rodent models. PMID:26463268

  6. Atmospheric oxidation of organic compounds: Gas-phase reactivity, gas-to-particle conversion, and particle aging

    NASA Astrophysics Data System (ADS)

    Sage, Amy M.

    The atmospheric oxidation of organic compounds has implications for both health and climate policy, In order to quantify these impacts, we must know the reactivity of organic pollutants throughout their atmospheric residence times. This reactivity encompasses both gas-phase and heterogeneous processes, carried out via complex radical reaction mechanisms, and involves more than 10,000 organic species. Creatively reducing the complexity of this system is a first-order priority in atmospheric chemistry. The work discussed here does that in the process of addressing three questions. In response to the need for large amounts of gas-phase kinetics data, a method is demonstrated that permits the extraction of the physical properties that control reactivity from experimental kinetics datasets. We demonstrate the strength of this method in extrapolating beyond measured temperature ranges and species. In response to observations that condensed-phase organic mass in the atmosphere dramatically exceeds expected values, we show that the consideration of a single additional molecular property can have profound influences on those expectations. By considering species volatility in addition to atmospheric abundance we can improve the agreement between models and measurements and chemical analysis verifies that this improvement is correct. In response to the need to study atmospheric particle chemistry in the laboratory, we have developed methods to examine long timescale chemistry in complex mixtures. These methods show that the reactivity of compounds in atmospheric particles is a strong function of the composition of those particles. Taken together, the work described here advances both the methods used in and our understanding of atmospheric chemistry.

  7. Tandem differential mobility analysis-mass spectrometry reveals partial gas-phase collapse of the GroEL complex.

    PubMed

    Hogan, Christopher J; Ruotolo, Brandon T; Robinson, Carol V; Fernandez de la Mora, Juan

    2011-04-01

    A parallel-plate differential mobility analyzer and a time-of-flight mass spectrometer (DMA-MS) are used in series to measure true mobility in dry atmospheric pressure air for mass-resolved electrosprayed GroEL tetradecamers (14-mers; ~800 kDa). Narrow mobility peaks are found (2.6-2.9% fwhm); hence, precise mobilities can be obtained for these ions without collisional activation, just following their generation by electrospray ionization. In contrast to previous studies, two conformers are found with mobilities (Z) differing by ~5% at charge state z ~ 79. By extrapolating to small z, a common mobility/charge ratio Z(0)/z = 0.0117 cm(2) V(-1) s(-1) is found for both conformers. When interpreted as if the GroEL ion surface were smooth and the gas molecule-protein collisions were perfectly elastic and specular, this mobility yields an experimental collision cross section, ?, 11% smaller than in an earlier measurement, and close to the cross section, A(C,crystal), expected for the crystal structure (determined by a geometric approximation). However, the similarity between ? and A(C,crystal) does not imply a coincidence between the native and gas-phase structures. The nonideal nature of protein-gas molecule collisions introduces a drag enhancement factor, ? = 1.36, with which the true cross section A(C) is related to ? via A(C) = ?/?. Therefore, A(C) for GroEL 14-mer ions determined by DMA measurements is 0.69A(C,crystal). The factor 1.36 used here is based on the experimental Stokes-Millikan equation, as well as on prior and new numerical modeling accounting for multiple scattering events via exact hard-sphere scattering calculations. Therefore, we conclude that the gas-phase structure of the GroEL complex as electrosprayed is substantially more compact than the corresponding X-ray crystal structure. PMID:21395304

  8. Novel tracer method to measure isotopic labeled gas-phase nitrous acid (HO15NO) in biogeochemical studies.

    PubMed

    Wu, Dianming; Kampf, Christopher J; Pöschl, Ulrich; Oswald, Robert; Cui, Junfang; Ermel, Michael; Hu, Chunsheng; Trebs, Ivonne; Sörgel, Matthias

    2014-07-15

    Gaseous nitrous acid (HONO), the protonated form of nitrite, contributes up to ?60% to the primary formation of hydroxyl radical (OH), which is a key oxidant in the degradation of most air pollutants. Field measurements and modeling studies indicate a large unknown source of HONO during daytime. Here, we developed a new tracer method based on gas-phase stripping-derivatization coupled to liquid chromatography-mass spectrometry (LC-MS) to measure the 15N relative exceedance, ?(15N), of HONO in the gas-phase. Gaseous HONO is quantitatively collected and transferred to an azo dye, purified by solid phase extraction (SPE), and analyzed using high performance liquid chromatography coupled to mass spectrometry (HPLC-MS). In the optimal working range of ?(15N)=0.2-0.5, the relative standard deviation of ?(15N) is <4%. The optimum pH and solvents for extraction by SPE and potential interferences are discussed. The method was applied to measure HO15NO emissions from soil in a dynamic chamber with and without spiking 15) labeled urea. The identification of HO15NO from soil with 15N urea addition confirmed biogenic emissions of HONO from soil. The method enables a new approach of studying the formation pathways of HONO and its role for atmospheric chemistry (e.g., ozone formation) and environmental tracer studies on the formation and conversion of gaseous HONO or aqueous NO2- as part of the biogeochemical nitrogen cycle, e.g., in the investigation of fertilization effects on soil HONO emissions and microbiological conversion of NO2- in the hydrosphere. PMID:24954648

  9. (129) Xe and (131) Xe nuclear magnetic dipole moments from gas phase NMR spectra.

    PubMed

    Makulski, W?odzimierz

    2015-04-01

    (3) He, (129) Xe and (131) Xe NMR measurements of resonance frequencies in the magnetic field B0=11.7586?T in different gas phase mixtures have been reported. Precise radiofrequency values were extrapolated to the zero gas pressure limit. These results combined with new quantum chemical values of helium and xenon nuclear magnetic shielding constants were used to determine new accurate nuclear magnetic moments of (129) Xe and (131) Xe in terms of that of the (3) He nucleus. They are as follows: ?((129) Xe)?=?-0.7779607(158)?N and ?((131) Xe)?=?+0.6918451(70)?N . By this means, the new 'helium method' for estimations of nuclear dipole moments was successfully tested. Gas phase NMR spectra demonstrate the weak intermolecular interactions observed on the (3) He and (129) Xe and (131) Xe shielding in the gaseous mixtures with Xe, CO2 and SF6 . PMID:25594841

  10. Structure and bonding of isoleptic coinage metal (Cu, Ag, Au) dimethylaminonitrenes in the gas phase.

    PubMed

    Fedorov, Alexey; Couzijn, Erik P A; Nagornova, Natalia S; Boyarkin, Oleg V; Rizzo, Thomas R; Chen, Peter

    2010-10-01

    Dimethylaminonitrene complexes of IMesM(+) (IMes =1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene; M = Cu, Ag, Au) were prepared in the gas phase and structurally characterized by high-resolution infrared spectroscopy of the cold species, ion-molecule reactions, and DFT computations. We measured the binding energies of the nitrene fragment to the IMesM(+) moiety by energy-resolved collision-induced dissociation experiments in the gas phase, affording a trend in bond strength of M = Cu ? Au > Ag. This trend is explained in terms of a detailed metal-nitrogen bonding analysis, from which relativistic effects on the bonding were assessed. Various density functionals were evaluated for reproducing the observed thermochemical data and Truhlar's M06 functional was found to give the best agreement. PMID:20843043

  11. Fundamental studies of gas phase ionic reactions by ion mobility spectrometry

    NASA Technical Reports Server (NTRS)

    Giles, K.; Knighton, W. B.; Sahlstrom, K. E.; Grimsrud, E. P.

    1995-01-01

    Ion mobility spectrometry (IMS) provides a promising approach to the study of gas phase ionic reactions in buffer gases at unusually high pressures. This point is illustrated here by studies of the Sn2 nucleophilic displacement reaction, Cl(-) + CH3Br yields Br + CH3Br, using IMS at atmospheric pressure. The equilibrium clustering reaction, Cl(-)(CHCI3)(n - 1) + CHCI3 yields Cl(-)(CHCI3)(n), where n = 1 and 2, and the effect of clustering on the Sn2 reaction with CH3Br have also been characterized by this IMS-based kinetic method. Present problems and anticipated improvements in the application of ion mobility spectrometry to studies of other gas phase ionic processes are discussed.

  12. Electronic Spectrum of C7H3+ in the Gas Phase at 10 K

    NASA Astrophysics Data System (ADS)

    Rice, C. A.; Hardy, F.-X.; Gause, O.; Maier, J. P.

    2015-10-01

    The analysis of the ?5797.1 diffuse interstellar band (DIB) by Huang & Oka concludes that the carrier is a chain-like molecule with five to seven heavy atoms with a large oscillator strength, f ? 1, for the electronic transition. The spectra of carbon chains of this size with transitions in the visible have been obtained in the gas phase, but the f-values are too small. We have now found that certain carbon-chain cations with transitions in the DIB range have large f-values. An example is the origin band at 4387.7 Å of the 1 1A{}1 ?ftarrow X{ }1A1 electronic transition of the H2C7H+ chain with f ? 0.3. This could be measured in the gas phase at 10 K in an ion trap. Astrophysical relevance of such cations is discussed.

  13. Elusive Sulfurous Acid: Gas-Phase Basicity and IR Signature of the Protonated Species.

    PubMed

    Sinha, Rajeev K; Scuderi, Debora; Maitre, Philippe; Chiavarino, Barbara; Crestoni, Maria Elisa; Fornarini, Simonetta

    2015-05-01

    The ion corresponding to protonated sulfurous acid, H3SO3(+), has been successfully delivered into the gas phase by electrospray ionization of the solution of a suitable precursor and an in-source fragmentation process. The neutral acid is a highly elusive molecule. However, its gas-phase basicity has been ascertained by means of a kinetic study of proton-transfer reactivity. The structure of the H3SO3(+) sampled ion has been probed by IRMPD spectroscopy in two complementary IR frequency ranges in conjunction with density functional theory calculations and found to conform to a trihydroxosulfonium ion. The characteristic IR signatures may aid in deciphering the presence of this species in extraterrestrial atmospheres. PMID:26263321

  14. Optical properties of Yb-doped fibers prepared by gas phase doping

    NASA Astrophysics Data System (ADS)

    Lindner, F.; Aichele, C.; Schwuchwo, A.; Leich, M.; Scheffel, A.; Unger, S.

    2014-03-01

    The active core diameter in silica preforms can be significantly increased by the deposition of ytterbium (Yb) and the most important codopant aluminum (Al) in the gas phase through the high-temperature evaporation of an Yb chelate compound and Al chloride in the Modified Chemical Vapor Deposition (MCVD) process. Here, we report on systematic investigations of the incorporation of Yb and Al into silica by gas phase doping technique. Preforms and fibers were prepared in a wide range of Yb and Al concentrations. The samples were characterized concerning the radial distribution of the refractive index and dopant concentrations, the efficiency of the deposition, and the absorption and emission properties in the NIR region. First laser experiments have demonstrated a slope efficiency of 80%, which is comparable to fibers made by MCVD/ solution doping and powder sinter technology.

  15. Targeting a Cross-Reactive Gly m 5 Soy Peptide as Responsible for Hypersensitivity Reactions in a Milk Allergy Mouse Model

    PubMed Central

    Curciarello, Renata; Smaldini, Paola L.; Candreva, Angela M.; González, Virginia; Parisi, Gustavo; Cauerhff, Ana; Barrios, Ivana; Blanch, Luis Bruno; Fossati, Carlos A.

    2014-01-01

    Background Cross-reactivity between soybean allergens and bovine caseins has been previously reported. In this study we aimed to map epitopes of the major soybean allergen Gly m 5 that are co-recognized by casein specific antibodies, and to identify a peptide responsible for the cross-reactivity. Methods Cow's milk protein (CMP)-specific antibodies were used in different immunoassays (immunoblotting, ELISA, ELISA inhibition test) to evaluate the in vitro recognition of soybean proteins (SP). Recombinant Gly m 5 (?), a truncated fragment containing the C-terminal domain (?-T) and peptides of ?-T were obtained and epitope mapping was performed with an overlapping peptide assay. Bioinformatics tools were used for epitope prediction by sequence alignment, and for modelling the cross-recognized soy proteins and peptides. The binding of SP to a monoclonal antibody was studied by surface Plasmon resonance (SPR). Finally, the in vivo cross-recognition of SP was assessed in a mouse model of milk allergy. Results Both ? and ?-T reacted with the different CMP-specific antibodies. ?-T contains IgG and IgE epitopes in several peptides, particularly in the peptide named PA. Besides, we found similar values of association and dissociation constants between the ?-casein specific mAb and the different milk and soy components. The food allergy mouse model showed that SP and PA contain the cross-reactive B and T epitopes, which triggered hypersensitivity reactions and a Th2-mediated response on CMP-sensitized mice. Conclusions Gly m 5 is a cross-reactive soy allergen and the ?-T portion of the molecule contains IgG and IgE immunodominant epitopes, confined to PA, a region with enough conformation to be bound by antibodies. These findings contribute to explain the intolerance to SP observed in IgE-mediated CMA patients, primarily not sensitised to SP, as well as it sets the basis to propose a mucosal immunotherapy for milk allergy using this soy peptide. PMID:24416141

  16. a Nucleoside Under Observation in the Gas Phase: a Rotational Study of Uridine

    NASA Astrophysics Data System (ADS)

    Peña, Isabel; Alonso, José L.

    2014-06-01

    The nucleoside of uridine has been placed in the gas phase by laser ablation and the most stable C2{'}-anti conformation characterized by broadband chirped pulse (CP-FTMW) and narrowband molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopies. The quadrupole hyperfine structure, originated by two 14N nuclei, has been completely resolved. Intramolecular hydrogen bonds involving uracil and ribose moieties have been found to play an important role in the stabilization of the nucleoside.

  17. {HIGH Resolution Electronic Spectroscopy of 2,6-DIAMINOPYRIDINE in the Gas PHASE}

    NASA Astrophysics Data System (ADS)

    Clements, Casey L.; Fleisher, Adam J.; Young, Justin W.; Thomas, Jessica A.; Pratt, David W.

    2009-06-01

    Ab initio calculations suggest that 2,6-diaminopyridine (26DAP) has several interesting low-frequency vibrations arising from motion of its amino groups. For this reason, 26DAP has been studied in the gas phase using both low resolution and high resolution electronic spectroscopy techniques. Presented here are the results of this study, which provide information about the structural and dynamical properties of 26DAP in both the ground and excited electronic states. The results will be discussed. footnote

  18. Method and apparatus for selective capture of gas phase analytes using metal .beta.-diketonate polymers

    SciTech Connect

    Harvey, Scott D

    2011-06-21

    A process and sensor device are disclosed that employ metal .beta.-diketonate polymers to selectively capture gas-phase explosives and weaponized chemical agents in a sampling area or volume. The metal .beta.-diketonate polymers can be applied to surfaces in various analytical formats for detection of: improvised explosive devices, unexploded ordinance, munitions hidden in cargo holds, explosives, and chemical weapons in public areas.

  19. Gas-phase UF/sub 6/ enrichment monitor for enrichment plant safeguards

    SciTech Connect

    Strittmatter, R.B.; Tape, J.W.

    1980-03-01

    An in-line enrichment monitor is being developed to provide real-time enrichment data for the gas-phase UF/sub 6/ feed stream of an enrichment plant. The nondestructive gamma-ray assay method can be used to determine the enrichment of natural UF/sub 6/ with a relative precision of better than 1% for a wide range of pressures.

  20. Gas phase heterogeneous catalytic oxidation of alkanes to aliphatic ketones and/or other oxygenates

    DOEpatents

    Lin, Manhua; Wang, Xiang; Yeom, Younghoon

    2015-09-29

    A catalyst, its method of preparation and its use for producing aliphatic ketones by subjecting alkanes C.sub.3 to C.sub.9 to a gas phase catalytic oxidation in the presence of air or oxygen, and, optionally, steam and/or one or more diluting gases. The catalyst comprises a catalytically active mixed metal oxide phase and a suitable support material onto and/or into which the active catalytic phase is dispersed.

  1. Gas phase heterogeneous catalytic oxidation of alkanes to aliphatic ketones and/or other oxygenates

    SciTech Connect

    Lin, Manhua; Wang, Xiang; Yeom, Younghoon

    2015-03-17

    A catalyst, its method of preparation and its use for producing aliphatic ketones by subjecting alkanes C.sub.3 to C.sub.9 to a gas phase catalytic oxidation in the presence of air or oxygen, and, optionally, steam and/or one or more diluting gases. The catalyst comprises a catalytically active mixed metal oxide phase and a suitable support material onto and/or into which the active catalytic phase id dispersed.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  3. GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

    SciTech Connect

    HALL, G.E.

    2006-05-30

    This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

  4. Atmospheric and indoor chemistry of gas-phase indole, quinoline, and isoquinoline

    NASA Astrophysics Data System (ADS)

    Atkinson, Roger; Tuazon, Ernesto C.; Arey, Janet; Aschmann, Sara M.

    The gas-phase chemistry of the nitrogen-containing organic compounds indole, quinoline and isoquinoline, which are present in environmental tobacco smoke, has been investigated. No photolysis of these nitrogen heterocycles was observed under indoor "white" fluorescent lighting conditions. Rate constants for the gas-phase reactions of these compounds with OH radicals, NO 3 radicals, NO 2, and O 3 were measured, and the rate constants obtained (in cm 3 molecule -1s -1 units) were: for reaction with the OH radical: indole, (1.54 ± 0.35) × 10 -10; quinoline, (1.16 ± 0.55) × 10 -11; isoquinoline, (8.5 ± 3.6) × 10 -12; for reaction with the NO 3 radical: indole, (1.3 ± 0.5) × 10 -10; for reaction with NO 2: indole,< 2 × 10 -19; quinoline, < 1.6 × 10 -20; isoquinoline,< 1.1 × 10 and for reaction with O 3: indole, (4.9 ± 1.8) × 10 -17; quinoline, < 1.0 × 10 -19; and isoquinoline, < 1.1 × 10 -19. Evidence was obtained that quinoline reacts with gas-phase nitric acid and this is also expected to be the case for isoquinoline. These data indicate that in indoor environments, quinoline and isoquinoline will be largely removed by air exchange unless gas-phase nitric acid is present, while indole will be removed by chemical reaction if NO 3 radicals are present at part-per-trillion levels. Products of the O 3 and OH radical reactions with indole have been studied and the possible O 3 reaction mechanism is discussed.

  5. Comparison of ozone determinations by ultraviolet photometry and gas-phase titration

    NASA Technical Reports Server (NTRS)

    Demore, W. B.; Patapoff, M.

    1976-01-01

    A comparison of ozone determinations based on ultraviolet absorption photometry and gas-phase titration (GPT) shows good agreement between the two methods. Together with other results, these findings indicate that three candidate reference methods for ozone, UV photometry, IR photometry, and GPT are in substantial agreement. However, the GPT method is not recommended for routine use by air pollution agencies for calibration of ozone monitors because of susceptibility to experimental error.

  6. Shear viscosity of neutron-rich nucleonic matter near its liquid-gas phase transition

    E-print Network

    Jun Xu; Lie-Wen Chen; Che Ming Ko; Bao-An Li; Yu-Gang Ma

    2013-09-26

    Within a relaxation time approach using free nucleon-nucleon cross sections modified by the in-medium nucleon masses that are determined from an isospin- and momentum-dependent effective nucleon-nucleon interaction, we investigate the specific shear viscosity ($\\eta/s$) of neutron-rich nucleonic matter near its liquid-gas phase transition. It is found that as the nucleonic matter is heated at fixed pressure or compressed at fixed temperature, its specific shear viscosity shows a valley shape in the temperature or density dependence, with the minimum located at the boundary of the phase transition. Moreover, the value of $\\eta/s$ drops suddenly at the first-order liquid-gas phase transition temperature, reaching as low as $4\\sim5$ times the KSS bound of $\\hbar/4\\pi$. However, it varies smoothly for the second-order liquid-gas phase transition. Effects of the isospin degree of freedom and the nuclear symmetry energy on the value of $\\eta/s$ are also discussed.

  7. Gas-Phase Oxidation, Particle Uptake, and Product Studies of Isoprene Epoxydiols

    NASA Astrophysics Data System (ADS)

    Bates, K. H.; Nguyen, T. B.; St Clair, J. M.; Crounse, J.; Zhang, X.; Coggon, M.; Schwantes, R.; Bennett, N.; Stoltz, B.; Wennberg, P. O.; Seinfeld, J.

    2013-12-01

    Isoprene epoxydiols (IEPOX), discovered in 2009 as low-NOx atmospheric oxidation products of the ubiquitous biogenic precursor isoprene, are key intermediates in the formation of secondary organic aerosol (SOA) from biogenic emissions. Recent studies carried out in the Caltech environmental chambers have elucidated the gas-phase OH oxidation rates and products, particle uptake rates, and particle-phase OH oxidation products of three isomers of IEPOX synthesized in-house. Gas-phase oxidation studies were conducted in 1 m3 chambers at both high- and low-NOx conditions, and were monitored by GC-FID, two types of chemical ionization mass spectrometry (CIMS), and GC-CIMS. Comparisons with previous studies on isoprene showed that the two ?-IEPOX isomers dominate over the ? isomers under atmospheric conditions, and the use of propene as an internal standard provided a robust estimate of OH oxidation rates between 0.99*10-11 and 1.67*10-11 cm3molec-1s-1 for the three isomers. Particle uptake and oxidation studies were conducted in 28 m3 chambers, and were monitored by GC-FID, CIMS, an aerosol mass spectrometer (AMS), and a differential mobility analyzer (DMA). Particle uptake showed a strong dependence on humidity, with no uptake on dry seed, and was faster on ammonium sulfate seed than sodium chloride seed. Particle-phase oxidation gave similar products to gas-phase oxidation by OH radicals.

  8. Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations.

    PubMed

    Aziz, Saadullah G; Osman, Osman I; Elroby, Shaaban A; Hilal, Rifaat H

    2015-01-01

    The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I) and imidazole-5-acetic (II) acids was monitored using the traditional hybrid functional (B3LYP) and the long-range corrected functionals (CAM-B3LYP and ?B97XD) with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital-Lowest Unoccupied Molecular Orbital (HOMO-LUMO) energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750-0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8??*O14-H15). This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS), TS1 and TS2, having energy barriers of 47.67-49.92 and 49.55-52.69 kcal/mol, respectively, and an sp³-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed. PMID:26556336

  9. Acid-catalysed glucose dehydration in the gas phase: a mass spectrometric approach.

    PubMed

    Ricci, Andreina; Di Rienzo, Brunella; Pepi, Federico; Troiani, Anna; Garzoli, Stefania; Giacomello, Pierluigi

    2015-01-01

    Understanding on a molecular level the acid-catalysed decomposition of the sugar monomers from hemicellulose and cellulose (e.g.?glucose, xylose), the main constituent of lignocellulosic biomass is very important to increase selectivity and reaction yields in solution, key steps for the development of a sustainable renewable industry. In this work we reported a gas-phase study performed by electrospray triple quadrupole mass spectrometry on the dehydration mechanism of D-glucose. In the gas phase, reactant ions corresponding to protonated D-glucose were obtained in the ESI source and were allowed to undergo collisionally activated decomposition (CAD) into the quadrupole collision cell. The CAD mass spectrum of protonated D-glucose is characterized by the presence of ionic dehydrated daughter ion (ionic intermediates and products), which were structurally characterized by their fragmentation patterns. In the gas phase D-glucose dehydration does not lead to the formation of protonated 5-hydroxymethyl-2-furaldehyde, but to a mixed population of m/z 127 isomeric ions. To elucidate the D-glucose dehydration mechanism, 3-O-methyl-D-glucose was also submitted to the mass spectrometric study; the results suggest that the C3 hydroxyl group plays a key role in the reaction mechanism. Furthermore, protonated levulinic acid was found to be formed from the monodehydrated D-glucose ionic intermediate, an alternative pathway other than the known route consisting of 5-hydroxymethyl-2-furaldehyde double hydration. PMID:25601697

  10. The ?-Effect and Competing Mechanisms: The Gas-Phase Reactions of Microsolvated Anions with Methyl Formate

    NASA Astrophysics Data System (ADS)

    Thomsen, Ditte L.; Nichols, Charles M.; Reece, Jennifer N.; Hammerum, Steen; Bierbaum, Veronica M.

    2013-12-01

    The enhanced reactivity of ?-nucleophiles, which contain an electron lone pair adjacent to the reactive site, has been demonstrated in solution and in the gas phase and, recently, for the gas-phase SN2 reactions of the microsolvated HOO-(H2O) ion with methyl chloride. In the present work, we continue to explore the significance of microsolvation on the ?-effect as we compare the gas-phase reactivity of the microsolvated ?-nucleophile HOO-(H2O) with that of microsolvated normal alkoxy nucleophiles, RO-(H2O), in reactions with methyl formate, where three competing reactions are possible. The results reveal enhanced reactivity of HOO-(H2O) towards methyl formate, and clearly demonstrate the presence of an overall ?-effect for the reactions of the microsolvated ?-nucleophile. The association of the nucleophiles with a single water molecule significantly lowers the degree of proton abstraction and increases the SN2 and BAC2 reactivity compared with the unsolvated analogs. HOO-(H2O) reacts with methyl formate exclusively via the BAC2 channel. While microsolvation lowers the overall reaction efficiency, it enhances the BAC2 reaction efficiency for all anions compared with the unsolvated analogs. This may be explained by participation of the solvent water molecule in the BAC2 reaction in a way that continuously stabilizes the negative charge throughout the reaction.

  11. Theoretical insight into the conversion of xylose to furfural in the gas phase and water.

    PubMed

    Wang, Meng; Liu, Chao; Li, Qibin; Xu, Xiaoxiao

    2015-11-01

    Furfural (FF) is a valuable ring-containing organic compound in the decomposition of xylose and can be produced massively in hydrothermal condition. In this study, density functional theory (DFT) methods are employed to investigate the formation mechanism of FF from xylose and the solvent effects on FF formation. Kinetic and thermodynamic analyses indicate that xylulose could be the intermediate that leads to the formation of FF in the gas phase and water. The formation of xylulose is initiated by a six-membered transition state with energy barriers of 163.6 and 150.8 kJ mol(-1) in the gas phase and water, respectively. It is found that the strong stabilization of the reactants and transition states and the overall energy barriers of formation pathways of FF are reduced in water. The formation of FF is more thermodynamically favored in water compared with that in the gas phase. In addition, the inclusion of an explicit water molecule transforms four-membered transition states of ring-opening reaction, hydrogenation-cyclization, and dehydrations into less distorted six-membered transition states, which leads to the significant reduction of reaction barriers of FF formation. PMID:26518688

  12. Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations

    PubMed Central

    Aziz, Saadullah G.; Osman, Osman I.; Elroby, Shaaban A.; Hilal, Rifaat H.

    2015-01-01

    The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I) and imidazole-5-acetic (II) acids was monitored using the traditional hybrid functional (B3LYP) and the long-range corrected functionals (CAM-B3LYP and ?B97XD) with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital–Lowest Unoccupied Molecular Orbital (HOMO–LUMO) energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750–0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8??*O14–H15). This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS), TS1 and TS2, having energy barriers of 47.67–49.92 and 49.55–52.69 kcal/mol, respectively, and an sp3-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed. PMID:26556336

  13. Accurate Benchmark Calculations on the Gas-Phase Basicities of Small Molecules

    PubMed Central

    He, Xiao; Fusti-Molnar, Laszlo; Merz, Kenneth M.

    2009-01-01

    Accurate benchmark calculations of gas-phase basicities of small molecules are presented and compared with available experimental results. The optimized geometries and thermochemical analyses were obtained from MP2/aug-cc-pVTZ calculations. Two different ab initio electron-correlated methods MP2 and CCSD(T) were employed for subsequent gas-phase basicity calculations and the single point energies were extrapolated to the complete basis set (CBS) limit. The overall accuracy for different ab initio methods are compared and the accuracy in descending order is CCSD(T)_CBS > CCSD(T)/aug-cc-pVDZ > (MP2/aug-cc-pVQZ ? MP2_CBS) > HF/ aug-cc-pVQZ. The best root-mean-squared-error obtained was 1.0 kcal mol?1 at the CCSD(T)_CBS//MP2/aug-cc-pVTZ level for a test set of 41 molecules. Clearly, accurate calculations for the electron correlation energy are important for the theoretical prediction of molecular gas-phase basicities. However, conformational effects were also found to be relevant in several instances when more complicated molecules were examined. PMID:19694482

  14. Thermodynamic analysis of fuels in gas phase: ethanol, gasoline and ethanol - gasoline predicted by DFT method.

    PubMed

    Neto, A F G; Lopes, F S; Carvalho, E V; Huda, M N; Neto, A M J C; Machado, N T

    2015-10-01

    This paper presents a theoretical study using density functional theory to calculate thermodynamics properties of major molecules compounds at gas phase of fuels like gasoline, ethanol, and gasoline-ethanol mixture in thermal equilibrium on temperature range up to 1500 K. We simulated a composition of gasoline mixture with ethanol for a thorough study of thermal energy, enthalpy, Gibbs free energy, entropy, heat capacity at constant pressure with respect to temperature in order to study the influence caused by ethanol as an additive to gasoline. We used semi-empirical computational methods as well in order to know the efficiency of other methods to simulate fuels through this methodology. In addition, the ethanol influence through the changes in percentage fractions of chemical energy released in combustion reaction and the variations on thermal properties for autoignition temperatures of fuels was analyzed. We verified how ethanol reduces the chemical energy released by gasoline combustion and how at low temperatures the gas phase fuels in thermal equilibrium have similar thermodynamic behavior. Theoretical results were compared with experimental data, when available, and showed agreement. Graphical Abstract Thermodynamic analysis of fuels in gas phase. PMID:26386958

  15. Peptides: Bicycling into cells

    NASA Astrophysics Data System (ADS)

    Liskamp, Rob M. J.

    2014-10-01

    Bicyclic peptides that are cell-permeable and can inhibit an intracellular target have been developed. These peptides consist of two rings: one enables the peptide to pass through the membrane, the other can inhibit the target.

  16. Aerosol and gas-phase characteristics in relation to meteorology: Case studies in populated arid settings

    NASA Astrophysics Data System (ADS)

    Crosbie, Ewan Colin

    Atmospheric aerosols and trace gases are a highly relevant component of the climate system affecting atmospheric radiative transfer and the hydrologic cycle. In arid and semi-arid regions, where cloud cover is often low and precipitation is generally scarce and sporadic, the driving processes accounting for the production, loss and transport of atmospheric constituents are often distinctly different from other climates. In arid regions, the same circulation dynamics that suppress cloud formation can be responsible for creating strong subsidence inversions, which cap atmospheric mixing and trap pollutants close to the surface, often placing populated arid regions high on global rankings of air pollution concerns. In addition, low soil moisture can encourage wind-blown dust emissions, which can be a significant fraction of the total aerosol loading in both coarse and fine modes on a mass basis. Three distinct focus regions are investigated over varying time scales, using a diverse set of techniques, and with wide-ranging primary goals. 1) the Tehran metropolitan area in Iran over a ten-year period from 2000-2009, 2) Tucson, Arizona over 2012-2014 with three intensive monitoring periods during summer 2014 and winter 2015 and 3) the San Joaquin Valley in California during the NASA DISCOVER-AQ campaign during Jan-Feb 2013. However, in all cases, local and regional scale meteorology play a significant role in controlling the spatiotemporal variability in trace gas and aerosol concentrations. Particular emphasis is placed on understanding transport pathways due to the local wind patterns and the importance of key meteorological parameters such as temperature, humidity and solar radiation on controlling production and loss mechanisms. While low in magnitude, the precipitation pattern is still an important sink mechanism that modulates gas phase and particle abundances in all three regions, either through scavenging or by promoting vertical mixing. The reported measurements and data analysis serve to improve the characterization of trace gases and aerosols in populated arid regions and offer process level understanding of dominant mechanisms for model validations and improvements.

  17. NMR based solvent exchange experiments to understand the conformational preference of intrinsically disordered proteins using FG-nucleoporin peptide as a model.

    PubMed

    Heisel, Kurt A; Krishnan, V V

    2014-01-01

    The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent, are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on (13)C?, (1)H?, and (1)HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water). PMID:24037535

  18. Phospholipid-driven differences determine the action of the synthetic antimicrobial peptide OP-145 on Gram-positive bacterial and mammalian membrane model systems.

    PubMed

    Malanovic, Nermina; Leber, Regina; Schmuck, Maria; Kriechbaum, Manfred; Cordfunke, Robert A; Drijfhout, Jan W; de Breij, Anna; Nibbering, Peter H; Kolb, Dagmar; Lohner, Karl

    2015-10-01

    OP-145, a synthetic antimicrobial peptide developed from a screen of the human cathelicidin LL-37, displays strong antibacterial activities and is--at considerably higher concentrations--lytic to human cells. To obtain more insight into its actions, we investigated the interactions between OP-145 and liposomes composed of phosphatidylglycerol (PG) and phosphatidylcholine (PC), resembling bacterial and mammalian membranes, respectively. Circular dichroism analyses of OP-145 demonstrated a predominant ?-helical conformation in the presence of both membrane mimics, indicating that the different membrane-perturbation mechanisms are not due to different secondary structures. Membrane thinning and formation of quasi-interdigitated lipid-peptide structures was observed in PG bilayers, while OP-145 led to disintegration of PC liposomes into disk-like micelles and bilayer sheets. Although OP-145 was capable of binding lipoteichoic acid and peptidoglycan, the presence of these bacterial cell wall components did not retain OP-145 and hence did not interfere with the activity of the peptide toward PG membranes. Furthermore, physiological Ca++ concentrations did neither influence the membrane activity of OP-145 in model systems nor the killing of Staphylococcus aureus. However, addition of OP-145 at physiological Ca++-concentrations to PG membranes, but not PC membranes, resulted in the formation of elongated enrolled structures similar to cochleate-like structures. In summary, phospholipid-driven differences in incorporation of OP-145 into the lipid bilayers govern the membrane activity of the peptide on bacterial and mammalian membrane mimics. PMID:26210299

  19. Mass spectrometric and peptide chip characterization of an assembled epitope: analysis of a polyclonal antibody model serum directed against the Sjøgren/systemic lupus erythematosus autoantigen TRIM21.

    PubMed

    Al-Majdoub, M; Koy, C; Lorenz, P; Thiesen, H-J; Glocker, M O

    2013-06-01

    We demonstrate the development of a mass spectrometry-based epitope-mapping procedure in combination with Western blot analysis that works also with antigens that are insoluble in nondenaturing buffers consuming minute amounts of antigen (approximately 200 pmol) and antibody (approximately 15 pmol), respectively. A polyclonal anti-TRIM21 rabbit antibody serum is applied as a model serum for future patient analyses to set up the system. The major epitope that is recognized by the anti-TRIM21 serum spans the central TRIM21 region LQ-ELEKDEREQLRILGE-KE, showing that immunization with a 139-amino acid residue long peptide resulted in a 'monospecific' polyclonal antibody repertoire. Protein structure investigations, secondary structure predictions, and surface area calculations revealed that the best matching partial sequence to fulfill all primary and secondary structure requirements was the four amino acid spanning motif 'L-E-Q-L', which is present in both the sequential and the ?-helical peptide conformation. Peptide chip analyses confirmed the mass spectrometric results and showed that the peptide chip platform is an appropriate method for displaying secondary structure-relying epitope conformations. As the same secondary structures are present in vivo, patient antibody screening, e.g., to identify subgroups of patients according to distinct epitope antibody reactivities, is feasible. PMID:23722955

  20. Selection and identification of ligand peptides targeting a model of castrate-resistant osteogenic prostate cancer and their receptors

    PubMed Central

    Mandelin, Jami; Cardó-Vila, Marina; Driessen, Wouter H. P.; Mathew, Paul; Navone, Nora M.; Lin, Sue-Hwa; Logothetis, Christopher J.; Rietz, Anna Cecilia; Dobroff, Andrey S.; Proneth, Bettina; Sidman, Richard L.; Pasqualini, Renata; Arap, Wadih

    2015-01-01

    We performed combinatorial peptide library screening in vivo on a novel human prostate cancer xenograft that is androgen-independent and induces a robust osteoblastic reaction in bonelike matrix and soft tissue. We found two peptides, PKRGFQD and SNTRVAP, which were enriched in the tumors, targeted the cell surface of androgen-independent prostate cancer cells in vitro, and homed to androgen receptor-null prostate cancer in vivo. Purification of tumor homogenates by affinity chromatography on these peptides and subsequent mass spectrometry revealed a receptor for the peptide PKRGFQD, ?-2-macroglobulin, and for SNTRVAP, 78-kDa glucose-regulated protein (GRP78). These results indicate that GRP78 and ?-2-macroglobulin are highly active in osteoblastic, androgen-independent prostate cancer in vivo. These previously unidentified ligand–receptor systems should be considered for targeted drug development against human metastatic androgen-independent prostate cancer. PMID:25762070