Sample records for model gas-phase peptide

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

    SciTech Connect

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

    2008-07-01

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

  2. Gas-phase dissociation pathways of multiply charged peptide clusters

    Microsoft Academic Search

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

    2003-01-01

    Numerous studies of cluster formation and dissociation have been conducted to determine properties of matter in the transition\\u000a from the condensed phase to the gas phase using materials as diverse as atomic nuclei, noble gasses, metal clusters, and amino\\u000a acids. Here, electrospray ionization is used to extend the study of cluster dissociation to peptides including leucine enkephalin\\u000a with 7–19 monomer

  3. 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

  4. Gas-phase helical peptides mimic solution-phase behavior.

    PubMed

    Morrison, Lindsay J; Wysocki, Vicki H

    2014-10-01

    In solution, ?-helices are stabilized at the termini by a variety of different capping interactions. Study of these interactions in the gas phase provides a unique means to explore the intrinsic properties that cause this stabilization. Evidence of helical and globular conformations is presented here for gas-phase, doubly charged peptides of sequence XAnK, wherein X is D, N, Q, or L. The relative abundance of the helical conformation is found to vary as a function of peptide length and the identity of the first amino acid, consistent with solution phase studies that have looked at the identity of the first amino acid. The N-terminal, b ion fragments of the doubly charged precursor peptides are shown to form helical and globular conformations. The stability of the helical fragments is examined as a function of fragment length, N-terminal amino acid, precursor conformation, and the activation energy used to generate the fragment. At lower collision energies, helical b ions preferentially form, particularly from helical precursors. The abundance of the helical b ion population is observed to dramatically decrease for NAn and DAn b ions smaller than the b10; simulations suggest this feature is due to the b10 having two complete turns of the helix, while the b9 and smaller ions have only a partial second turn, suggesting the b10 is the lower limit for stable helical conformations in b ions. Use of higher collision energies promotes the formation of globular structures in the b ions. This characteristic is attributed to increased conformational dynamics and subsequently improved proton transfer kinetics from the b ion's C-terminal oxazolone ring to the N-terminus. PMID:25203898

  5. Gas Phase Dissociation Behavior of Acyl-Arginine Peptides

    PubMed Central

    McGee, William M.; McLuckey, Scott A.

    2013-01-01

    The gas phase dissociation behavior of peptides containing acyl-arginine residues is investigated. These acylations are generated via a combination of ion/ion reactions between arginine-containing peptides and N-hydroxysuccinimide (NHS) esters and subsequent tandem mass spectrometry (MS/MS). Three main dissociation pathways of acylated arginine, labeled Paths 1-3, have been identified and are dependent on the acyl groups. Path 1 involves the acyl-arginine undergoing deguanidination, resulting in the loss of the acyl group and dissociation of the guanidine to generate an ornithine residue. This pathway generates selective cleavage sites based on the recently discussed “ornithine effect”. Path 2 involves the coordinated losses of H2O and NH3 from the acyl-arginine side chain while maintaining the acylation. We propose that Path 2 is initiated via cyclization of the ?-nitrogen of arginine and the C-terminal carbonyl carbon, resulting in rapid rearrangement from the acyl-arginine side chain and the neutral losses. Path 3 occurs when the acyl group contains ?-hydrogens and is observed as a rearrangement to regenerate unmodified arginine while the acylation is lost as a ketene. PMID:24465154

  6. Investigation of the effect of intra-molecular interactions on the gas-phase conformation of peptides as probed by ion mobility-mass spectrometry, gas-phase hydrogen/deuterium exchange, and molecular mechanics 

    E-print Network

    Sawyer, Holly Ann

    2006-04-12

    Ion mobility-mass spectrometry (IM-MS), gas-phase hydrogen/deuterium (H/D) exchange ion molecule reactions and molecular modeling provide complimentary information and are used here for the characterization of peptide ion structure, including fine...

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

    E-print Network

    Clemmer, David E.

    Cis-Trans Signatures of Proline-Containing Tryptic Peptides in the Gas Phase Anne E. Counterman digest peptide ions obtained from digestion of common proteins. Here, we report a mobility signature that aids in identifying proline-containing peptides containing 4-10 residues. Of 129 peptides (e10 residues

  8. 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.

  9. Gas Phase Radical Migration in Peptides and Proteins

    E-print Network

    Moore, Benjamin Nathan

    2013-01-01

    of  peptide  radical  cations  an  ergodic   process?  J.  peptide   is   typically   dominated   by   radical-­??directed   processes,  peptides  and  proteins.  The  thermodynamic  factors  controlling   this  process  

  10. Spectroscopic Evidence for Gas Phase Formation of Successive -turns in a Three-Residue Peptide Chain

    E-print Network

    Paris-Sud XI, Université de

    Spectroscopic Evidence for Gas Phase Formation of Successive -turns in a Three-Residue Peptide MN Nieuwegein, The Netherlands Author E-mail : mmons@cea.fr Gas phase studies of small biomolecules1 between secondary structures such as -strands, -turns, 27 ribbons, - and 310 helices. In the present

  11. Efficient and directed peptide bond formation in the gas phase via ion/ion reactions

    PubMed Central

    McGee, William M.; McLuckey, Scott A.

    2014-01-01

    Amide linkages are among the most important chemical bonds in living systems, constituting the connections between amino acids in peptides and proteins. We demonstrate the controlled formation of amide bonds between amino acids or peptides in the gas phase using ion/ion reactions in a mass spectrometer. Individual amino acids or peptides can be prepared as reagents by (i) incorporating gas phase–labile protecting groups to silence otherwise reactive functional groups, such as the N terminus; (ii) converting the carboxyl groups to the active ester of N-hydroxysuccinimide; and (iii) incorporating a charge site. Protonation renders basic sites (nucleophiles) unreactive toward the N-hydroxysuccinimide ester reagents, resulting in sites with the greatest gas phase basicities being, in large part, unreactive. The N-terminal amines of most naturally occurring amino acids have lower gas phase basicities than the side chains of the basic amino acids (i.e., those of histidine, lysine, or arginine). Therefore, reagents may be directed to the N terminus of an existing “anchor” peptide to form an amide bond by protonating the anchor peptide’s basic residues, while leaving the N-terminal amine unprotonated and therefore reactive. Reaction efficiencies of greater than 30% have been observed. We propose this method as a step toward the controlled synthesis of peptides in the gas phase. PMID:24474750

  12. Gas-phase separations of complex tryptic peptide mixtures.

    PubMed

    Taraszka, J A; Counterman, A E; Clemmer, D E

    2001-02-01

    High-resolution ion mobility and time-of-flight mass spectrometry techniques have been used to analyze complex mixtures of peptides generated from tryptic digestion of fourteen common proteins (albumin, bovine, dog, horse, pig, and sheep; aldolase, rabbit; beta-casein, bovine; cytochrome c, horse; beta-lactoglobulin, bovine; myoglobin, horse; hemoglobin, human, pig, rabbit, and sheep). In this approach, ions are separated based on differences in mobilities in helium in a drift tube and on differences in their mass-to-charge ratios in a mass spectrometer. From data recorded for fourteen individual proteins (over a m/z range of 405 to 1,000), we observe 428 peaks, of which 205 are assigned to fragments that are expected from tryptic digestion. In a separate analysis, the fourteen mixtures have been combined and analyzed as one system. In the single dataset, we resolve 260 features and are able to assign 168 peaks to unique peptide sequences. Many other unresolved features are observed. Methods for assigning peptides based on the use of m/z information and existing mobilities or mobilities that are predicted by use of intrinsic size parameters are described. PMID:11293699

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

    PubMed

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

    1999-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  15. Native like helices in a specially designed ? peptide in the gas phase.

    PubMed

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

    2015-02-21

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

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

    SciTech Connect

    Webb, S.W.

    1998-09-01

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

  17. Gas-phase Structure and Fragmentation Pathways of Singly Protonated Peptides with N-terminal Arginine

    PubMed Central

    Bythell, Benjamin J.; Csonka, István P.; Suhai, Sándor; Barofsky, Douglas F.; Paizs, Béla

    2010-01-01

    The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b2 ions or facilely rearrange to form anhydrides from which both b2 and b2+H2O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b2 and b2+H2O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc., 2009, 131, 14057–14065.). In addition to these findings we also report on the mechanisms for the formation of the b1 ion, neutral loss (H2O, NH3, guanidine) fragment ions and the d3 ion. PMID:20973555

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

    PubMed

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

    2015-07-01

    The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H](4+) ions exhibit two major conformer types with collision cross sections of 418 Å(2) and 446 Å(2); the [M + 3H](3+) ions also yield two different conformer types having collision cross sections of 340 Å(2) and 367 Å(2). Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H](3+) ions show faster HDX rate contributions compared with [M + 4H](4+) ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H](4+) ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS). Graphical Abstract ?. PMID:25895891

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

    NASA Astrophysics Data System (ADS)

    Gaigeot, Marie-Pierre

    2009-03-01

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

  20. Loss of ammonia during electron-transfer dissociation of deuterated peptides as an inherent gauge of gas-phase hydrogen scrambling.

    PubMed

    Rand, Kasper D; Zehl, Martin; Jensen, Ole N; Jørgensen, Thomas J D

    2010-12-01

    The application of electron-transfer dissociation (ETD) to obtain single-residue resolution in hydrogen exchange-mass spectrometry (HX-MS) experiments has recently been demonstrated. For such measurements, it is critical to ensure that the level of gas-phase hydrogen scrambling is negligible. Here we utilize the abundant loss of ammonia upon ETD of peptide ions as a universal reporter of positional randomization of the exchangeable hydrogens (hydrogen scrambling) during HX-ETD experiments. We show that the loss of ammonia from peptide ions proceeds without depletion of deuterium when employing optimized mild electrospray ion source settings for the HX-ETD analysis of a selectively labeled model peptide and peptides derived from fully labeled ?(2)-microglobulin. Hydrogen scrambling, as induced by excessive vibrational excitation of peptide ions during harsh declustering conditions, is easily detected by a depletion of deuterium when deuterated ammonia is lost from peptides during ETD. This straightforward method requires no modifications to the experimental workflow and has the great advantage that the occurrence of hydrogen scrambling can be directly detected in the actual peptides analyzed in the HX-ETD experiment. PMID:21033729

  1. Gas-phase binding energies for non-covalent A?-40 peptide/small molecule complexes from CID mass spectrometry and RRKM theory.

    PubMed

    Mayer, Paul M; Martineau, Eric

    2011-03-21

    The gas-phase binding of small molecules to the Amyloid ?-40 peptide generated by electrospray ionization has been explored with collision-induced dissociation mass spectrometry and kinetic rate theory. This study discusses a simple procedure used to theoretically model the experimental breakdown diagrams for the A?-40 peptide complexed with a series of aminosulfonate small molecules, namely homotaurine, 3-cyclohexylamino-2-hydroxy-1-propanesulfonic acid (CAPSO), 3-(1,3,4,9-tetrahydro-2H-?-carbolin-2-yl)propane-1-sulfonic acid, 3-(1,3,4,9-tetrahydro-2H-?-carbolin-2-yl)butane-1-sulfonic acid, and 3-(cyclohexylamino)propane-1-sulfonic acid. An alternative procedure employing an extrapolation procedure for k(E) is also discussed. PMID:21298155

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

    E-print Network

    Slaton, James Garrett

    2009-05-15

    Peptide synthesis and metal doping, combined with mass spectrometric and ion mobility spectrometric techniques, have provided a picture of the fragmentation behavior of a large field of homologous peptide ions, represented ...

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

    E-print Network

    Slaton, James Garrett

    2009-05-15

    ], and in particular, the charge derivatization study of Allison [16]. Our objectives are to 1) determine the location of the charge within the peptide ions, 2) assess differences in the fragmentation chemistry of the protonated and metalated peptides, 3) establish...

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

    PubMed Central

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

    2005-01-01

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

  5. Steady-State and Dynamic Modeling of Gas-Phase Polypropylene Processes Using Stirred-Bed Reactors

    E-print Network

    Liu, Y. A.

    Steady-State and Dynamic Modeling of Gas-Phase Polypropylene Processes Using Stirred-Bed Reactors for the continuous gas-phase synthesis of polypropylene using stirred-bed reactors. The model considers the important and techniques used to develop a comprehensive model for a gas-phase polypropylene process using stirred

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

    SciTech Connect

    Malandra, J.

    1993-05-01

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

  7. Gas-phase structure of amyloid-? (12-28) peptide investigated by infrared spectroscopy, electron capture dissociation and ion mobility mass spectrometry.

    PubMed

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

    2013-12-01

    The gas-phase structures of doubly and triply protonated Amyloid-?12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - C? bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and ?-helix motifs. PMID:24043520

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    We present evidence that following near-UV excitation, protonated tyrosine- or phenylalanine-containing peptides undergo intersystem crossing to produce a triplet species. This pathway competes with direct dissociation from the excited electronic state and with dissociation from the electronic ground state subsequent to internal conversion. We employ UV-IR double-resonance photofragment spectroscopy to record conformer-specific vibrational spectra of cold peptides pre-excited to their S1 electronic state. The absorption of tunable IR light by these electronically excited peptides leads to a drastic increase in fragmentation, selectively enhancing the loss of neutral phenylalanine or tyrosine side-chain, which are not the lowest dissociation channels in the ground electronic state. The recorded IR spectra evolve upon increasing the time delay between the UV and IR pulses, reflecting the dynamics of the intersystem crossing on a timescale of ˜80 ns and <10 ns for phenylalanine- and tyrosine-containing peptides, respectively. Once in the triplet state, phenylalanine-containing peptides may live for more than 100 ms, unless they absorb IR photons and undergo dissociation by the loss of an aromatic side-chain. We discuss the mechanism of this fragmentation channel and its possible implications for photofragment spectroscopy and peptide photostability.

  9. Mobile protons versus mobile radicals: gas-phase unimolecular chemistry of radical cations of cysteine-containing peptides.

    PubMed

    Lam, Adrian K Y; Ryzhov, Victor; O'Hair, Richard A J

    2010-08-01

    A combination of electrospray ionization (ESI), multistage, and high-resolution mass spectrometry experiments are used to examine the gas-phase fragmentation reactions of radical cations of cysteine containing di- and tripeptides. Two different chemical methods were used to form initial populations of radical cations in which the radical sites were located at different positions: (1) sulfur-centered cysteinyl radicals via bond homolysis of protonated S-nitrosocysteine containing peptides; and (2) alpha-carbon backbone-centered radicals via Siu's sequence of reactions (J. Am. Chem. Soc.2008, 130, 7862). Comparison of the fragmentation reactions of these regiospecifically generated radicals suggests that hydrogen atom transfer (HAT) between the alpha C-H of adjacent residues and the cysteinyl radical can occur. In addition, using accurate mass measurements, deuterium labeling, and comparison with an authentic sample, a novel loss of part of the N-terminal cysteine residue was shown to give rise to the protonated, truncated N-formyl peptide (an even-electron x(n) ion). DFT calculations were performed on the radical cation [GCG]*(+) to examine: the relative stabilities of isomers with different radical and protonation sites; the barriers associated with radical migration between four possible radical sites, [G*CG](+), [GC*G](+), [GCG*](+), and [GC(S*)G](+); and for dissociation from these sites to yield b(2)-type ions. PMID:20189828

  10. Modeling gas phase nitric oxide release in lung epithelial cells Jingjing Jiang a

    E-print Network

    George, Steven C.

    Modeling gas phase nitric oxide release in lung epithelial cells Jingjing Jiang a , Steven C Revised 21 April 2011 Available online xxxx Keywords: Arginase Nitric oxide synthase L-Arginine a b s t r a c t Nitric oxide (NO) is present in exhaled breath and is generally considered to be a noninvasive

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  12. Mobile protons versus mobile radicals: Gas-phase unimolecular chemistry of radical cations of cysteine-containing peptides

    Microsoft Academic Search

    Adrian K. Y. Lam; Victor Ryzhov; Richard A. J. O’Hair

    2010-01-01

    A combination of electrospray ionization (ESI), multistage, and high-resolution mass spectrometry experiments are used to\\u000a examine the gas-phase fragmentation reactions of radical cations of cysteine containing di- and tripeptides. Two different\\u000a chemical methods were used to form initial populations of radical cations in which the radical sites were located at different\\u000a positions: (1) sulfur-centered cysteinyl radicals via bond homolysis of

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

    SciTech Connect

    Ge, Hai-Wen [Engine Research Center, University of Wisconsin-Madison, 1500 Engineering Drive, Madison, WI 53706 (United States); Gutheil, Eva [Interdisziplinaeres Zentrum fuer Wissenschaftliches Rechnen, Universitaet Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg (Germany)

    2008-04-15

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

  14. Kinetic study of model reactions in the gas phase at the early stage of coke formation

    SciTech Connect

    Nohara, D.; Sakai, T. (Dept. of Chemical Reaction Engineering, Faculty of Pharmaceutical Sciences, Nagoya City Univ., Mizuho-ku, Nagoya 467 (JP))

    1992-01-01

    This paper reports that the most probable gas-phase reactions at the early stage of coke formation were elucidated by kinetic study on the model reactions adopted for formation of cyclic compounds and growth of ring. It was revealed that the formation and growth of ring proceeded mainly through cycloaddition of butadiene or allyl radicals to unsaturated hydrocarbons at relatively low temperatures ({approximately}600{degrees}C), i.e., through a Diels-Alder type reaction. On the other hand, such growth of ring as formation of biphenyl accompanying dehydrogenation from benzene can proceed only at the higher temperatures. It was also revealed that in the growth of the ring, cycloaddition of butadiene favors a cyclic olefin molecule that possesses a nonconjugated double bond and a nearly planar structure.

  15. Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations

    PubMed Central

    Fadda, Elisa; Woods, Robert J.

    2014-01-01

    In this work we analyze the effect of the inclusion of an empirical dispersion term to standard DFT (DFT-D) in the prediction of the conformational energy of the alanine dipeptide (Ala2) and in assessing the relative stabilities of short polyala-nine peptides in helical conformations, i.e., ? and 310 helices, from Ala4 to Ala16. The Ala2 conformational energies obtained with the dispersion-corrected GGA functional B97-D are compared to previously published high level MP2 data. Meanwhile, the B97-D performance on larger polyalanine peptides is compared to MP2, B3LYP and RHF calculations obtained at a lower level of theory. Our results show that electron correlation affects the conformational energies of short peptides with a weight that increases with the peptide length. Indeed, while the contribution of vdW forces is significant for larger peptides, in the case of Ala2 it is negligible when compared to solvent effects. Even for short peptides, the inclusion of an empirical dispersion term greatly improves accuracy of DFT methods, providing results that correlate very well with the MP2 reference at no additional computational cost. PMID:25418993

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

  17. 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.

  18. Modeling gas-phase nucleation in inductively coupled silane-oxygen S.-M. Suh, S. L. Girshick,a)

    E-print Network

    Zachariah, Michael R.

    Modeling gas-phase nucleation in inductively coupled silane-oxygen plasmas S.-M. Suh, S. L. An inductively coupled plasma reactor was modeled in a one-dimensional multicomponent two-temperature framework while also having the capability of anisotropic deep etching. Inductively coupled plasmas ICPs

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

    PubMed

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

    2014-01-01

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

  20. 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...

  1. Challenges in Modeling Gas-Phase Flow in Microchannels: From Slip to Transition

    Microsoft Academic Search

    Robert W. Barber; David R. Emerson

    2006-01-01

    It has long been recognized that the fluid mechanics of gas-phase microflows can differ significantly from the macroscopic world. Non-equilibrium effects such as rarefaction and gas-surface interactions need to be taken into account, and it is well known that the no-slip boundary condition of the Navier-Stokes equations is no longer valid. Following ideas proposed by Maxwell, it is generally accepted

  2. Intrinsic Folding of Small Peptide Chains: Spectroscopic Evidence for the Formation of -turns

    E-print Network

    Boyer, Edmond

    1 Intrinsic Folding of Small Peptide Chains: Spectroscopic Evidence for the Formation of -turns running head "Spectroscopy of -turns in the gas phase" #12;2 Abstract Laser desorption of model peptides structures of biology. Spectroscopic evidence for the formation of - turns in gas phase peptide chains

  3. 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 -pinene reactions in the presence of sunlight, ozone (O3), and oxides of nitrogen (NO ...

  4. 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

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

    PubMed

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

    2012-01-01

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

  6. 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

  7. Numerical modelling of the carrier gas phase in a laboratory-scale coal classifier model

    Microsoft Academic Search

    Lanre Afolabi; Abdelwahab Aroussi; Nora Mat Isa

    2011-01-01

    The pneumatic transport of fine ideally combustible coal dust to the burner furnace is an important process in coal fired power plants. The strongly swirling air phase responsible for the particle separation and transport in a coal pulverising mill was characterised experimentally and numerically. Measurements of the swirl velocity component were taken in a scaled laboratory model of the device

  8. Determination of the Gas-phase Acidities of Oligopeptides

    PubMed Central

    Ren, Jianhua; Sawhney, Ashish; Tian, Yuan; Padda, Bhupinder; Batoon, Patrick

    2013-01-01

    Amino acid residues located at different positions in folded proteins often exhibit different degrees of acidities. For example, a cysteine residue located at or near the N-terminus of a helix is often more acidic than that at or near the C-terminus 1-6. Although extensive experimental studies on the acid-base properties of peptides have been carried out in the condensed phase, in particular in aqueous solutions 6-8, the results are often complicated by solvent effects 7. In fact, most of the active sites in proteins are located near the interior region where solvent effects have been minimized 9,10. In order to understand intrinsic acid-base properties of peptides and proteins, it is important to perform the studies in a solvent-free environment. We present a method to measure the acidities of oligopeptides in the gas-phase. We use a cysteine-containing oligopeptide, Ala3CysNH2 (A3CH), as the model compound. The measurements are based on the well-established extended Cooks kinetic method (Figure 1) 11-16. The experiments are carried out using a triple-quadrupole mass spectrometer interfaced with an electrospray ionization (ESI) ion source (Figure 2). For each peptide sample, several reference acids are selected. The reference acids are structurally similar organic compounds with known gas-phase acidities. A solution of the mixture of the peptide and a reference acid is introduced into the mass spectrometer, and a gas-phase proton-bound anionic cluster of peptide-reference acid is formed. The proton-bound cluster is mass isolated and subsequently fragmented via collision-induced dissociation (CID) experiments. The resulting fragment ion abundances are analyzed using a relationship between the acidities and the cluster ion dissociation kinetics. The gas-phase acidity of the peptide is then obtained by linear regression of the thermo-kinetic plots 17,18. The method can be applied to a variety of molecular systems, including organic compounds, amino acids and their derivatives, oligonucleotides, and oligopeptides. By comparing the gas-phase acidities measured experimentally with those values calculated for different conformers, conformational effects on the acidities can be evaluated. PMID:23851399

  9. 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.

  10. 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.

  11. GEM-AQ, an on-line global multiscale chemical weather modelling system: model description and evaluation of gas phase chemistry processes

    Microsoft Academic Search

    J. W. Kaminski; L. Neary; J. Struzewska; J. C. McConnell; A. Lupu; J. Jarosz; K. Toyota; S. L. Gong; J. Côté; X. Liu; K. Chance; A. Richter

    2008-01-01

    Tropospheric chemistry and air quality processes were implemented on-line in the Global Environmental Multiscale weather prediction model. The integrated model, GEM-AQ, was developed as a platform to investigate chemical weather at scales from global to urban. The current chemical mechanism is comprised of 50 gas-phase species, 116 chemical and 19 photolysis reactions, and is complemented by a sectional aerosol module

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

    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 six-year 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

    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 six-year simulation (2000-2005). For the episode analysis, model simulations show good agreement with European Monitoring and Evaluation Programme (EMEP) observations of hourly ozone over different regions in Europe and capture ozone concentrations during and after the summer 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.

  14. 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.

  15. 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...

  16. 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).

  17. 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.

  18. Computer-Aided Derivation of Gas-Phase Oxidation Mechanisms: Application to the Modeling of the Oxidation of n-Butane

    Microsoft Academic Search

    V. Warth; N. Stef; P. A. Glaude; F. Battin-Leclerc; G. Scacchi; G. M. Côme

    1998-01-01

    This paper describes a system that permits the computer-aided formulation of comprehensive primary mechanisms and simplified secondary mechanisms, coupled with the relevant thermochemical and kinetic data in the case of the gas-phase oxidation of alkanes and ethers. This system has been demonstrated by modeling the oxidation of n-butane at temperatures between 554 and 737 K, i.e., in the negative temperature

  19. Experimental validation of CFD models for fluidized beds: Influence of particle stress models, gas phase compressibility and air inflow models

    Microsoft Academic Search

    K. Johansson; B. G. M. van Wachem; A. E. Almstedt

    2006-01-01

    This work compares numerical simulations of fluid dynamics in fluidized beds using different closure models and air feed system models. The numerical results are compared to experiments by means of power spectral density distributions of fluctuating pressure signals and bubble statistics obtained from capacitance probe measurements. Two different particle rheology models are tested in combination with two different values of

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  1. Gas-phase separations of protease digests.

    PubMed

    Valentine, S J; Counterman, A E; Hoaglund, C S; Reilly, J P; Clemmer, D E

    1998-11-01

    A mixture of peptides from a complete tryptic digest of ubiquitin has been analyzed by ion mobility/time-of-flight mass spectrometry techniques. All components of the mixture were electrosprayed and ions were separated in the gas phase based on differences in their mobilities through helium before being dispersed into a time-of-flight mass spectrometer for mass-to-charge analysis. The data show that ions separate into families primarily according to differences in their charge states and, to a lesser extent, differences in conformation. This approach reduces spectral congestion typically associated with electrosprayed mixtures and provides charge assignments for mass-to-charge ratio data. Gas-phase separations of ions appear to provide a new physical basis for characterizing components of biological mixtures. PMID:9794086

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  3. Fundamentals of gas phase plasmas for treatment of human tissue.

    PubMed

    Kushner, Mark J; Babaeva, Natalia Yu

    2011-01-01

    The use of gas phase plasmas for treating human tissue is at the intersection of two disciplines - plasma physics and engineering, and medicine. In this paper, a primer will be provided for the medical practitioner on the fundamentals of generating gas phase plasmas at atmospheric pressure in air for the treatment of human tissue. The mechanisms for gas phase plasmas interacting with tissue and biological fluids will also be discussed using results from computer modeling. PMID:21335808

  4. 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. [Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Environmental Sciences and Engineering] [Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Environmental Sciences and Engineering

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  6. 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

  7. 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 reactions...

  8. 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 ...

  9. On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems With the Gas Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models

    PubMed Central

    Kamerlin, Shina C. L.; Chu, Zhen T.; Warshel, A.

    2010-01-01

    Oxyanion holes play a major role in catalyzing enzymatic reactions, yet the corresponding energetics is frequently misunderstood. The main problem may be associated with the non-trivial nature of the electrostatic preorganization effect, without following the relevant formulation. That is, although the energetics of oxyanion holes have been fully quantified in early studies (which include both the enzymatic and reference solution reactions), the findings of these studies are sometimes overlooked, and, in some cases, it is assumed that gas-phase calculations with a fixed model of an oxyanion hole are sufficient for assessing the corresponding effect in the protein. Herein, we present a systematic analysis of this issue, clarifying the problems associated with modeling oxyanions by means of two fixed water molecules (or related constructs). We then re-emphasize the point that the effect of the oxyanion hole is mainly due to the fact that the relevant dipoles are already set in an orientation that stabilizes the TS charges, whereas the corresponding dipoles in solution are randomly oriented, resulting in the need to pay a very large reorganization energy. Simply calculating interaction energies with relatively fixed species cannot capture this crucial point, and considering it may help in advancing rational enzyme design. PMID:20825150

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  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. Liquid-gas phase transition in hypernuclei

    NASA Astrophysics Data System (ADS)

    Mallik, S.; Chaudhuri, G.

    2015-05-01

    The fragmentation of excited hypernuclear systems formed in heavy ion collisions has been described by the canonical thermodynamical model extended to three-component systems. The multiplicity distribution of the fragments has been analyzed in detail and it has been observed that the hyperons tend to get attached to the heavier fragments. Another important observation is the phase coexistence of the hyperons, a phenomenon which is linked to the liquid-gas phase transition in strange matter.

  16. Development and initial evaluation of a dynamic species-resolved model for gas phase chemistry and size-resolved gas\\/particle partitioning associated with secondary organic aerosol formation

    Microsoft Academic Search

    Robert J. Griffin; Donald Dabdub; John H. Seinfeld

    2005-01-01

    A module for predicting the dynamic evolution of the gas phase species and the aerosol size and composition distribution during formation of secondary organic aerosol (SOA) is presented. The module is based on the inorganic gas-aerosol equilibrium model Simulating the Composition of Atmospheric Particles at Equilibrium 2 (SCAPE2) and updated versions of the lumped Caltech Atmospheric Chemistry Mechanism (CACM) and

  17. Investigation of the ellipsoidal-statistical Bhatnagar-Gross-Krook kinetic model applied to gas-phase transport of heat and tangential momentum between parallel walls

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

    The ellipsoidal-statistical Bhatnagar-Gross-Krook (ES-BGK) kinetic model is investigated for steady gas-phase transport of heat, tangential momentum, and mass between parallel walls (i.e., Fourier, Couette, and Fickian flows). This investigation extends the original study of Cercignani and Tironi, who first applied the ES-BGK model to heat transport (i.e., Fourier flow) shortly after this model was proposed by Holway. The ES-BGK model is implemented in a molecular-gas-dynamics code so that results from this model can be compared directly to results from the full Boltzmann collision term, as computed by the same code with the direct simulation Monte Carlo (DSMC) algorithm of Bird. A gas of monatomic molecules is considered. These molecules collide in a pairwise fashion according to either the Maxwell or the hard-sphere interaction and reflect from the walls according to the Cercignani-Lampis-Lord model with unity accommodation coefficients. Simulations are performed at pressures from near-free-molecular to near-continuum. Unlike the BGK model, the ES-BGK model produces heat-flux and shear-stress values that both agree closely with the DSMC values at all pressures. However, for both interactions, the ES-BGK model produces molecular-velocity-distribution functions that are qualitatively similar to those determined for the Maxwell interaction from Chapman-Enskog theory for small wall temperature differences and moment-hierarchy theory for large wall temperature differences. Moreover, the ES-BGK model does not produce accurate values of the mass self-diffusion coefficient for either interaction. Nevertheless, given its reasonable accuracy for heat and tangential-momentum transport, its sound theoretical foundation (it obeys the H-theorem), and its available extension to polyatomic molecules, the ES-BGK model may be a useful method for simulating certain classes of single-species noncontinuum gas flows, as Cercignani suggested.

  18. Multiphysics modeling of carbon gasification processes in a well-stirred reactor with detailed gas-phase chemistry

    E-print Network

    Qiao, Li

    Multi-physics numerical modeling a b s t r a c t Fuel synthesis through coal and biomass gasification parameters for syngas production, we developed a multiphysics model to simulate the gasification processes

  19. 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

  20. Gas phase atmospheric bromine photochemistry

    Microsoft Academic Search

    D. J. Lary

    1996-01-01

    This paper reviews the current knowledge of gas phase bromine photochemistry and presents a budget study of atmospheric bromine species. The effectiveness of the ozone catalytic loss cycles involving bromine is quantified by considering their chain length and effectiveness. The chain effectiveness is a new variable defined as the chain length multiplied by the rate of the cycle's rate-limiting step.

  1. 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

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

    SciTech Connect

    Lindberg, S.E. [Oak Ridge National Lab., TN (United States). Environmental Sciences Div.; Stratton, W.J. [Earlham Coll., Richmond, IN (United States). Dept. of Chemistry; Pai, P. [Atmospheric and Environmental Research, San Ramon, CA (United States); Allan, M.A. [Electric Power Research Inst., Palo Alto, CA (United States)

    1997-12-31

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

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

    PubMed Central

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-08-01

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

  6. Development and initial evaluation of a dynamic species-resolved model for gas phase chemistry and size-resolved gas//particle

    E-print Network

    Dabdub, Donald

    biogenic and anthropogenic sources. [3] The gas phase oxidation chemistry of SOA-forming VOCs is complex of the semivolatile or nonvolatile products of VOC oxidation between the gas and particle phases. Chem- ical analysis are presented in which a single salt (either dry or aqueous), a volatile organic compound, and oxides

  7. HLA-peptide binding prediction using structural and modeling principles.

    PubMed

    Kangueane, Pandjassarame; Sakharkar, Meena Kishore

    2007-01-01

    Short peptides binding to specific human leukocyte antigen (HLA) alleles elicit immune response. These candidate peptides have potential utility in peptide vaccine design and development. The binding of peptides to allele-specific HLA molecule is estimated using competitive binding assay and biochemical binding constants. Application of this method for proteome-wide screening in parasites, viruses, and virulent bacterial strains is laborious and expensive. However, short listing of candidate peptides using prediction approaches have been realized lately. Prediction of peptide binding to HLA alleles using structural and modeling principles has gained momentum in recent years. Here, we discuss the current status of such prediction. PMID:18450009

  8. Nonextensive nuclear liquid-gas phase transition

    NASA Astrophysics Data System (ADS)

    Lavagno, A.; Pigato, D.

    2013-10-01

    We study an effective relativistic mean-field model of nuclear matter with arbitrary proton fraction at finite temperature in the framework of nonextensive statistical mechanics, characterized by power-law quantum distributions. We investigate the presence of thermodynamic instability in a warm and asymmetric nuclear medium and study the consequent nuclear liquid-gas phase transition by requiring the Gibbs conditions on the global conservation of baryon number and electric charge fraction. We show that nonextensive statistical effects play a crucial role in the equation of state and in the formation of mixed phase also for small deviations from the standard Boltzmann-Gibbs statistics.

  9. Coulomb-Assisted Dissociative Electron Attachment:  Application to a Model Peptide

    Microsoft Academic Search

    Monika Sobczyk; Iwona Anusiewicz; Joanna Berdys-Kochanska; Agnieszka Sawicka; Piotr Skurski; Jack Simons

    2005-01-01

    The fragmentation of positively charged gas-phase samples of peptides is used to infer the primary structure of such molecules. In electron capture dissociation (ECD) experiments, very low-energy electrons attach to the sample and rupture bonds to effect the fragmentation. It turns out that ECD fragmentation tends to produce cleavage of very specific types of bonds. In earlier works by this

  10. Antibiotic activity of Leu-Lys rich model peptides

    Microsoft Academic Search

    Dong Gun Lee; Kyung-Soo Hahm

    2003-01-01

    To develop novel antibiotic peptides useful as therapeutic drugs, short model peptides rich in Leu and Lys were designed by changing not only the net positive charge by Lys-deletion but also in the hydrophobic helix region by Leu-deletion from a peptide analogue of cecropin A (1–8)-magainin 2 (1–12) (CA-MA) known as P5. In particular, one peptide (P6), which was obtained

  11. 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.

  12. SVOC partitioning between the gas phase and settled dust indoors

    NASA Astrophysics Data System (ADS)

    Weschler, Charles J.; Nazaroff, William W.

    2010-09-01

    Semivolatile organic compounds (SVOCs) are a major class of indoor pollutants. Understanding SVOC partitioning between the gas phase and settled dust is important for characterizing the fate of these species indoors and the pathways by which humans are exposed to them. Such knowledge also helps in crafting measurement programs for epidemiological studies designed to probe potential associations between exposure to these compounds and adverse health effects. In this paper, we analyze published data from nineteen studies that cumulatively report measurements of dustborne and airborne SVOCs in more than a thousand buildings, mostly residences, in seven countries. In aggregate, measured median data are reported in these studies for 66 different SVOCs whose octanol-air partition coefficients ( Koa) span more than five orders of magnitude. We use these data to test a simple equilibrium model for estimating the partitioning of an SVOC between the gas phase and settled dust indoors. The results demonstrate, in central tendency, that a compound's octanol-air partition coefficient is a strong predictor of its abundance in settled dust relative to its gas phase concentration. Using median measured results for each SVOC in each study, dustborne mass fractions predicted using Koa and gas-phase concentrations correlate reasonably well with measured dustborne mass fractions ( R2 = 0.76). Combined with theoretical understanding of SVOC partitioning kinetics, the empirical evidence also suggests that for SVOCs with high Koa values, the mass fraction in settled dust may not have sufficient time to equilibrate with the gas phase concentration.

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

    E-print Network

    Minnesota, University of

    2005-01-01

    calculated to determine the characteristics that confer their antimicrobial activity. A structure­activity: Antimicrobial peptide; Homology modeling; Structure­activity relationships 1. Introduction 1.1. AntimicrobialPeptides 26 (2005) 197­206 Protegrin structure­activity relationships: using homology models

  14. Evolutionary Sequence Modeling for Discovery of Peptide Hormones

    Microsoft Academic Search

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

    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

  15. Autoxidation of MMH at Room Temperature in the Gas Phase

    Microsoft Academic Search

    Laurent Catoire; Claude Paillard

    2000-01-01

    The objective of this study is to characterize the lifetime of monomethylhydrazine mixed with O2, both in the gas phase, at 298 K. A detailed kinetic model has been built to allow a numerical study of the homogeneous MMH\\/O2 reactivity.

  16. Photodissociation and spectroscopy of gas phase bimetallic clusters

    Microsoft Academic Search

    1992-01-01

    Focus of the research program is the study of gas phase metal clusters for modeling fundamental interactions on metal surfaces. We characterize the chemical bonding between component atoms in clusters as well as the bonding in adsorption on cluster surfaces. Electronic spectra, vibrational frequencies and bond dissociation energies are measured for both neutral and ionized clusters with laser\\/mass spectrometry techniques.

  17. 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.

  18. 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.

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

    PubMed

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

    2015-01-01

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

  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

    (i.e., peptides and proteins) produced upon ESI and provide new insight into their solution to gas phase evolution. First, fundamental principles of periodic focusing ion mobility spectrometry are comprehensively discussed. Radial ion confinement...

  1. Modelling Studies With a Coupled Canopy Atmospheric Chemistry Emission Model on Trace Gas Exchange and Gas Phase Chemistry in a Norway Spruce Forest

    NASA Astrophysics Data System (ADS)

    Forkel, R.; Klemm, O.; Graus, M.; Rappengl{Ü}Ck, B.; Stockwell, W. R.; Grabmer, W.; Held, A.; Hansel, A.; Steinbrecher, R.

    2006-12-01

    Within the joint project BEWA2000 modelling studies were performed in combination with field campaigns in a Norway spruce forest at the Waldstein site in NE Bavaria. Although located in a comparatively remote region the Waldstein site is still affected by a certain background of anthropogenic pollution which can influence BVOC degradation and product formation. The role of chemical degradation of biogenic volatile organic compounds and the effect of dynamical processes on BVOC and product mixing ratios within and above forest canopies have been investigated by applying the one-dimensional canopy-chemistry model CACHE. The simulations with CACHE permit the interpretation of observed features of the diurnal cycles of ozone and VOC mixing ratios by investigating the effect of turbulent exchange, chemical formation and degradation, emission, and deposition during the course of the day. For the conditions given at the Waldstein site chemical BVOC degradation within the canopy was found to reduce the BVOC fluxes into the atmosphere by 10 - 15 % as compared to the emission fluxes on branch basis. Furthermore, the simulations show that BVOC degradation by the NO3 can occur in the lower part of the canopy also during daytime and that this effect is strongly influenced by the presence of advected NOx and local NO emissions from the soil. The simulation results emphasize the role of deposition for the concentrations of BVOC oxidation products and indicate that further research is still necessary concerning the emission and deposition of aldehydes and ketones.

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

    SciTech Connect

    Ali, A.N.; Son, S.F.; Asay, B.W.; Sander, R.K. [Los Alamos National Laboratory, MS C920, Los Alamos, New Mexico 87544 (United States)

    2005-03-15

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

  3. Conformational Transitions in Model Silk Peptides

    Microsoft Academic Search

    Donna Wilson; Regina Valluzzi; David Kaplan

    2000-01-01

    Protein structural transitions and ?-sheet formation are a common problem both in vivo and in vitro and are of critical relevance in disparate areas such as protein processing and ?-amyloid and prion behavior. Silks provide a “databank” of well-characterized polymorphic sequences, acting as a window onto structural transitions. Peptides with conformationally polymorphic silk-like sequences, expected to exhibit an intractable ?-sheet

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  5. Coulomb-assisted dissociative electron attachment: application to a model peptide.

    PubMed

    Sobczyk, Monika; Anusiewicz, Iwona; Berdys-Kochanska, Joanna; Sawicka, Agnieszka; Skurski, Piotr; Simons, Jack

    2005-01-13

    The fragmentation of positively charged gas-phase samples of peptides is used to infer the primary structure of such molecules. In electron capture dissociation (ECD) experiments, very low-energy electrons attach to the sample and rupture bonds to effect the fragmentation. It turns out that ECD fragmentation tends to produce cleavage of very specific types of bonds. In earlier works by this group, it has been suggested that the presence of positive charges produces stabilizing Coulomb potentials that allow low-energy electrons to exothermically attach to sigma orbitals of certain bonds and thus to cleave those bonds. In the present effort, the stabilizing effects of Coulomb potentials due to proximal positive charges are examined for a small model peptide molecule that contains a wide range of bond types. Direct attachment of an electron to the sigma orbitals of eight different bonds as well as indirect sigma bond cleavage, in which an electron first binds to a carbonyl C=O pi orbital, are examined using ab initio methods. It is found that direct attachment to and subsequent cleavage of any of the eight sigma bonds is not likely except for highly positively charged samples. It is also found that attachment to a C=O pi orbital followed by cleavage of the nitrogen-to-alpha-carbon bond is the most likely outcome. Interestingly, this bond cleavage is the one that is seen most commonly in ECD experiments. So, the results presented here seem to offer good insight into one aspect of the ECD process, and they provide a means by which one can estimate (on the basis of a simple Coulomb energy formula) which bonds may be susceptible to cleavage by low-energy electron attachment. PMID:16839114

  6. A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation

    PubMed Central

    Kang, Myungshim

    2010-01-01

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

  7. A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation

    NASA Astrophysics Data System (ADS)

    Kang, Myungshim; Smith, Paul Edward

    2010-05-01

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

  8. Gas-Phase Polymerization: Ultraslow Chemistry

    Microsoft Academic Search

    Howard Reiss

    1987-01-01

    The mechanism of formation of polymer molecules in the gas phase is difficult to study because the involatile polymers tend to condense out of that phase. However, new techniques, involving the use of cloud chambers, have enabled workers to use the nucleation of liquid drops in supersaturated monomer vapors to detect single polymer molecules and therefore to work with so

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

    SciTech Connect

    Zilber, B.; Scherf, T.; Anglister, J. (The Weizmann Institute of Science (Israel)); Levitt, M. (Stanford Univ. School of Medicine, CA (USA))

    1990-10-01

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

  10. 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.

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

    E-print Network

    Tao, Lei

    2011-08-08

    Society for Mass Spectrometry, 18, 1232-1238, Copyright [2007] by Elsevier. 9 proteomics, i.e., high throughput analysis of peptides/proteins, and most of this work has utilized ?bottom-up? proteomics or the identification of proteins by enzymatic... INVESTIGATION ON GAS-PHASE ION STRUCTURES OF BIOMOLECULES USING ION MOBILITY-MASS SPECTROMETRY A Dissertation by LEI TAO Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment...

  12. Simulation of Gas-Phase Kinetics in CHF3:H2: O2 Mixtures

    Microsoft Academic Search

    Dmitry G. Voloshin; Konstantin S. Klopovskiy; Yuri A. Mankelevich; Nikolay A. Popov; Tatyana V. Rakhimova; Alexander T. Rakhimov

    2007-01-01

    A gas-phase reaction model for and mixtures was developed. Self-consistent electron impact cross-section set for was introduced. The original total and partial dissociation cross sections were received. A developed gas-phase kinetic scheme was tested on the experimental data. An important role of the chain reactions in the kinetics of F and H atoms and radicals was revealed.

  13. pH-dependent coarse-grained model of peptides

    E-print Network

    Enciso, Marta; Site, Luigi Delle

    2012-01-01

    We propose a coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving interactions using reference data from atomistic simulations and experimental databases and transferring its main physical features to the coarse-grained resolution according the principle of consistency across the scales. After refining the coarse-grained model appropriately this was achieved by finding a unique set of parameters for the coarse-grained model that, when applied to peptides with different sequences and experimental properties, reproduces the experimental and atomistic data of reference. We used the such parametrized model for performing several numerical tests to check the universality of the model. We have tried systems with rather different response to pH variations, showing a highly satisfactory performance of the model.

  14. 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.

  15. Ultrafast gas-phase electron diffraction

    Microsoft Academic Search

    Joseph Charles Williamson

    1998-01-01

    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

  16. Self-assembly of model DNA-binding peptide amphiphiles.

    PubMed

    Bitton, Ronit; Schmidt, Judith; Biesalski, Markus; Tu, Raymond; Tirrell, Matthew; Bianco-Peled, Havazelet

    2005-12-01

    Peptide amphiphiles combine the specific functionality of proteins with the engineering convenience of synthetic amphiphiles. These molecules covalently link a peptide headgroup, typically from an active fragment of a larger protein, to a hydrophobic alkyl tail. Our research is aimed at forming and characterizing covalently stabilized, self-assembled, peptide-amphiphile aggregates that can be used as a platform for the examination and modular design and construction of systems with engineering biological activity. We have studied the self-assembly properties of a model DNA-binding amphiphile, having a GCN4 peptide as the headgroup and containing a polymerizable methacrylic group in the tail region, using a combination of small-angle X-ray scattering, small-angle neutron scattering, and cryo- transmission electron microscopy. Our results reveal a variety of morphologies in this system. The peptide amphiphiles assembled in aqueous solution to helical ribbons and tubules. These structures transformed into lamella upon DNA binding. In contrast with common surfactants, the specific interaction between the headgroups seems to play an important role in determining the microstructure. The geometry of the self-assembled aggregate can be controlled by means of adding a cosurfactant. For example, the addition of SDS induced the formation of spherical micelles. PMID:16316129

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

    PubMed

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

    2002-12-01

    The most important natural sources of new leads are plant extracts, bacterial broths, animal venoms and peptides isolated from living organisms. However, only the three first have been used extensively in the development of new therapeutic agents. This is probably due to the low pharmacological profile exhibited by peptides, that requires a lengthy transformation to make them suitable as new leads. In contrast, bioactive compounds isolated from the other sources are regularly closer to be used as lead compounds. Nevertheless, the sources for compounds of this category are nowadays scarce. In contrast, there are new bioactive peptides discovered quite often and reported as ligands for different receptors. Under these circumstances peptides appear as an attractive source of prospective new leads. In order to reduce the time involved in the design of a potential lead from a peptide, molecular modeling tools have been developed in the last few years. The purpose of the present work is to review the different techniques available and to report various successful examples of design of new peptidomimetics published in the literature. PMID:12470243

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  19. Substrate-Free Gas-Phase Synthesis of Graphene Sheets

    E-print Network

    Frenklach, Michael

    Substrate-Free Gas-Phase Synthesis of Graphene Sheets Albert Dato,*, Velimir Radmilovic, Zonghoon in the gas phase, and the entire synthesis process took place in fractions of a second, in an atmospheric graphene sheets in the gas phase using a substrate-free, atmospheric-pressure microwave plasma reactor

  20. Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry John T. Halloran

    E-print Network

    Noble, William Stafford

    /MS as a physical process. The model traverses an observed MS/MS spec- trum and a peptide-based theoretical spectrum that serves as a generative model of the process by which peptides produce spectra in MS/MS. DRIP explicitly not model the underlying process by which peptides produce MS/MS spectra. Rather, in Didea both theoretical

  1. A Peptide-Spectrum Alignment Model for Tandem Mass Spectrometry: Extended Version

    E-print Network

    Noble, William Stafford

    fragmentation in MS/MS as a physical process. The model traverses an observed MS/MS spec- trum and a peptide of Peptides (DRIP), a database search method that serves as a generative model of the process by which, was recently proposed [3], but this method does not model the underlying process by which peptides produce MS

  2. Performance of Ecient Minimization Algorithms as Applied to Models of Peptides and Proteins

    E-print Network

    Aluffi, Paolo

    Performance of EÆcient Minimization Algorithms as Applied to Models of Peptides and Proteins CÆciency. Keywords: energy minimization; cyclic peptides and proteins; implicit solvation models; truncated and quasi, as applied to peptide and protein models. Such a study is necessary because the performance of minimization

  3. Low energy electron-induced reactions in gas phase 1,2,3,5-tetra-O-acetyl-?-D-ribofuranose: A model system for the behavior of sugar in DNA

    NASA Astrophysics Data System (ADS)

    Bald, Ilko; Kopyra, Janina; D?bkowska, Iwona; Antonsson, Egill; Illenberger, Eugen

    2007-02-01

    Dissociative electron attachment to 1,2,3,5-tetra-O-acetyl-?-D-ribofuranose (TAR) is studied in a crossed electron-molecular beam experiment with mass spectrometric detection of the observed fragment ions. Since in TAR acetyl groups are coupled at the relevant positions to the five membered ribose ring, it may serve as an appropriate model compound to study the response of the sugar unit in DNA towards low energy electrons. Intense resonances close to 0eV are observed similar to the pure gas phase sugars (2-deoxyribose, ribose, and fructose). Further strong resonances appear in the range of 1.6-1.8eV (not present in the pure sugars). Based on calculations on transient anions adopting the stabilization method, this feature is assigned to a series of closely spaced shape resonances of ?* character with the extra electron localized on the acetyl groups outside the ribose ring system. Further but weaker resonant contributions are observed in the range of 7-11eV, representing core excited resonances and/or ?* shape resonances. The decomposition processes involve single bond ruptures but also more complex reactions associated with substantial rearrangement. The authors hence propose that the sugar unit in DNA plays an active role in the molecular mechanism towards single strand breaks induced by low energy electrons.

  4. Miniature free-piston homogeneous charge compression ignition engine-compressor concept—Part II: modeling HCCI combustion in small scales with detailed homogeneous gas phase chemical kinetics

    Microsoft Academic Search

    H. T. Aichlmayr; D. B. Kittelson; M. R. Zachariah

    2002-01-01

    Operational maps for crankshaft-equipped miniature homogeneous charge compression ignition engines are established using performance estimation, detailed chemical kinetics, and diffusion models for heat transfer and radical loss. In this study, radical loss was found to be insignificant. In contrast, heat transfer was found to be increasingly significant for 10, 1, and 0.1W engines, respectively. Also, temperature–pressure trajectories and ignition delay

  5. Trace gas exchange and gas phase chemistry in a Norway spruce forest: A study with a coupled 1-dimensional canopy atmospheric chemistry emission model

    NASA Astrophysics Data System (ADS)

    Forkel, Renate; Klemm, Otto; Graus, Martin; Rappenglück, Bernhard; Stockwell, William R.; Grabmer, Wolfgang; Held, Andreas; Hansel, Armin; Steinbrecher, Rainer

    Numerical modelling is an efficient tool to investigate the role of chemical degradation of biogenic volatile organic compounds (BVOC) and the effect of dynamical processes on BVOC and product mixing ratios within and above forest canopies. The present study shows an application of the coupled canopy-chemistry model CACHE to a Norway spruce forest at the Waldstein (Fichtelgebirge, Germany). Simulated courses of temperature, trace gas mixing ratios, and fluxes are compared with measurements taken during the BEWA2000 field campaigns. The model permits the interpretation of the observed diurnal course of ozone and VOC by investigating the role of turbulent exchange, chemical formation and degradation, emission, and deposition during the course of the day. The simulation results show that BVOC fluxes into the atmosphere are 10-15% lower than the emission fluxes on branch basis due to chemical BVOC degradation within the canopy. BVOC degradation by the NO 3 radical was found to occur in the lower part of the canopy also during daytime. Furthermore, the simulations strongly indicate that further research is still necessary concerning the emission and deposition of aldehydes and ketones.

  6. Gas-phase Conformational Analysis of (R,R)-Tartaric Acid, its Diamide, N,N,N',N'- Tetramethyldiamide and Model Compounds

    NASA Astrophysics Data System (ADS)

    Hoffmann, Marcin; Szarecka, Agnieszka; Rychlewski, Jacek

    A review over most recent ab initio studies carried out at both RHF and MP2 levels on (R,R)-tartaric acid (TA), its diamide (DA), tetramethyldiamide (TMDA) and on three prototypic model systems (each of them constitutes a half of the respective parental molecule), i.e. 2-hydroxyacetic acid (HA), 2-hydroxyacetamide (HD) and 2-hydroxy-N,N-dimethylacetamide (HMD) is presented. (R,R)-tartaric acid and the derivatives have been completely optimized at RHF/6-31G* level and subsequently single-point energies of all conformers have been calculated with the use of second order perturbation theory according to the scheme: MP2/6-31G*//RHF/6-31G*. In the complete optimization of the model molecules at RHF level we have employed relatively large basis sets, augmented with polarisation and diffuse functions, namely 3-21G, 6-31G*, 6-31++G** and 6-311++G**. Electronic correlation has been included with the largest basis set used in this study, i.e. MP2/6-311++G**//RHF/6-311++G** single-point energy calculations have been performed. General confomational preferences of tartaric acid derivatives have been analysed as well as an attempt has been made to define main factors affecting the conformational behaviour of these molecules in the isolated state, in particular, the role and stability of intramolecular hydrogen bonding. In the case of the model compounds, our study principally concerned the conformational preferences and hydrogen bonding structure within the [alpha]-hydroxy-X moiety, where X=COOH, CONH2, CON(CH3)2.

  7. Gas phase hydrogen-bonded complexes of aromatic molecules

    NASA Astrophysics Data System (ADS)

    Mons, Michel; Dimicoli, Iliana; Piuzzi, François

    The present review discusses the possibility of measuring the dissociation energy of gas phase complexes from their dissociative photoionization. A compilation of recent results on hydrogen-bonded complexes of aromatic molecules, with a polar solvent molecule (water, alcohol, NH 3 , HCl, etc.), playing the role of either proton donor or proton acceptor is presented. We show that laser experiments begin to provide a consistent set of energetic data that can be considered as benchmarks to assess quantum calculations as well as to parametrize the force field models used in biochemistry.

  8. 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 ...

  9. Gas phase thermochemistry of organogermanium compounds

    SciTech Connect

    Engel, J.P.

    1993-12-07

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

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

    NASA Astrophysics Data System (ADS)

    Balucani, Nadia; Ceccarelli, Cecilia; Taquet, Vianney

    2015-04-01

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

  11. UV Damage of Collagen: Insights from Model Collagen Peptides

    PubMed Central

    Jariashvili, Ketevan; Madhan, Balaraman; Brodsky, Barbara; Kuchava, Ana; Namicheishvili, Louisa; Metreveli, Nunu

    2012-01-01

    Fibrils of type I collagen in the skin are exposed to ultraviolet (UV) light and there have been claims that collagen photo-degradation leads to wrinkles and may contribute to skin cancers. To understand the effects of UV radiation on collagen, type I collagen solutions were exposed to the UV-C wavelength of 254 nm for defined lengths of time at 4°C. Circular dichroism (CD) experiments show that irradiation of collagen leads to high loss of triple helical content with a new lower thermal stability peak and SDS-gel electrophoresis indicates breakdown of collagen chains. To better define the effects of UV radiation on the collagen triple-helix, the studies were extended to peptides which model the collagen sequence and conformation. CD studies showed irradiation for days led to lower magnitudes of the triple-helix maximum at 225 nm and lower thermal stabilities for two peptides containing multiple Gly-Pro-Hyp triplets. In contrast, the highest radiation exposure led to little change in the Tm values of (Gly-Pro-Pro)10 and (Ala-Hyp-Gly)10, although (Gly-Pro-Pro)10 did show a significant decrease in triple helix intensity. Mass spectroscopy indicated preferential cleavage sites within the peptides, and identification of some of the most susceptible sites of cleavage. The effect of radiation on these well defined peptides gives insight into the sequence and conformational specificity of photo-degradation of collagen. PMID:22002434

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

    PubMed

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

    2015-06-01

    Human milk is a highly valuable food for newborns and infants. Its protein fraction plays an important role for the development of the newborn. In the present study, an in vitro digestive model, developed for resembling closely the digestive system of an infant, was applied to human milk in order to identify and characterize the peptide profile. The peptide profile obtained after digestion was analyzed by ?LC-LTQ-Orbitrap-MS. A total of 149 peptides from ?-casein, 30 peptides from ?-lactalbumin, 26 peptides from ?s1-casein, 24 peptides from ?-casein, 28 peptides from osteopontin, and 29 from lactoferrin was recovered. The identified peptide profile of partially hydrolyzed proteins, such as caseins, ?-lactalbumin, and osteopontin, was different from that previously reported demonstrating a different performance of the developed neonatal digestive system with respect to other previously applied. These results would be useful as a starting point to investigate the physiological function of breast milk peptides. PMID:26017322

  13. Coarse-Grained Peptide Modeling Using a Systematic Multiscale Approach

    Microsoft Academic Search

    Jian Zhou; Ian F. Thorpe; Sergey Izvekov; Gregory A. Voth

    2007-01-01

    A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically detailed simulations to derive CG forces and associated effective potentials. In this work, the MS-CG methodology is extended to study two peptides representing distinct structural motifs, ?-helical polyalanine and the ?-hairpin V5PGV5. These studies represent the first known application of

  14. Peptide self-assembly as a model of proteins in the pre-genomic world

    E-print Network

    Ghosh, Indraneel

    -a-amino-g-nucleobase-butyric acid PNA peptide nucleic acid Introduction The nature of the molecular origins of life is a research hexopyranosyl analogs of RNA [5] and peptide nucleic acids (PNA) [6]. Research into prebiotic chemistry hasPeptide self-assembly as a model of proteins in the pre-genomic world Indraneel Ghosh1 and Jean

  15. Electron scattering from gas-phase glycine molecules.

    PubMed

    Tashiro, Motomichi

    2008-10-28

    Low-energy electron collisions with gas-phase glycine molecules have been studied using the fixed-nuclei R-matrix method based on state-averaged complete-active-space self-consistent-field orbitals. A total of 40 electronic states of neutral glycine, including 3s and 3p Rydberg excited states, are included in the R-matrix model. A large peak is observed in the A(") partial elastic cross section around 3.4 eV, which originates from the pi( *) shape resonance. In addition, many sharp narrow peaks coming from core excited resonances are seen in the elastic and inelastic cross sections at energies above 5 eV. Although the effect of the Rydberg orbitals on the elastic cross section is insignificant, these orbitals are crucial to represent core excited resonances in the inelastic cross sections. In previous experiments on dissociative electron attachment to gas-phase glycine, noticeable product ion peaks have been observed at electron collision energies around 1-2 and 5-10 eV. The resonance positions obtained in our calculations are generally close to these experimental results. PMID:19045267

  16. Gas phase hyper-Rayleigh scattering measurements

    NASA Astrophysics Data System (ADS)

    Shelton, David P.

    2012-07-01

    Measurements of hyper-Rayleigh scattering intensities and polarization ratios are presented for nine small molecules in the gas phase [CH4, CF4, CCl4, N2O, NH3, D2O, SO2, CF2Cl2, and (CH3)2CO]. In four cases [CH4, CF4, CCl4, and N2O] all molecular hyperpolarizability tensor components can be determined from the measurements. The results of this experiment are compared with the results of previous ab initio calculations, finding discrepancies up to 60%. Including vibrational contributions decreases the discrepancies for CH4 and CF4 and increases them for CCl4, D2O, and NH3.

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

    NASA Astrophysics Data System (ADS)

    Giovangigli, Vincent; Rahman, Shihab

    2013-01-01

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

  18. Gas phase and surface reactions in subatmospheric chemical vapor deposition of tetraethylorthosilicate-ozone

    SciTech Connect

    Gill, W.N.; Ganguli, S. [Department of Chemical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180-3590 (United States)] [Department of Chemical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180-3590 (United States)

    1997-07-01

    A new physical-chemical model, which applies over a wide range of operating pressures, describes the gas phase and surface reactions in subatmospheric chemical vapor deposition of silicon dioxide for producing inter-layer dielectrics in a cold-wall reactor. Tetraethylorthosilicate (TEOS) reacts in the gas phase to form an intermediate which is adsorbed and reacts on the surface to produce a silicon dioxide film. The results compare favorably with experimental data over a pressure range of 100{endash}600 Torr and a temperature range of 370{endash}500{degree}C. The concentration distributions of TEOS, intermediate and ozone in the gas phase and their ratios at the surface of the wafer are determined to study gas phase nucleation and the relationship between composition distributions and film quality. Previous models based on low pressure data in the range of 30{endash}90 Torr need to be modified to predict accurately the rates of deposition from 100 Torr to atmospheric pressure. Gas phase reactions cause the maximum in the deposition rates to shift to higher pressures at lower deposition temperatures, both in the model and experiments. At higher pressures, particulates are formed by the gas phase reactions which must be included to represent properly the chemical dynamics of the process. The deposition rate increases up to an asymptotic value as the TEOS flow rate is increased; above this level no further increase in growth rate occurs. This is a consequence of the basic mechanism of the surface reaction which predicts the asymptotic behavior observed. {copyright} {ital 1997 American Vacuum Society.}

  19. Simulation of the transfer of water with a fine-disperse gas phase in porous media

    NASA Astrophysics Data System (ADS)

    Dem'yanov, A. Yu.; Dinariev, O. Yu.; Ivanov, E. N.

    2012-11-01

    The problem on the transfer of a three-phase water-gas-oil mixture in a porous medium was solved for the case where the water contains a fine-disperse gas phase in the form of microsized or nanosized bubbles. It was suggested that the transfer of bubbles is mainly due to the flow of the disperse phase (water). In this case, the large aggregates of the gas phase in the porous space, in the water, and in the oil are transferred in accordance with the modified Darcy law for multiphase mixtures. A mathematical model of movement of the indicated mixture has been constructed for the case where the main phases (water, gas, and oil) adhere to the filtration equations and the fine-disperse gas phase is defined by a kinetic equation like the Boltzmann equation. Some one-dimensional numerical solutions of the indicated problem were analyzed.

  20. Modeling of mixed-mode chromatography of peptides.

    PubMed

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

    2013-03-29

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

  1. 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.

  2. 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.

  3. 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

  4. 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...

  5. 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.

  6. Sugar synthesis from a gas-phase formose reaction.

    PubMed

    Jalbout, Abraham F; Abrell, Leif; Adamowicz, Ludwik; Polt, Robin; Apponi, A J; Ziurys, L M

    2007-06-01

    Prebiotic possibilities for the synthesis of interstellar ribose through a protic variant of the formose reaction under gas-phase conditions were studied in the absence of any known catalyst. The ion-molecule reaction products, diose and triose, were sought by mass spectrometry, and relevant masses were observed. Ab initio calculations were used to evaluate protic formose mechanism possibilities. A bilateral theoretical and experimental effort yielded a physical model for glycoaldehyde generation whereby a hydronium cation can mediate formaldehyde dimerization followed by covalent bond formation leading to diose and water. These results advance the possibility that ion-molecule reactions between formaldehyde (CH(2)O) and H(3)O(+) lead to formose reaction products and inform us about potential sugar formation processes in interstellar space. PMID:17630839

  7. Instabilities in Lean Gas-Phase Combustion

    NASA Astrophysics Data System (ADS)

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

    2005-06-01

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

  8. Transferring pharmaceuticals into the gas phase

    NASA Astrophysics Data System (ADS)

    Christen, Wolfgang; Krause, Tim; Rademann, Klaus

    2008-11-01

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

  9. Gas-phase reactions of halogen species of atmospheric importance

    NASA Astrophysics Data System (ADS)

    Heard, Anne C.

    A low-pressure discharge-flow technique, with various optical detection methods, has been used to determine bimolecular rate coefficients for a number of reactions in the gas-phase between OH radicals and organic halogen-containing molecules and between NO3 radicals and the iodine species I2 and I. These experiments have shown that: (1) the reaction of methyl iodide with OH accounts for approximately 2 percent of the removal of CH3I from the troposphere as compared with photolysis; (2) abstraction of I-atoms from a C-I bond by OH is probable in the gas-phase; (3) the halogen-containing anaesthetic substances halothane CF3CClBrH, enflurane CF2HOCF2CFClH, isoflurane CF2HOCClHCF3 and sevoflurane (CF3)2CHOCFH2 have significantly shorter tropospheric lifetimes than the fully halogenated CFCs and halons because of reaction with the OH radical and are thus unlikely to be transported up to the stratosphere where they could contribute to the depletion of ozone. Data obtained for reactions between OH and some 'CFC alternatives' along with measurements of the integrated absorption cross-sections of the compounds in the spectral region 800-1200 cm(exp -1) were used to calculate ozone depletion potentials (ODP) and greenhouse warming potentials relative to CFCl3 for each compound. The study of the reactions between OH and CF3CFBrH and CF2BrH was used to provide a useful first estimate of the environmental acceptability of these compounds in the context of their possible use as replacements for the conventional CFCs. A method was developed to provide a first estimate of the ODP of a halogenated alkane without use of a complicated (and expensive) computer modeling scheme. A reaction between molecular iodine and the nitrate radical in the gas-phase was discovered and the kinetics of this reaction have been studied. No temperature or pressure dependence was observed for the rate of reaction, the rate constant of which was found to be (1.5 +/- 0.5) x 10(exp -12)/cu cm/molecule/s. The reaction between I and NO3 was found to occur at a rate of about 60 percent of the hard-sphere collision frequency for the two species. The rate constant for reaction between I and NO3 was found to be (4.5 +/- 1.9) x 10(exp -10)/cu cm/molecule/s. An upper limit for the heat of formation of IONO2 of (21 +/- 3) kJmol(exp -1) was also derived.

  10. 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.

  11. Knowledge-based grouping of modeled HLA peptide complexes

    Microsoft Academic Search

    Pandjassarame Kangueane; Meena K Sakharkar; Kuan S Lim; Han Hao; Kui Lin; Ren E Chee; Prasanna R Kolatkar

    2000-01-01

    Human leukocyte antigens are the most polymorphic of human genes and multiple sequence alignment shows that such polymorphisms are clustered in the functional peptide binding domains. Because of such polymorphism among the peptide binding residues, the prediction of peptides that bind to specific HLA molecules is very difficult. In recent years two different types of computer based prediction methods have

  12. Simulating electron transfer attachment to a positively charged model peptide.

    PubMed

    Anusiewicz, Iwona; Berdys-Kochanska, Joanna; Skurski, Piotr; Simons, Jack

    2006-02-01

    Ab initio electronic structure methods, including stabilization method tools for handling electronically metastable states, are used to treat a model system designed to probe the electron-transfer event characterizing electron-transfer dissociation (ETD) mass spectroscopic studies of peptides. The model system consists of a cation H(3)C-(C=O)NH-CH(2)-CH(2)-NH(3)(+), containing a protonated amine site and an amide site, that undergoes collisions with a CH(3)(-) anion. Cross-sections for electron transfer from CH(3)(-) to the protonated amine site are shown to exceed those for transfer to the Coulomb-stabilized amide site by 2 orders of magnitude. Moreover, it is shown that the fates of the amine-attached and amide-attached species are similar in that both eventually lead to the same carbon-centered radical species H(3)C-((*)C-OH)NH-CH(2)-CH(2)-NH(2), although the reaction pathways by which the two species produce this radical are somewhat different. The implications for understanding peptide fragmentation patterns under ETD conditions are also discussed in light of this work's findings. PMID:16435786

  13. Methane-to-Methanol Conversion by Gas-Phase Transition Metal Oxide Cations: Experiment and Theory

    E-print Network

    Metz, Ricardo B.

    Methane-to-Methanol Conversion by Gas-Phase Transition Metal Oxide Cations: Experiment and Theory-phase transition metal oxide cations can convert methane to methanol. Methane activation by MO+ is discussed-phase transition metal oxides with methane are thus a simple model system for the direct conversion of methane

  14. Investigation of the formation of iron nanoparticles from the gas phase by molecular dynamics simulation

    Microsoft Academic Search

    N. Lümmen; T. Kraska

    2004-01-01

    The formation of iron particles from the supersaturated gas phase is investigated by molecular dynamics simulation. The atomic interaction is modelled with a recent parameterization of the embedded atom method which is able to describe the bcc phase of bulk iron. The influence of the state conditions such as temperature and density on the growth mechanisms of the iron particles

  15. Photodissociation and spectroscopy of gas phase bimetallic clusters. Annual progress report

    Microsoft Academic Search

    1992-01-01

    Focus of the research program is the study of gas phase metal clusters for modeling fundamental interactions on metal surfaces. We characterize the chemical bonding between component atoms in clusters as well as the bonding in adsorption on cluster surfaces. Electronic spectra, vibrational frequencies and bond dissociation energies are measured for both neutral and ionized clusters with laser\\/mass spectrometry techniques.

  16. The photochemistry of 1,4-cyclohexadiene in solution and in the gas phase: conical intersections and the origin of the `helicopter-type'

    E-print Network

    Haas, Yehuda

    The photochemistry of 1,4-cyclohexadiene in solution and in the gas phase: conical intersections photochemistry of 1,4-cyclohexadiene (CHDN) in solution and in the gas phase is analyzed using a model is proposed, and its properties are calculated. I. Introduction The photochemistry of 1,4-cyclohexadiene (CHDN

  17. Chiral recognition in gas-phase cyclodextrin: Amino acid complexes—Is the three point interaction still valid in the gas phase?

    Microsoft Academic Search

    Seonghee Ahn; Javier Ramirez; Gabriela Grigorean; Carlito B. Lebrilla

    2001-01-01

    The validity of the “three-point interaction” model is examined in the guest exchange reaction involving complexes of cyclodextrins\\u000a and amino acids. The amino acid guest is exchanged in the gas phase in the presence of a gaseous alkyl amine. The net reaction\\u000a is proton transfer between the protonated amino acid and the alkyl amine. The amino acid is lost as

  18. 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 ...

  19. Comparison of catalytic ethylene polymerization in slurry and gas phase

    Microsoft Academic Search

    Majid Daftaribesheli

    2009-01-01

    Polyethylene (PE) with the annual consumption of 70 million tones in 2007 is mostly produced in slurry, gas-phase or combination of both processes.\\u000aThis work focuses on a comparison between the slurry and gas phase processes. Why does PE produced in theses two processes can show extremely different properties and extremely different reaction behaviour even if the same Ziegler-Natta (ZN)

  20. Quantitative structure activity relationship modelling of peptides and proteins as a tool in food science

    Microsoft Academic Search

    Are Hugo Pripp; Tomas Isaksson; Leszek Stepaniak; Terje Sørhaug; Ylva Ardö

    2005-01-01

    Peptides and proteins contribute to physical properties, biological activities and sensory characteristics of foods. Studies on the isolation and characterisation of peptides and proteins allow compilation of data sets on their structures and properties\\/activities. Quantitative structure activity relationship (QSAR) modelling provides methodology to find mathematical expressions for such relationships which may then be useful for estimating activities of any related

  1. Computational Modeling Studies of Peptides and Proteins on Inorganic Surfaces

    NASA Astrophysics Data System (ADS)

    Farmer, Barry

    2013-03-01

    Biological moieties offer exquisite sensitivity and selectivity in their interactions with small molecules, offering considerable potential in applications as chemical sensors. To detect binding events between the peptide and the intended molecule, a transduction mechanism is needed. This often involves an association of the peptide with an inorganic surface, such as a metal nanoparticle, a carbon nanotube, or graphene. Understanding the nature of the association of the peptide with the surface and its effect on the conformational (and thus, binding) properties of the peptide are key to optimizing the sensing mechanism. We utilized computational approaches ranging from ab initio to molecular dynamics to bond-fluctuation Monte Carlo methods to study the adsorption of peptides and proteins on inorganic surfaces to develop an understanding of the role that composition and substrate character plays in the adsorption process, and in turn, the effects on the binding events with the molecules of interest.

  2. Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

    PubMed Central

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2011-01-01

    By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ? dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the ? system of C? substituents and the ? system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed. PMID:21949726

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

    PubMed

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

    2015-06-01

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

  4. Atomic and molecular physics in the gas phase.

    PubMed

    Toburen, L H

    1991-01-01

    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 circumstance has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions 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, and lead to knowledge of the regions of energy deposition where molecular and phase effects are important-knowledge that guides development in appropriate theory. In this report, studies of the doubly differential cross sections, which are crucial to the development of stochastic energy deposition calculations and track structure simulation, are reviewed. We discuss areas of understanding and address directions for future work. 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. PMID:1811483

  5. Gas-Phase Reactions of Halogen Species of Atmospheric Importance.

    NASA Astrophysics Data System (ADS)

    Heard, Anne C.

    Available from UMI in association with The British Library. Requires signed TDF. A low-pressure discharge-flow technique, with various optical detection methods, has been used to determine bimolecular rate coefficients for a number of reactions in the gas-phase between OH radicals and organic halogen -containing molecules and between NO_3 radicals and the iodine species I_2 and I. These experiments have shown that: (i) the reaction of methyl iodide with OH accounts for approximately 2% of the removal of CH_3I from the troposphere as compared with photolysis; (ii) abstraction of I-atoms from a C-I bond by OH is probable in the gas -phase; (iii) the halogen-containing anaesthetic substances halothane CF_3CCl BrH, enflurane CF_2HOCF _2CFClH, isoflurane CF_2HOCClHCF _3 and sevoflurane (CF_3) _2CHOCFH_2 have significantly shorter tropospheric lifetimes than the fully halogenated CFCs and halons because of reaction with the OH radical and are thus unlikely to be transported up to the stratosphere where they could contribute to the depletion of ozone. Data obtained for reactions between OH and some 'CFC alternatives' along with measurements of the integrated absorption cross -sections of the compounds in the spectral region 800-1200 cm^{-1} were used to calculate ozone depletion potentials (ODP) and greenhouse warming potentials relative to CFCl_3 for each compound. The study of the reactions between OH and CF_3CFBrH and CF _2BrH was used to provide a useful first estimate of the environmental acceptability of these compounds in the context of their possible use as replacements for the conventional CFCs. A method was developed to provide a first estimate of the ODP of a halogenated alkane without use of a complicated (and expensive) computer modeling scheme. A reaction between molecular iodine and the nitrate radical in the gas-phase was discovered and the kinetics of this reaction have been studied. No temperature or pressure dependence was observed for the rate of reaction, the rate constant of which was found to be (1.5 +/- 0.5) times 10 ^{-12}cm^{ -3}molecule^{-1}s ^{-1}. The reaction between I and NO_3 was found to occur at a rate of about 60% of the hard-sphere collision frequency for the two species. The rate constant for reaction between I and NO_3 was found to be (4.5 +/- 1.9) times 10^{-10}cm^3 molecule^{-1}s ^{-1}. An upper limit for the heat of formation of IONO_2 of (21 +/- 3) kJmol^ {-1} was also derived. (Abstract shortened by UMI.).

  6. 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.

  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. 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

  10. Interaction studies of novel cell selective antimicrobial peptides with model membranes and E. coli ATCC 11775.

    PubMed

    Joshi, Seema; Bisht, Gopal Singh; Rawat, Diwan S; Kumar, Anil; Kumar, Rita; Maiti, Souvik; Pasha, Santosh

    2010-10-01

    Cationic antimicrobial peptides (CAMPs) are novel candidates for drug development. Here we describe design of six short and potent CAMPs (SA-1 to SA-6) based on a minimalist template of 12 residues H+HHG+HH+HH+NH2 (where H: hydrophobic amino acid and +: charged hydrophilic amino acid). Designed peptides exhibit good antibacterial activity in micro molar concentration range (1-32 mug/ml) and rapid clearance of Gram-positive and Gram-negative bacterial strains at concentrations higher than MIC. For elucidating mode of action of designed peptides various biophysical studies including CD and Trp fluorescence were performed using model membranes. Further based on activity, selectivity and membrane bound structure; modes of action of Trp rich peptide SA-3 and template based peptide SA-4 were compared. Calcein dye leakage and transmission electron microscopic studies with model membranes exhibited selective membrane active mode of action for peptide SA-3 and SA-4. Extending our work from model membranes to intact E. coli ATCC 11775 in scanning electron micrographs we could visualize different patterns of surface perturbation caused by peptide SA-3 and SA-4. Further at low concentration rapid translocation of FITC-tagged peptide SA-3 into the cytoplasm of E. coli cells without concomitant membrane perturbation indicates involvement of intracellular targeting mechanism as an alternate mode of action as was also evidenced in DNA retardation assay. For peptide SA-4 concentration dependent translocation into the bacterial cytoplasm along with membrane perturbation was observed. Establishment of a non specific membrane lytic mode of action of these peptides makes them suitable candidates for drug development. PMID:20599694

  11. Gas phase radiative effects in diffusion flames

    Microsoft Academic Search

    Hasan Bedir

    1998-01-01

    Several radiation models are evaluated for a stagnation point diffusion flame of a solid fuel in terms of accuracy and computational time. Narrowband, wideband, spectral line weighted sum of gray gases (SLWSGG), and gray gas models are included in the comparison. Radiative heat flux predictions by the nongray narrowband, wideband, and SLWSGG models are found to be in good agreement

  12. 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.

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

    PubMed

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

    2015-05-28

    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. PMID:26026459

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

    PubMed

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

    2005-07-01

    Degradation of formaldehyde with different initial concentration over titanium dioxide was carried out in a photocatalytic reactor. Photocatalytic rates were well described by the simplified Langmuir-Hinshelwood model. The kinetic analysis shows that the apparent first-order reaction coefficient is lower and half-life of photocatalysis is longer for low concentration than for high concentration formaldehyde. A network formation model of the photocatalytic products was established. Experimental results and analysis demonstrate that carbon dioxide concentration and carbon monoxide concentration in gas phase vary exponentially with the illumination time and may be even higher than gas-phase formaldehyde concentration if there is much pre-adsorbed formaldehyde in adsorption equilibrium on catalysts before illumination. Carbon monoxide is found to be one of the by-products during formaldehyde photooxidation. PMID:15963801

  15. Gas-phase dissociation pathways of a tetrameric protein complex

    NASA Astrophysics Data System (ADS)

    Sobott, Frank; McCammon, Margaret G.; Robinson, Carol V.

    2003-12-01

    The gas-phase dissociation of the tetrameric complex transthyretin (TTR) has been investigated with tandem-mass spectrometry (tandem-MS) using a nanoflow-electrospray interface and a quadrupole time-of-flight (Q-TOF) mass spectrometer. The results show that highly charged monomeric product ions dissociate from the macromolecular complex to form trimeric products. Manipulating the pressure conditions within the mass spectrometer facilitates the formation of metastable ions. These were observed for the transitions from tetrameric to monomeric and trimeric product ions and additionally for losses of small molecules associated with the protein complex in the gas phase. These results are interpreted in the light of recent mechanisms for the electrospray process and provide insight into the composition and factors governing the stability of macromolecular ions in the gas phase.

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

    SciTech Connect

    Schmidt, Michael W. [Ames Laboratory; Gordon, Mark S. [Ames Laboratory

    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.

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

    SciTech Connect

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

    2005-10-01

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

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

    PubMed

    Bouchoux, Guy

    2015-09-01

    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. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 493-534, 2015. PMID:24399766

  19. 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.

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

    PubMed Central

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

    1996-01-01

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

  1. A Variational Model for Oligomer-Formation Process of GNNQQNY Peptide from Yeast Prion Protein Sup35

    E-print Network

    Zhang, Yang

    A Variational Model for Oligomer-Formation Process of GNNQQNY Peptide from Yeast Prion Protein Sup-like fibrous proteins. However, the processes by which the randomly diffused monomer peptides aggregate is determined to be three peptides for the homogeneous nucleation process, whereas the zig-zag growth pattern

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

    PubMed Central

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

    2011-01-01

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

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

    ERIC Educational Resources Information Center

    Perez, J. M.; Quereda, R.

    1983-01-01

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

  4. Gas-phase terpene oxidation products: a review

    Microsoft Academic Search

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

    1999-01-01

    Terpenes are emitted in large quantities from vegetation into the troposphere, where they react readily with ozone, OH and NO3 radicals leading to a number of oxidation products. The current knowledge about gas-phase terpene oxidation products is reviewed. Their formation and decomposition pathways, their products and their relevance for the troposphere, and their chemical analysis are discussed. Data on oxidation

  5. Gas phase pulse radiolysis. [Reaction with hydroxyl radical

    SciTech Connect

    Jonah, C.D.; Andong Liu; Mulac, W.A.

    1987-01-01

    Gas phase pulse radiolysis, a technique which can be used to study many different phenomena in chemistry and physics, is discussed. As a source of small radicals, pulse radiolysis is important to the field of chemistry, particularly to combustion and atmospheric kinetics. The reactions of 1,3-butadiene, allene, ethylene and acetylene with OH are presented. 52 refs., 1 fig., 1 tab.

  6. Extended sugar synthesis from a gas phase formose reaction

    Microsoft Academic Search

    Abraham F. Jalbout; Leif Abrell; Ludwik Adamowicz; Robin Polt; L. M. Ziurys

    2007-01-01

    The prebiotic possibilities for the synthesis of interstellar ribose through a protic variant of the formose reaction under gas phase conditions were studied with the use of a proton source as a known catalyst. Mass spectrometry was sought as a method to probe the synthesis of higher order sugars. Ab initio calculations were used to evaluate protic formose mechanism possibilities

  7. Sugar Synthesis from a Gas-Phase Formose Reaction

    Microsoft Academic Search

    Abraham F. Jalbout; Leif Abrell; Ludwik Adamowicz; Robin Polt; A. J. Apponi; L. M. Ziurys

    2007-01-01

    Prebiotic possibilities for the synthesis of interstellar ribose through a protic variant of the formose reaction under gas-phase conditions were studied in the absence of any known catalyst. The ion-molecule reaction products, diose and triose, were sought by mass spectrometry, and relevant masses were observed. Ab initio calculations were used to evaluate protic formose mechanism possibilities. A bilateral theoretical and

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

    EPA Science Inventory

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

  9. Selected examples of gas-phase ion chemistry studies.

    PubMed

    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

  10. Printing nanoparticle building blocks from the gas phase using nanoxerography

    Microsoft Academic Search

    Chad R. Barry; Nyein Z. Lwin; Wei Zheng; Heiko O. Jacobs

    2003-01-01

    This letter reports on the electrostatic driven self-assembly of nanoparticles onto charged surface areas ~receptors! from the gas phase for nanoparticle based device fabrication. The charged areas were generated by a parallel technique that uses a ?exible, conductive electrode to pattern electrons and holes in a thin film electret. Samples, 1 cm, in size, were patterned with charge in 10

  11. Printing nanoparticles from the liquid and gas phases using nanoxerography

    Microsoft Academic Search

    Chad R Barry; Michael G Steward; Nyein Z Lwin; Heiko O Jacobs

    2003-01-01

    This paper reports on the directed self-assembly of nanoparticles onto charged surface areas with a resolution of 200 nm from the liquid phase and 100 nm from the gas phase. The charged areas required for this type of nanoxerographic printing were fabricated using a parallel method that employs a flexible, electrically conductive, electrode to charge a thin-film electret. As electrodes,

  12. 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)

  13. 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.

  14. 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

  15. A model for the controlled assembly of semiconductor peptides

    NASA Astrophysics Data System (ADS)

    Kim, Se Hye; Parquette, Jon R.

    2012-10-01

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

  16. 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.

  17. Slow insertion kinetics during interaction of a model antimicrobial peptide with unilamellar phospholipid vesicles.

    PubMed

    Ningsih, Zubaidah; Hossain, Mohammed Akhter; Wade, John D; Clayton, Andrew H A; Gee, Michelle L

    2012-01-31

    The mechanism of interaction between a model antimicrobial peptide and phospholipid unilamellar vesicle membranes was studied using fluorescence spectroscopy, fluorescence lifetime measurements, and light scattering. The peptide, a mellitin mutant, was labeled at position K14 with the polarity-sensitive probe AlexaFluor 430. The kinetics of the interaction of this derivative with various concentrations of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) vesicles was examined. Our work unveiled two novel aspects of peptide-lipid interactions. First, the AB plot or phasor analysis of the fluorescence lifetime studies revealed at least three different peptide states, the population of which depended on the lipid to peptide (L:P) concentration ratio. Second, complex fluorescence kinetics were observed over extended time-scales from 30 s to 2 h. The extended kinetics was only observed at particular lipid concentrations (L:P ratios 20:1 and 10:1) and not at others (30, 40, 50 and 100:1 L:P ratio). Analysis of the complex kinetics revealed several intermediates. We assign these to distinct states of the peptide formed during helix insertion into the vesicle membrane that are intermediate to lytic pore formation. PMID:22148887

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

    PubMed Central

    Larsson, Per; Kasson, Peter M.

    2013-01-01

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

  19. 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.

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

    SciTech Connect

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

    2000-04-12

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

  1. Kinetic analysis of the gas-phase pyrolysis of carbohydrates

    Microsoft Academic Search

    Eun-Jae Shin; Mark R. Nimlos; Robert J. Evans

    2001-01-01

    Cellulose-derived pyrolysis products and selected primary products, 5-hydroxymethyl furfural (5-HMF), levoglucosan and hydroxyacetaldehyde (HAA) were used as starting materials for kinetic studies of gas-phase pyrolysis by using flow tube reactors and product detection with molecular beam mass spectrometry (MBMS). Multivariate data analysis was used to identify major product classes for lumped product kinetic analysis. The methodology employed in this work

  2. Molecular dynamics of gas phase hydrogen-bonded complexes 

    E-print Network

    Wofford, Billy Alan

    1987-01-01

    of rovibrational bands in hydrogen- bonded complexes have been recorded. Static gas phase infrared spec- troscopic analysis of fundamental, overtone, combination and hot bands in the common and some isotopically substituted species have been per- formed using a... necessitates rovibrational analysis of a plethora of vibrational bands. Observa- tion of the 2vl overtone band in the hydrogen-bonded complex HCN---HF permits evaluation of the anharmonicity constant Xll ? -116. 9(1) cm and determination...

  3. 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.

  4. Photodissociation of condensed carbon dioxide below the gas phase thresholds

    Microsoft Academic Search

    J. M. Coquel; L. Siller; J. Wilkes; R. Carrapa; C. L. A. Lamont; T. Almeida Gasche; R. E. Palmer; A. M. C. Moutinho

    1998-01-01

    We have investigated photodesorption from condensed carbon dioxide for photon energies ranging from 13 to 35 eV using synchrotron radiation. We report the desorption of O2+ ions at energies as low as 13 eV, and discuss this behaviour in terms of ion–molecule reactions. The desorbed CO+ ion yield shows resonances at ?15.4 and ?17 eV, below the gas-phase thermodynamic threshold

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

    Microsoft Academic Search

    Munday

    1993-01-01

    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

  6. Decay Pathways of Pyrimidine Bases: From Gas Phase to Solution

    Microsoft Academic Search

    Wei Kong; Yonggang He; Chengyin Wu

    We use a variation of the pump-probe technique to unravel the photodynamics of nucleic acid bases and their water complexes.\\u000a Our work aims at bridging studies from the gas phase with those in the solution phase. Our results indicate that the intrinsic\\u000a properties of the pyrimidine bases can be dramatically modified by the surrounding environment. As isolated species, the bases

  7. Gas-phase dissociation reactions of protonated saxitoxin and neosaxitoxin

    Microsoft Academic Search

    Lekha Sleno; Dietrich A. Volmer; Borislav Kova?evi?; Zvonimir B. Maksi?

    2004-01-01

    The aim of this study was to investigate the behavior of the protonated paralytic shellfish poisons saxitoxin (STX) and neosaxitoxin\\u000a (NEO) in the gas-phase after ion activation using different tandem mass spectrometry techniques. STX and NEO belong to a group\\u000a of neurotoxins produced by several strains of marine dinoflagellates. Their chemical structures are based on a tetrahydropurine\\u000a skeleton to which

  8. 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.

  9. 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.

  10. DEMONSTRATION OF GAS-PHASE COMBUSTION SYNTHESIS OF NANOSIZED PARTICLES USING

    E-print Network

    Wooldridge, Margaret S.

    DEMONSTRATION OF GAS-PHASE COMBUSTION SYNTHESIS OF NANOSIZED PARTICLES USING A HYBRID BURNER) Abstract--A new approach for gas-phase combustion synthesis of nanosized particles using a novel hybrid. Introduction Gas-phase combustion synthesis is an important methodology for the production of nanosized

  11. Phase transfer catalysis in solid phase peptide synthesis. Preparation of cyclo[Xxx-Pro-Gly-Yyy-Pro-Gly] model peptides and their conformational analysis.

    PubMed

    Spatola, A F; Anwer, M K; Rao, M N

    1992-01-01

    Relatively small cyclic peptides that contain functionalized side chains provide interesting model compounds for studying side chain-side chain interactions, peptide backbone flexibility (especially if X-Pro bonds are included), and as potential enzyme mimetics. In order to develop more efficient synthetic routes to compounds such as cyclo(Xxx-Pro-Gly-Yyy-Pro-Gly), using the Merrifield method, we have investigated several orthogonal solid phase synthesis strategies and contrasted the use of two solid phase peptide-resin cleavage techniques for preparing partially protected linear sequences. Phase transfer catalysis using tetrabutyl ammonium hydrogen sulfate in THF with saturated aqueous K2CO3 provides peptide acid salts in which most of the common protecting groups (Arg(NO2), Tyr(Bzl), Z-Lys, Lys(Boc), and Glu(tBu)) are not affected. Using 500 MHz proton NMR, peptides having a cyclo (L-L-Gly-L-L-Gly) sequence generally display two conformers in DMSO-d6 with the major isomer being the bis-cis conformer, while the minor form contains two beta turns. For peptides with a cyclo(D-L-Gly-L-L-Gly) sequence, the major conformer contains one cis and one trans X-Pro bond and one Type II beta turn, as previously predicted for related structure by Kopple and others. PMID:1478790

  12. A minimal model of peptide binding predicts ensemble properties of serum antibodies

    PubMed Central

    2012-01-01

    Background The importance of peptide microarrays as a tool for serological diagnostics has strongly increased over the last decade. However, interpretation of the binding signals is still hampered by our limited understanding of the technology. This is in particular true for arrays probed with antibody mixtures of unknown complexity, such as sera. To gain insight into how signals depend on peptide amino acid sequences, we probed random-sequence peptide microarrays with sera of healthy and infected mice. We analyzed the resulting antibody binding profiles with regression methods and formulated a minimal model to explain our findings. Results Multivariate regression analysis relating peptide sequence to measured signals led to the definition of amino acid-associated weights. Although these weights do not contain information on amino acid position, they predict up to 40-50% of the binding profiles' variation. Mathematical modeling shows that this position-independent ansatz is only adequate for highly diverse random antibody mixtures which are not dominated by a few antibodies. Experimental results suggest that sera from healthy individuals correspond to that case, in contrast to sera of infected ones. Conclusions Our results indicate that position-independent amino acid-associated weights predict linear epitope binding of antibody mixtures only if the mixture is random, highly diverse, and contains no dominant antibodies. The discovered ensemble property is an important step towards an understanding of peptide-array serum-antibody binding profiles. It has implications for both serological diagnostics and B cell epitope mapping. PMID:22353141

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

    EPA Science Inventory

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

  14. Photodissociation and spectroscopy of gas phase bimetallic clusters. Final report, September 15, 1990--September 14, 1993

    SciTech Connect

    Duncan, M.A.

    1993-12-31

    Focus is the study of gas phase metal clusters to evaluate their potential to model fundamental interactions on metal surfaces. Chemical bonding between component atoms in metal clusters and physisorption on cluster surfaces are studied. Electronic spectra, vibrational frequencies, and bond dissociation energies are measured for both neutral and ionized clusters using laser/mass spectrometry. Interest is on bimetallic cluster systems and how they compare to pure metal clusters. The following were studied: Bi/Cr, Bi/Fe, Pb/Sb, Ag{sub 2}-rare gas, Ag-Al, Ag-K, Ag-Na, Ag-Li, and Ag{sub 3}.

  15. 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.

  16. Source apportionment of wintertime gas-phase and particle-phase air pollutants using organic compounds as tracers

    Microsoft Academic Search

    James J. Schauer; Glen R. Cass

    2000-01-01

    Two chemical mass balance receptor models are developed which can determine the source contributions to atmospheric pollutant concentrations using organic compounds as tracers. The first model uses particle-phase organic compounds to apportion the primary source contribution to atmospheric fine particulate organic carbon concentrations and fine particle mass concentrations. The second receptor model simultaneously uses both volatile gas-phase hydrocarbon and particle-phase

  17. A computationally efficient aerosol nucleation/condensation method: Pseudo-steady state gas phase sulfuric acid

    NASA Astrophysics Data System (ADS)

    Adams, P. J.; Pierce, J. R.

    2007-12-01

    Aerosol nucleation and condensation are two processes that compete for gas phase sulfuric acid when it is formed in the atmosphere. Without approximations, accurate numerical integration of aerosol microphysics requires time steps on the order of seconds or less when nucleation is occurring, significantly shorter than the time steps required by other processes governing aerosol microphysics. This computational burden makes the explicit numerical simulation burdensome in 3-dimensional atmospheric models. We have developed an efficient method for simulating nucleation/condensation by assuming that gas phase sulfuric acid is at a pseudo- steady state (PSS) concentration determined by chemical generation and its loss by nucleation and condensation. The time step for nucleation/condensation is then governed by 1) the change in the condensation sink, 2) the change in the generation rate of sulfuric acid, 3) the coagulation timescale, or 4) a master time step in the model. The PSS assumption fails only when the time for sulfuric acid to reach its PSS state concentration is not significantly shorter than the four timescales above. This may occur when the following conditions are met 1) the condensation sink is less than 10-3-10-4 s-1, 2) nucleation is not occurring, and 3) the gas phase production rate is changing. These conditions are not frequently met for a long period of time in the atmosphere. The PSS assumption allows for time step increases of two to three orders of magnitude during nucleation events in typical atmospheric conditions and has been shown to reduce the nucleation/condensation computational time by a factor of 10-100.

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  1. X-ray scattering and optical ellipsometric studies of collagen-model peptides

    Microsoft Academic Search

    Georgie Georgiev; Peggy Cebe; Regina Valluzzi; David Kaplan

    2003-01-01

    We report results of optical ellipsometry and X-ray scattering studies of structure in collagen-model peptides. Proline and hydroxyproline residues stabilize the triple-helical conformation of collagen proteins in the collagen consensus sequence. Regular modifications have been introduced into the collagen consensus sequence, forming model systems for the study of bio-macromolecular organization. The model systems are oligomers with hexapeptide sequences of the

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

    PubMed

    Irikura, Karl K

    2013-02-14

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

  3. 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.

  4. 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.

  5. MODELING OF THE ENDOSOMOLYTIC ACTIVITY OF HA2-TAT PEPTIDES WITH RED BLOOD CELLS AND GHOSTS†

    PubMed Central

    Lee, Ya-Jung; Johnson, Gregory; Pellois, Jean-Philippe

    2011-01-01

    HA2-TAT is a peptide-based delivery agent that combines the pH-sensitive HA2 fusion peptide from Influenza and the cell-penetrating peptide TAT from HIV. This chimeric peptide is engineered to induce the cellular uptake of macromolecules into endosomes via the TAT moiety and to respond to the acidifying lumen of endosomes to cause membrane leakage and release of macromolecules into cells via the HA2 moiety. The question of how HA2 and TAT affect the properties of one another remains, however, unanswered and the behavior of the peptide inside endosomes is mostly uncharacterized. To address these issues, the binding and membrane leakage activity of a glutamic acid-enriched analogue E5-TAT was assessed with red blood cells and giant unilamellar vesicles as membrane models for endosomes. Hemolysis and microscopy assays reveal that E5-TAT binds to membranes in a pH-dependent manner and causes membrane leakage by inducing the formation of pores through which macromolecules can escape. The TAT moiety contributes to this activity by causing a shift in the pH response of E5 and by binding to negatively charged phospholipids. On the other hand, TAT binding to glycosaminoglycans reduces the lytic activity of E5-TAT. Addition of TAT to the C-terminus of E5 can therefore either increase or inhibit the activity of E5 depending on the cellular components present at the membrane. Taken together, these results suggest a model for the endosomolytic activity of the peptide and provide the basis for the molecular design of future delivery agents. PMID:20704453

  6. An elementary reaction-kinetic model for the gas-phase formation of 1,3,6,8- and 1,3,7,9-tetrachlorinated dibenzo- p-dioxins from 2,4,6–trichlorophenol

    Microsoft Academic Search

    Lavrent Khachatryan; Alexander Burcat; Barry Dellinger

    2003-01-01

    A 71-step reaction-kinetic model for the formation of 1,3,6,8- and 1,3,7,9-tetrachlorodibenzo-p-dioxins (TCDDs) from the oxidation of 2,4,6-trichlorophenol in the presence of hexane is developed based on experimental data and a simpler model that was previously published in the literature. The rate of reaction of phenoxyl-radicals with molecular oxygen has recently been experimentally demonstrated to be at least five orders of

  7. 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.

  8. Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS\\/MS and Database Search

    Microsoft Academic Search

    Andrew Keller; Alexey I. Nesvizhskii; Eugene Kolker; Ruedi Aebersold

    2002-01-01

    We present a statistical model to estimate the accuracy of peptide assignments to tandem mass (MS\\/MS) spectra made by database search applications such as SEQUEST. Employing the expectation maximization algorithm, the analysis learns to distinguish correct from incorrect database search results, computing probabilities that peptide assignments to spectra are correct based upon database search scores and the number of tryptic

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

    SciTech Connect

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

    2009-03-31

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

  10. Gas phase reaction of sulfur trioxide with water vapor

    SciTech Connect

    Kolb, C.E.; Molina, M.J.; Jayne, J.T.; Meads, R.F.; Worsnop, D.R.

    1994-12-31

    Sulfur trioxide (SO3) has long been known to react with water to produce sulfuric acid (H2S04). It has been commonly assumed that the gas phase reaction in the Earth`s atmosphere between SO3 and water vapor to produce sulfuric acid vapor is an important step in the production of sulfuric acid aerosol particles. The kinetics of the gas phase reaction of SO3 with water vapor have previously been studied by Castleman and co-workers, Wang et al and Reiner and Arnold. Each of these studies was carried out in a flow reactor, with the first two studies performed at low pressure (1-10 Torr) and the latter from approx. 30 to 260 Torr. Each of these studies measured SO3 decays over a range of H2O vapor levels, obtaining data consistent with interpreting the reaction of gaseous SO3 and H2O as a bimolecular process. It is not clear why previous experimental studies failed to observe a nonlinear dependence of SO3 consumption on water vapor concentration. It is probable that sufficient water dimer exists in much of the Earth`s atmosphere to allow dimer reactions to participate in sulfuric acid vapor formation.

  11. Probing Guanine and Cytosine Tautomers in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Pena, I.; Vaquero, V.; López, J. C.; Alonso, J. L.

    2009-06-01

    Using laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) we have recently studied the nucleic acid bases uracil and thymine. We have now successfully probed in isolation conditions in the gas phase cytosine and guanine which are solids with high melting points (m.p.>300°C) and a low vapour pressure, and consequently, they are elusive to gas-phase rotational studies. Five rotational species have been detected in the supersonic expansion of cytosine. The unambiguous assignment of the observed species to the various tautomer/conformer structures is based on the markedly different values of the quadrupole coupling constants of the three ^{14}N nuclei, which act as fingerprints for the identification of the various species. Four species have been observed in the rotational spectra of Guanine. The comparison between the experimental rotational constants and those calculated ab initio provide a definitive test for the identification of the four lowest energy forms. The planarity of the tautomers is discussed on the basis of the inertial defect values (?=I_c-I_a-I_b). V. Vaquero, M.E. Sanz, J.C. López and J.L. Alonso, J. Phys. Chem. A 111, 3443 (2007) J.C. López, M.I. Peña, M.E. Sanz and J.L. Alonso, J. Chem. Phys. 126, 191103 (2007)

  12. 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.

  13. Gas-phase pyridylamination of saccharides: development and applications.

    PubMed

    Nakakita, Shin-ichi; Sumiyoshi, Wataru; Miyanishi, Nobumitsu; Natsuka, Shunji; Hase, Sumihiro; Hirabayashi, Jun

    2007-04-01

    Pyridylamination is a versatile method for fluorescence labeling of oligosaccharides. The technique affords sensitive detection of saccharides with reducing termini and high-resolution separation by high-performance liquid chromatography. The conventional method, based on a liquid-phase reaction, has been extensively used in various aspects of glycobiology and glycotechnology. Unfortunately, the necessity for removing excess 2-aminopyridine makes the technique both laborious and time-consuming. Furthermore, removal of excess reagent can result in a significant loss of short saccharide components. In the present paper, we report an alternative methodology based on a "gas-phase" reaction, in which dried saccharides are reacted with vaporized 2-aminopyridine. The resultant Schiff base was also reduced in the gas phase within the same reaction microtube using a purpose-built device. The newly developed procedure was applied to both monosaccharide (GlcNAc) and oligosaccharides (isomalto-oligosaccharides) at quantitative yields with no requirement to remove excess reagent. The acid-labile sialyl linkages of alpha2-6-disialobiantennary oligosaccharides proved to be fully stable during the procedure. The developed method was also successfully applied to profiling N-linked oligosaccharides liberated from glycoproteins by hydrazinolysis and, thus, should contribute to various fields of glycomics. PMID:17335182

  14. Intramembrane molecular dipoles affect the membrane insertion and folding of a model amphiphilic peptide.

    PubMed Central

    Cladera, J; O'Shea, P

    1998-01-01

    The relationship between the dipole potential and the interaction of the mitochondrial amphipathic signal sequence known as p25 with model membranes has been studied using 1-(3-sulfonatopropyl)-4-[beta[2-(di-n-octyl-amino)-6-naphthyl]viny l] pyridinium betaine (di-8-ANEPPS) as a fluorescent probe. The dipole potential of phosphatidylcholine membranes was modified by incorporating into the bilayer the sterols phloretin and 6-ketocholestanol (KC), which decrease and increase the dipole potential, respectively. The results derived from the application of a dual-wavelength ratiometric fluorescence method for following the variation of the membrane dipole potential have shown that when p25 inserts into the lipidic bilayer, a decrease in the dipole potential takes place. The magnitude of this decrease depends on the initial value of the dipole potential, i.e., before interaction with the peptide. Thus, when KC was incorporated into the bilayer, the decrease caused by the membrane insertion of p25 was larger than that caused in PC membranes. Alternatively, in the presence of phloretin, the decrease in the potential caused by the peptide insertion was smaller. Complementary studies involving attenuated total reflectance-Fourier transform infrared spectroscopy of the peptide membrane interactions have shown that modification of the dipole potential affects the conformation of the peptide during the course of its interaction with the membrane. The presence of KC induces a higher amount of helicoidal structure. The presence of phloretin, however, does not appear to affect the secondary structure of the peptide. The differences observed in the dipole potential decreases caused by the presence of the peptide with the PC membranes and phloretin-PC membranes, therefore, must involve differences in the tertiary and, perhaps, quaternary conformations of p25. PMID:9591669

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

    PubMed Central

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

    1985-01-01

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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. Formation of secondary aerosols over Europe: comparison of two gas-phase chemical mechanisms

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Sartelet, K.; Seigneur, C.

    2011-01-01

    The impact of two recent gas-phase chemical kinetic mechanisms (CB05 and RACM2) on the formation of secondary inorganic and organic aerosols is compared for simulations of PM2.5 over Europe between 15 July and 15 August 2001. The host chemistry transport model is Polair3D of the Polyphemus air-quality platform. Particulate matter is modeled with a sectional aerosol model (SIREAM), which is coupled to the thermodynamic model ISORROPIA for inorganic species and to a module (MAEC) that treats both hydrophobic and hydrophilic species for secondary organic aerosol (SOA). Modifications are made to the gas-phase chemical mechanisms to handle the formation of SOA. In order to isolate the effect of the original chemical mechanisms on PM formation, the addition of reactions and chemical species needed for SOA formation was harmonized to the extent possible between the two gas-phase chemical mechanisms. Model performance is satisfactory with both mechanisms for speciated PM2.5. The monthly-mean difference of the concentration of PM2.5 is less than 1 ?g m-3 (6%) over the entire domain. Secondary chemical components of PM2.5 include sulfate, nitrate, ammonium and organic aerosols, and the chemical composition of PM2.5 is not significantly different between the two mechanisms. Monthly-mean concentrations of inorganic aerosol are higher with RACM2 than with CB05 (+16% for sulfate, +11% for nitrate, and +10% for ammonium), whereas the concentrations of organic aerosols are slightly higher with CB05 than with RACM2 (+22% for anthropogenic SOA and +1% for biogenic SOA). Differences in the inorganic and organic aerosols result primarily from differences in oxidant concentrations (OH, O3 and NO3). Nitrate formation tends to be HNO3-limited over land and differences in the concentrations of nitrate are due to differences in concentration of HNO3. Differences in aerosols formed from aromatic SVOC are due to different aromatic oxidation between CB05 and RACM2. The aromatic oxidation in CB05 leads to more cresol formation, which then leads to more SOA. Differences in the aromatic aerosols would be significantly reduced with the recent CB05-TU mechanism for toluene oxidation. Differences in the biogenic aerosols are due to different oxidant concentrations (monoterpenes) and different particulate organic mass concentrations affecting the gas-particle partitioning of SOA (isoprene). These results show that the formulation of a gas-phase chemical kinetic mechanism for ozone can have significant direct (e.g., cresol formation) and indirect (e.g., oxidant levels) effects on PM formation. Furthermore, the incorporation of SOA into an existing gas-phase chemical kinetic mechanism requires the addition of reactions and product species, which should be conducted carefully to preserve the original mechanism design and reflect current knowledge of SOA formation processes (e.g., NOx dependence of some SOA yields). The development of chemical kinetic mechanisms, which offer sufficient detail for both oxidant and SOA formation is recommended.

  1. 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

  2. Valence anions of N-acetylproline in the gas phase: Computational and anion photoelectron spectroscopic studies

    PubMed Central

    Chomicz, Lidia; Rak, Janusz; Paneth, Piotr; Sevilla, Michael; Ko, Yeon Jae; Wang, Haopeng; Bowen, Kit H.

    2011-01-01

    We report the photoelectron spectrum of anionic N-acetylproline, (N-AcPro)?, measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that N-acetylproline forms a valence anion in the gas phase. The neutrals and anions of N-AcPro were also studied computationally at the B3LYP/6-31++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the ?* orbital localized at the acetyl group of N-AcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic N-AcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue. PMID:21950856

  3. 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.

  4. Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution.

    PubMed

    Meliá, Conchín; Ferrer, Silvia; Moliner, Vicent; Tuñón, Iñaki; Bertrán, Juan

    2012-09-15

    We are presenting a theoretical study of the hydrolysis of a ?-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06-2X functionals. Inclusion of the full molecule of the antibiotic, Cefotaxime, in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate a nucleophilic water molecule. Moreover, the flexibility of the substrate implies the existence of a huge number of possible conformers, some of them implying formation of intramolecular hydrogen bond interaction that can determine the energetics of the conformers defining the different states along the reaction profile. The results show PM3 provides results that are in qualitative agreement with DFT calculations. The free energy profiles show a step-wise mechanism that is kinetically determined by the nucleophilic attack of a water molecule activated by the proton transfer to the carboxylate group of the substrate (the first step). However, since the main role of the ?-lactamase would be reducing the free energy barrier of the first step, and keeping in mind the barrier obtained from second intermediate to products, population of this second intermediate could be significant and consequently experimentally detected in ?-lactamases, as shown in the literature. PMID:22674452

  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. UV spectroscopy of DNA duplex and quadruplex structures in the gas phase.

    PubMed

    Rosu, Frédéric; Gabelica, Valérie; De Pauw, Edwin; Antoine, Rodolphe; Broyer, Michel; Dugourd, Philippe

    2012-06-01

    UV absorption spectroscopy is one of the most widely used methods to monitor nucleic acid folding in solution, but the absorption readout is the weighted average contribution of all species present in solution. Mass spectrometry, on the other hand, is able to separate constituents of the solution based on their mass, but methods to probe the structure of each constituent are needed. Here, we explored whether gas-phase UV spectroscopy can give an indication of DNA folding in ions isolated by electrospray mass spectrometry. Model DNA single strands, duplexes, and G-quadruplexes were extracted from solution by electrospray; the anions were stored in a quadrupole ion trap and irradiated by a tunable laser to obtain the UV action spectra of each complex. We found that the duplex and quadruplex spectra are significantly different from the spectra of single strands, thereby suggesting that electronic spectroscopy can be used to probe the DNA gas-phase structure and obtain information about the intrinsic properties of high-order DNA structure. PMID:22568521

  7. Gas-phase hydrolysis of SOF2 and SOF4

    NASA Astrophysics Data System (ADS)

    Van Brunt, R. J.; Sauers, I.

    1986-10-01

    The rates for gas-phase hydrolysis of SOF2 (thionylfluoride) and SOF4 (thionyl tetrafluoride) have been measured at a temperature of 298 K. The second order rate constant for SOF2 hydrolysis in SF6 buffer gas was found to have the value (1.2±0.3)×10-23 cm3/s which agrees with previous estimates of Sauers et al., but is three orders of magnitude lower than the value obtained by Rüegsegger et al. at 340 K. The rate constant for SOF4 hydrolysis has not previously been measured and its value in both SF6 and N2 buffer gases was found here to be (1.0±0.3)×10-21 cm3/s.

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

    PubMed Central

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

    2014-01-01

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

  9. 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.

  10. Molecular ions of ionic liquids in the gas phase.

    PubMed

    Gross, Jürgen H

    2008-09-01

    Ionic liquids form neutral ion pairs (CA) upon evaporation. The softness of the gas-phase ionization of field ionization has been used to generate "molecular ions," CA(+*), of ionic liquids, most probably by neutralization of the anion. In detail, 1-ethyl-3-methylimidazolium-thiocyanate, [C(6)H(11)N(2)](+) [SCN](-), 1-butyl-3-methylimidazolium-tricyanomethide, [C(8)H(15)N(2)](+) [C(4)N(3)](-), N-butyl-3-methylpyridinium-dicyanamide, [C(10)H(16)N](+) [C(2)N(3)](-), and 1-butyl-1-methylpyrrolidinium-bis[(trifluormethyl)sulfonyl]amide, [C(9)H(20)N](+) [C(2)F(6)NO(4)S(2)](-) were used. The assignment as CA(+*) ions, which has been confirmed by accurate mass measurements and misassignments due to thermal decomposition of the ionic liquids, has been ruled out by field desorption and electrospray ionization mass spectrometry of the residues. PMID:18650101

  11. Spin effects in gas-phase organometallic chemistry

    SciTech Connect

    Armentrout, P.B.; Wight, C.A.; Dalleska, N.; Schultz, R.H. [Univ. of Utah, Salt Lake City, UT (United States)

    1993-12-31

    Recent work providing evidence of spin-effects on organometallic chemistry in the gas-phase will be presented. The authors` studies have found such effects in three areas. First, different electronic states of atomic transition metal ions can exhibit very different reactivity with small molecules. Second, sequential bond dissociation energies for cationic metal ligand complexes are found to vary nonmonotonically, an observation that has been explained in terms of changes in spin as ligands are removed. Studies that vary the ligand field strength by changing the ligand support this explanation. Third, in the multiphoton dissociation multiphoton ionization (MPD-MPI) spectroscopy of a series of cobalt complexes, the authors have found that increasing the complexity of the ligands or decreasing the photon flux increases the likelihood that the cobalt atom is formed in an excited electronic state. This counterintuitive result can be explained in terms of a propensity for spin-conservation.

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

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

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

  13. 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.

  14. Tautomeric properties and gas-phase structure of acetylacetone.

    PubMed

    Belova, Natalya V; Oberhammer, Heinz; Trang, Nguen Hoang; Girichev, Georgiy V

    2014-06-20

    The tautomeric and structural properties of acetylacetone, CH3C(O)CH2C(O)CH3, have been studied by gas-phase electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximation with different basis sets up to aug-cc-pVTZ). The analysis of GED intensities resulted in the presence of 100(3)% of the enol tautomer at 300(5) K and 64(5)% of the enol at 671(7) K. The enol tautomer possesses Cs symmetry with a planar ring and strongly asymmetric hydrogen bond. The diketo form possesses C2 symmetry. The experimental geometric parameters of both tautomeric forms are reproduced very closely by B3LYP/aug-cc-pVTZ and MP2/cc-pVTZ methods. PMID:24758690

  15. Efficient model chemistries for peptides. II. Basis set convergence in the B3LYP method

    E-print Network

    Pablo Echenique; Gregory A. Chass

    2008-11-17

    Small peptides are model molecules for the amino acid residues that are the constituents of proteins. In any bottom-up approach to understand the properties of these macromolecules essential in the functioning of every living being, to correctly describe the conformational behaviour of small peptides constitutes an unavoidable first step. In this work, we present an study of several potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The PESs are calculated using the B3LYP density-functional theory (DFT) method, with Dunning's basis sets cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, aug-cc-pVTZ, and cc-pVQZ. These calculations, whose cost amounts to approximately 10 years of computer time, allow us to study the basis set convergence of the B3LYP method for this model peptide. Also, we compare the B3LYP PESs to a previous computation at the MP2/6-311++G(2df,2pd) level, in order to assess their accuracy with respect to a higher level reference. All data sets have been analyzed according to a general framework which can be extended to other complex problems and which captures the nearness concept in the space of model chemistries (MCs).

  16. Feasibility of gas-phase decontamination of gaseous diffusion equipment

    SciTech Connect

    Munday, E.B.; Simmons, D.W.

    1993-02-01

    The five buildings at the K-25 Site formerly involved in the gaseous diffusion process contain 5000 gaseous diffusion stages as well as support facilities that are internally contaminated with uranium deposits. The gaseous diffusion facilities located at the Portsmouth Gaseous Diffusion Plant and the Paducah Gaseous Diffusion Plant also contain similar equipment and will eventually close. The decontamination of these facilities will require the most cost-effective technology consistent with the criticality, health physics, industrial hygiene, and environmental concerns; the technology must keep exposures to hazardous substances to levels as low as reasonably achievable (ALARA). This report documents recent laboratory experiments that were conducted to determine the feasibility of gas-phase decontamination of the internal surfaces of the gaseous diffusion equipment that is contaminated with uranium deposits. A gaseous fluorinating agent is used to fluorinate the solid uranium deposits to gaseous uranium hexafluoride (UF{sub 6}), which can be recovered by chemical trapping or freezing. The lab results regarding the feasibility of the gas-phase process are encouraging. These results especially showed promise for a novel decontamination approach called the long-term, low-temperature (LTLT) process. In the LTLT process: The equipment is rendered leak tight, evacuated, leak tested, and pretreated, charged with chlorine trifluoride (ClF{sub 3}) to subatmospheric pressure, left for an extended period, possibly > 4 months, while processing other items. Then the UF{sub 6} and other gases are evacuated. The UF{sub 6} is recovered by chemical trapping. The lab results demonstrated that ClF{sub 3} gas at subatmospheric pressure and at {approx} 75{degree}F is capable of volatilizing heavy deposits of uranyl fluoride from copper metal surfaces sufficiently that the remaining radioactive emissions are below limits.

  17. The antimicrobial peptide microcin J25 stabilizes the gel phase of bacterial model membranes.

    PubMed

    Rintoul, M R; Morero, R D; Dupuy, F G

    2015-05-01

    The bacterial membrane interaction of the antimicrobial peptide microcin J25 was studied with the probe-free techniques Langmuir monolayers and infrared spectroscopy. Membrane model systems composed by phosphatidylethanolamine:phosphatidylglycerol 7:3, which mimic the cytoplasmic membrane of Gram negative bacteria, were used in both monolayer and bilayer approaches. The peptide reduced the transition surface pressure of the expanded-to-condensed lipid monolayer states, as well as increased the gel-to-liquid crystalline transition temperature in bilayers, indicating a stabilization of membrane ordered state. In addition, a reduction of the surface pressure at which condensed domains appeared was observed upon mixed monolayers compression after microcin J25 adsorption. The results indicate a favorable interaction of microcin J25 with bacterial membrane model systems. Also, the effects on the ordered phases stabilization are discussed in terms of the biological effects observed in membranes of sensitive cells. PMID:25863710

  18. 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

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

    Microsoft Academic Search

    Leonor Saiz; Michael L. Klein

    2005-01-01

    We have studied the structure and properties of a bundle of ?-helical peptides embedded in a 1,2-dimyristoyl-3-phosphatidylcholine phospholipid bilayer by molecular dynamics simulations. The bundle of five transmembrane ?M2 segments constitutes the model for the pore region of the nicotinic acetylcholine receptor, which is the neurotransmitter-gated ion-channel responsible for the fast propagation of electrical signals between cells at the nerve-muscle

  20. 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

  1. 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

  2. Gas-Phase Separations of Protein and Peptide Ion Fragments Generated by Collision-Induced

    E-print Network

    Clemmer, David E.

    University, Bloomington, Indiana 47405 Ion mobility/time-of-flight mass spectrometry techniques have been dissociation of multiply charged proteins, a combined ion mobility/time-of-flight (TOF) mass spectrometry) in a quadrupole ion trap. The mobility-based separation step prior to mass-to-charge (m/z) analysis reduces

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  5. Spatial expression patterns of peptide transporters in the human and rat gastrointestinal tracts, Caco-2 In Vitro cell culture model, and multiple human tissues

    Microsoft Academic Search

    Dea Herrera-Ruiz; Qing Wang; Thomas J. Cook; Gregory T. Knipp; Olafur S. Gudmundsson; Ronald L. Smith; Teresa N. Faria

    2001-01-01

    This study sought to identify the spatial patterns of expression of peptide transporter 1 (PepT1), peptide transporter 3 (PTR3),\\u000a peptide\\/histidine transporter 1 (PHT1), and the human peptide transporter 1 (HPT-1) mRNA in complementary DNA (cDNA) libraries\\u000a of the human and rat gastrointestinal tracts (GIT), Caco-2 in vitro cell culture model, and in a human multiple tissue panel. Human PTR3 and

  6. 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.

  7. Vibrational spectroscopy of C 7 H-bonded structures: studies on peptide and glycopeptide models

    NASA Astrophysics Data System (ADS)

    Vass, E.; Samu, J.; Majer, Zs.; Hollósi, M.

    1997-06-01

    This paper reports FTIR spectroscopic studies on cyclic peptides and N-glycosylated bridged cyclic peptides {cyclo[Gly-Pro-Xxx(GlcNAc)-Gly- ?-Ava], Xxx = Asn, Gln} with possible H-bonded ?-(C 10) and/or ?-turn (C 7) structures, as well as on model compounds which are capable of forming C 7 intramolecular hydrogen bonds (IHBs), such as Ac-Gly-NHMe and N-acetyl-2-acetamido-2-deoxy-?- D-glucopyranosylamine (GlcNAc-NHAc). In certain cases, the assignment of the characteristic amide I frequencies to the acceptor amide carbonyls was assisted by 13C isotope labelling or by additional structural information inferred from NMR measurements. The influence of solvent (trifluoroethanol and dimethyl sulphoxide) on the stability of C 10 and C 7 IHBs is also discussed.

  8. 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.

  9. In Situ Spectroscopic Investigation of Gas Phase Chemistry During Silicon Chemical Vapor Deposition

    Microsoft Academic Search

    James E. Maslar; Wilbur S. Hurst

    2003-01-01

    During silicon thermal chemical vapor deposition, reactions occurring in the gas phase above the wafer surface can strongly influence the deposited film quality. Depending on the process conditions, e.g., temperature, silicon precursor, carrier gas, pressure, etc., gas phase reactions can include not only precursor decomposition but also nucleation of silicon nanoparticles above the wafer surface. Optical diagnostics were employed to

  10. Gas Phase Nanomaterial Integration Lead P.I. Heiko O. Jacobs*

    E-print Network

    Jacobs, Heiko O.

    1 Gas Phase Nanomaterial Integration Lead P.I. Heiko O. Jacobs* University of Minnesota Engineering Abstract: This letter reports on a new gas phase printing approach to deposit nanomaterials the assembly of nanomaterials into the openings. Directed assembly was observed due to a naturally occurring

  11. 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 pancreatic trypsin inhibitor) and cytochrome c ions in the gas phase, as a function of charge. For BPTI into place by three covalent disulfide bridges. For cytochrome c, geometries with cross sections close

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

    SciTech Connect

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

    2006-05-15

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

  13. 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.

  14. High-order-harmonic generation using gas-phase H{sub 2}O molecules

    SciTech Connect

    Zhao Songfeng [J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506 (United States); Key Laboratory of Atomic and Molecular Physics and Functional Materials of Gansu Province, College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070 (China); Jin, Cheng; Le, Anh-Thu; Lin, C. D. [J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506 (United States); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

    2011-03-15

    We investigate high-order-harmonic generation of isotropically distributed gas-phase H{sub 2}O molecules exposed to an intense laser field. The induced dipole of each individual molecule by the laser field is first calculated using the recently developed quantitative rescattering theory. In a thin medium, harmonic spectra generated coherently from all the molecules are then calculated by solving Maxwell's equation of propagation. By using accurate transition dipoles of H{sub 2}O, we show that the harmonics in the lower plateau region are quite different from models that employ the simpler strong-field approximation. We also examine the magnitude and phase of the harmonics and their dependence on laser focusing conditions.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  16. High-order-harmonic generation using gas-phase H2O molecules

    NASA Astrophysics Data System (ADS)

    Zhao, Song-Feng; Jin, Cheng; Lucchese, R. R.; Le, Anh-Thu; Lin, C. D.

    2011-03-01

    We investigate high-order-harmonic generation of isotropically distributed gas-phase H2O molecules exposed to an intense laser field. The induced dipole of each individual molecule by the laser field is first calculated using the recently developed quantitative rescattering theory. In a thin medium, harmonic spectra generated coherently from all the molecules are then calculated by solving Maxwell’s equation of propagation. By using accurate transition dipoles of H2O, we show that the harmonics in the lower plateau region are quite different from models that employ the simpler strong-field approximation. We also examine the magnitude and phase of the harmonics and their dependence on laser focusing conditions.

  17. Molecular Mechanisms of RADA16-1 Peptide on Fast Stop Bleeding in Rat Models

    PubMed Central

    Wang, Ting; Zhong, Xiaozhong; Wang, Songtao; Lv, Fei; Zhao, Xiaojun

    2012-01-01

    Ionic self-assembly of the peptide RADARADARADARADA (RADA16-1) may form a well-defined nanofiber and eventually a hydrogel scaffold, with a water content of over 99.5%. This leads to the establishment of a nanofiber barrier that can be used to achieve complete hemostasis in less than 20 s in multiple tissues and in a variety of different wounds. In the present study, the nanofiber scaffolds of RADA16-1 peptide were sonicated into smaller fragments to identify possible molecular mechanisms underlying the rapid cessation of bleeding associated with these materials. Atomic force microscopy (AFM), circular dichroism (CD), and rheometry were also used to evaluate the re-assembly kinetics of this peptide. A bleeding control experiment was performed in animal models to uncover the molecular mechanisms underlying this fast hemostasis. In this way, these sonicated fragments not only quickly reassembled into nanofibers indistinguishable from the original material, but the degree of reassembly was also correlated with an increase in the rigidity of the scaffold and increased as the time required for hemostasis increased. PMID:23203125

  18. Molecular mechanisms of RADA16-1 peptide on fast stop bleeding in rat models.

    PubMed

    Wang, Ting; Zhong, Xiaozhong; Wang, Songtao; Lv, Fei; Zhao, Xiaojun

    2012-01-01

    Ionic self-assembly of the peptide RADARADARADARADA (RADA16-1) may form a well-defined nanofiber and eventually a hydrogel scaffold, with a water content of over 99.5%. This leads to the establishment of a nanofiber barrier that can be used to achieve complete hemostasis in less than 20 s in multiple tissues and in a variety of different wounds. In the present study, the nanofiber scaffolds of RADA16-1 peptide were sonicated into smaller fragments to identify possible molecular mechanisms underlying the rapid cessation of bleeding associated with these materials. Atomic force microscopy (AFM), circular dichroism (CD), and rheometry were also used to evaluate the re-assembly kinetics of this peptide. A bleeding control experiment was performed in animal models to uncover the molecular mechanisms underlying this fast hemostasis. In this way, these sonicated fragments not only quickly reassembled into nanofibers indistinguishable from the original material, but the degree of reassembly was also correlated with an increase in the rigidity of the scaffold and increased as the time required for hemostasis increased. PMID:23203125

  19. New experimental evidence for in-chain amino acid racemization of serine in a model peptide.

    PubMed

    Demarchi, Beatrice; Collins, Matthew; Bergström, Ed; Dowle, Adam; Penkman, Kirsty; Thomas-Oates, Jane; Wilson, Julie

    2013-06-18

    The facile racemization of protein-bound amino acids plays an important role in the aging and pathologies of living tissues, and it can be exploited for protein geochronological studies in subfossil biominerals. However, the in-chain degradation pathways of amino acids are complex and difficult to elucidate. Serine has proven to be particularly elusive, and its ability to racemize as a peptide-bound residue (like asparagine and aspartic acid) has not been demonstrated. This study investigates the patterns of degradation of a model peptide (WNSVWAW) at elevated temperatures, quantifying the extent of racemization and peptide bond hydrolysis using reverse-phase high-performance liquid chromatography (RP-HPLC) and tracking the presence of degradation products by MALDI-MS. We provide direct evidence that, under these experimental conditions, both serine and asparagine are able to undergo racemization as internally bound residues, which shows their potential for initiating protein breakdown and provides an explanation for the presence of d-enantiomers in living mammalian tissues. PMID:23705982

  20. The topology of lysine-containing amphipathic peptides in bilayers by circular dichroism, solid-state NMR, and molecular modeling.

    PubMed Central

    Vogt, B; Ducarme, P; Schinzel, S; Brasseur, R; Bechinger, B

    2000-01-01

    In order to better understand the driving forces that determine the alignment of amphipathic helical polypeptides with respect to the surface of phospholipid bilayers, lysine-containing peptide sequences were designed, prepared by solid-phase chemical synthesis, and reconstituted into membranes. CD spectroscopy indicates that all peptides exhibit a high degree of helicity in the presence of SDS micelles or POPC small unilamellar vesicles. Proton-decoupled (31)P-NMR solid-state NMR spectroscopy demonstrates that in the presence of peptides liquid crystalline phosphatidylcholine membranes orient well along glass surfaces. The orientational distribution and dynamics of peptides labeled with (15)N at selected sites were investigated by proton-decoupled (15)N solid-state NMR spectroscopy. Polypeptides with a single lysine residue adopt a transmembrane orientation, thereby locating this polar amino acid within the core region of the bilayer. In contrast, peptides with > or = 3 lysines reside along the surface of the membrane. With 2 lysines in the center of an otherwise hydrophobic amino acid sequence the peptides assume a broad orientational distribution. The energy of lysine discharge, hydrophobic, polar, and all other interactions are estimated to quantitatively describe the polypeptide topologies observed. Furthermore, a molecular modeling algorithm based on the hydrophobicities of atoms in a continuous hydrophilic-hydrophobic-hydrophilic potential describes the experimentally observed peptide topologies well. PMID:11053137

  1. 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.

  2. 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.

  3. 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

  4. Antidiabetic effect of novel modulating peptides of G-protein-coupled kinase in experimental models of diabetes

    Microsoft Academic Search

    Y. Anis; O. Leshem; H. Reuveni; I. Wexler; R. Ben Sasson; B. Yahalom; M. Laster; I. Raz; S. Ben Sasson; E. Shafrir; E. Ziv

    2004-01-01

    Aims\\/hypothesis  G-protein-coupled receptor kinases (GRKs) play a key role in agonist-induced desensitisation of G-protein-coupled receptors (GPCRs) that are involved in metabolic regulation and glucose homeostasis. Our aim was to examine whether small peptides derived from the catalytic domain of GRK2 and -3 would ameliorate Type 2 diabetes in three separate animal models of diabetes.Methods  Synthetic peptides derived from a kinase-substrate interaction site

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

    PubMed Central

    Montenegro, Javier

    2013-01-01

    CONSPECTUS Compartmentalization and isolation from external media facilitates the sophisticated functionality and connectivity of all the different biological processes accomplished by living entities. The lipid bilayer membranes are the dynamic structural motifs selected by Nature to individualize cells and keep ions, proteins, biopolymers and metabolites confined in the appropriate location. However, cellular interaction with the exterior and the regulation of its internal environment requires the assistance of minimal energy short cuts for the transport of molecules across membranes. Ion channels and pores stand out from all other possible transport mechanisms due to their high selectivity and efficiency in discriminating and transporting ions or molecules across membrane barriers. Nevertheless, the complexity of these smart “membrane holes” has been a significant driving force to develop artificial structures with comparable performance to the natural systems. The emergence of the broad range of supramolecular interactions as efficient tools for the rational design and preparation of stable 3D superstructures has boosted the possibilities and stimulated the creativity of chemists to design synthetic mimics of natural active macromolecules and even to develop artificial functions and properties. In this account we highlight results from our laboratories on the construction of artificial ion channel models that exploit the self-assembling of flat cyclic peptides into supramolecular nanotubes. The straightforward synthesis of the cyclic peptide monomers and the complete control over the internal diameter and external surface properties of the resulting hollow tubular suprastructure make CPs the optimal candidates for the fabrication of ion channels. Ion channel activities and selective transport of small molecules are examples of the huge potential of cyclic peptide nanotubes for the construction of functional transmembrane ion channels or pores. Our experience to date suggests that the topological control over cyclic peptide assembly together with the lumen functionalization should be the next steps to achieve conceptual devices with better performance and selectivity. PMID:23898935

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

    PubMed

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

    2013-12-17

    The lipid bilayer membranes are Nature's dynamic structural motifs that individualize cells and keep ions, proteins, biopolymers and metabolites confined in the appropriate location. The compartmentalization and isolation of these molecules from the external media facilitate the sophisticated functions and connections between the different biological processes accomplished by living organisms. However, cells require assistance from minimal energy shortcuts for the transport of molecules across membranes so that they can interact with the exterior and regulate their internal environments. Ion channels and pores stand out from all other possible transport mechanisms due to their high selectivity and efficiency in discriminating and transporting ions or molecules across membrane barriers. Nevertheless, the complexity of these smart "membrane holes" has driven researchers to develop simpler artificial structures with comparable performance to the natural systems. As a broad range of supramolecular interactions have emerged as efficient tools for the rational design and preparation of stable 3D superstructures, these results have stimulated the creativity of chemists to design synthetic mimics of natural active macromolecules and even to develop artificial structures with functions and properties. In this Account, we highlight results from our laboratories on the construction of artificial ion channel models that exploit the self-assembly of conformationally flat cyclic peptides (CPs) into supramolecular nanotubes. Because of the straightforward synthesis of the cyclic peptide monomers and the complete control over the internal diameter and external surface properties of the resulting hollow tubular suprastructure, CPs are the optimal candidates for the fabrication of ion channels. The ion channel activity and selective transport of small molecules by these structures are examples of the great potential that cyclic peptide nanotubes show for the construction of functional artificial transmembrane transporters. Our experience to date suggests that the next steps for achieving conceptual devices with better performance and selectivity will derive from the topological control over cyclic peptide assembly and the functionalization of the lumen. PMID:23898935

  7. 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

  8. Antimicrobial peptides in 2014.

    PubMed

    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

  9. Antimicrobial Peptides in 2014

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2004-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

    This study concerns the gas phase rovibrational spectroscopy of organosulfide and organophosphorous which are considered as non toxic model compounds in the analysis of chemical weapon materials, high pathogenic and mutagenic agents, and other environmentally interesting air-borne species. The coupling of the synchrotron radiation with multipass cells and the FTIR spectrometer allowed to obtain very conclusive results in term of sensitivity and resolution and improved the previous results obtained with classical sources. For DMSO, using an optical path of 150 m the spectra have been recorded at the ultimate resolution of 0.001 Cm-1 allowing to fully resolve the rotational structure of the lowest vibrational modes observed in the THz region. In the 290 - 420 Cm-1 region, the rovibrational spectrum of the "perpendicular" and "parallel" vibrational bands associated with, respectively, the asymmetric ?23 and symmetric ?11 bending modes of DMSO have been recorded with a resolution of 1.5× 10-3 Cm-1. The gas phase vibrational spectra of organophosphorous compounds were measured by FTIR spectroscopy using the vapor pressure of the compounds. Except for TBP, the room temperature vapor pressure was sufficient to detect all active vibrational modes from THz to NIR domain. Contrary to DMSO, the rotational patterns of alkyl phosphates and alkyl phosphonates could not be resolved; only a vibrational analysis may be performed. Nevertheless, the spectral fingerprints observed in the THz region allowed a clear discrimination between the molecules and between the different molecular conformations. A. Cuisset, G. Mouret, O. Pirali, P. Roy, F. Cazier, H. Nouali, J. Demaison, J. Phys. Chem. B, 2008, 112:, 12516-12525 A. Cuisset, L. Nanobashvili, I. Smirnova, R. Bocquet, F. Hindle, G. Mouret, O. Pirali, P. Roy and D. A. Sadovskií, Chem. Phys. Lett., 2010, 492: 30-34 I. Smirnova, A. Cuisset, R. Bocquet, F. Hindle, G. Mouret, O. Pirali, P. Roy, J. Phys. Chem. B, 2010, 114: 16936-16947.

  12. Immunomodulatory monoclonal antibodies combined with peptide vaccination provide potent immunotherapy in an aggressive murine neuroblastoma model

    PubMed Central

    Williams, Emily L.; Dunn, Stuart N.; James, Sonya; Johnson, Peter W.; Cragg, Mark. S.; Glennie, Martin J.; Gray, Juliet C.

    2013-01-01

    Purpose Neuroblastoma is one of the commonest extra-cranial tumors of childhood. The majority of patients present with metastatic disease for which outcome remains poor. Immunotherapy is an attractive therapeutic approach for this disease, and a number of neuroblastoma tumor antigens have been identified. Here we examine the therapeutic potential of combining immunomodulatory monoclonal antibodies (mAb) with peptide vaccination in murine neuroblastoma models. Experimental design Neuroblastoma bearing mice were treated with mAb targeting 4-1BB, CD40 and CTLA-4 alone, or in combination with a peptide derived from the tumor antigen survivin (GWEDPPNDI). Survivin-specific immune response and therapeutic efficacy was assessed. Results In the Neuro2a model, treatment of established tumor with either anti-4-1BB, anti-CD40 or anti-CTLA-4 mAb results in tumor regression and long-term survival in 40-60% of mice. This is dependent on NK and CD8+ T cells and is associated with tumor CD8+ lymphocyte infiltrate. Successful therapy is achieved only if mAb is given to mice once tumors are established, suggesting dependence on sufficient tumor to provide antigen. In the more aggressive AgN2a and NXS2 models, single agent mAb therapy provides ineffective therapy. However if mAb (anti-CTLA-4) is given in conjunction with survivin peptide vaccination then 60% long term survival is achieved. This is associated with the generation of survivin-specific T cell immunity, which again is only demonstrated in the presence of tumor antigen. Conclusions These data suggest the combination of antigen and co-stimulatory mAb may provide effective immunotherapy against neuroblastoma and may be of particular use in the minimal-residual disease setting. PMID:23649004

  13. Prediction and analysis of cell-penetrating peptides using pseudo-amino acid composition and random forest models.

    PubMed

    Chen, Lei; Chu, Chen; Huang, Tao; Kong, Xiangyin; Cai, Yu-Dong

    2015-07-01

    Cell-penetrating peptides, a group of short peptides, can traverse cell membranes to enter cells and thus facilitate the uptake of various molecular cargoes. Thus, they have the potential to become powerful drug delivery systems. The correct identification of peptides as cell-penetrating or non-cell-penetrating would accelerate this application. In this study, we determined which features were important for a peptide to be cell-penetrating or non-cell-penetrating and built a predictive model based on the key features extracted from this analysis. The investigated peptides were retrieved from a previous study, and each was encoded as a numeric vector according to six properties of amino acids-amino acid frequency, codon diversity, electrostatic charge, molecular volume, polarity, and secondary structure-by the pseudo-amino acid composition method. Methods of minimum redundancy maximum relevance and incremental feature selection were then employed to analyze these features, and some were found to be key determinants of cell penetration. In parallel, an optimal random forest prediction model was built. We hope that our findings will provide new resources for the study of cell-penetrating peptides. PMID:25894890

  14. 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.

  15. Gas-phase chemistry of technetium carbonyl complexes.

    PubMed

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

    2015-05-28

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

  16. Proton irradiation of DNA nucleosides in the gas phase.

    PubMed

    Poully, Jean-Christophe; Miles, Jordan; De Camillis, Simone; Cassimi, Amine; Greenwood, Jason B

    2015-03-21

    The four DNA nucleosides guanosine, adenosine, cytidine and thymidine have been produced in the gas phase by a laser thermal desorption source, and irradiated by a beam of protons with 5 keV kinetic energy. The molecular ions as well as energetic neutrals formed have been analyzed by mass spectrometry in order to shed light on the ionization and fragmentation processes triggered by proton collision. A range of 8-20 eV has been estimated for the binding energy of the electron captured by the proton. Glycosidic bond cleavage between the base and sugar has been observed with a high probability for all nucleosides, resulting in predominantly intact base ions for guanosine, adenosine, and cytidine but not for thymidine where intact sugar ions are dominant. This behavior is influenced by the ionization energies of the nucleobases (G < A < C < T), which seems to determine the localization of the charge following the initial ionization. This charge transfer process can also be inferred from the production of protonated base ions, which have a similar dependence on the base ionization potential, although the base proton affinity might also play a role. Other dissociation pathways have also been identified, including further fragmentation of the base and sugar moieties for thymidine and guanosine, respectively, and partial breakup of the sugar ring without glycosidic bond cleavage mainly for adenosine and cytidine. These results show that charge localization following ionization by proton irradiation is important in determining dissociation channels of isolated nucleosides, which could in turn influence direct radiation damage in DNA. PMID:25691342

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Dawley, M. Michele; Tanzer, Katrin; Carmichael, Ian; Denifl, Stephan; Ptasi?ska, Sylwia

    2015-06-01

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

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

    PubMed

    Dawley, M Michele; Tanzer, Katrin; Carmichael, Ian; Denifl, Stephan; Ptasi?ska, Sylwia

    2015-06-01

    We present high-resolution measurements of the dissociative electron attachment (DEA) to isolated gas-phase hypoxanthine (C5H4N4O, Hyp), a tRNA purine base. The anion mass spectra and individual ion efficiency curves from Hyp were measured as a function of electron energy below 9 eV. The mass spectra at 1 and 6 eV exhibit the highest anion yields, indicating possible common precursor ions that decay into the detectable anionic fragments. The (Hyp - H) anion (C5H3N4O(-)) exhibits a sharp resonant peak at 1 eV, which we tentatively assign to a dipole-bound state of the keto-N1H,N9H tautomer in which dehydrogenation occurs at either the N1 or N9 position based upon our quantum chemical computations (B3LYP/6-311+G(d,p) and U(MP2-aug-cc-pVDZ+)) and prior studies with adenine. This closed-shell dehydrogenated anion is the dominant fragment formed upon electron attachment, as with other nucleobases. Seven other anions were also observed including (Hyp - NH)(-), C4H3N4 (-)/C4HN3O(-), C4H2N3 (-), C3NO(-)/HC(HCN)CN(-), OCN(-), CN(-), and O(-). Most of these anions exhibit broad but weak resonances between 4 and 8 eV similar to many analogous anions from adenine. The DEA to Hyp involves significant fragmentation, which is relevant to understanding radiation damage of biomolecules. PMID:26049525

  1. Minimalistic Hybrid Models for the Adsorption of Polymers and Peptides to Solid Substrates

    E-print Network

    Michael Bachmann; Wolfhard Janke

    2007-10-24

    We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the adsorption process. Primarily focusing on the dependence of the conformational behavior on temperature and solubility we obtained pseudophase diagrams with a detailed structure of conformational subphases. In the study of hydrophobic-polar peptides in the vicinity of different types of substrates, we found a noticeable substrate specificity of the assembly of hydrophobic domains in the conformations dominating the adsorption subphases.

  2. Mixtures of a series of homologous hydrophobic peptides with lipid bilayers: a simple model system for examining the protein-lipid interface.

    PubMed

    Jacobs, R E; White, S H

    1986-05-01

    The interactions of several members of a homologous series of peptides with the phospholipid bilayer have been examined by using fluorescence and deuterium NMR spectroscopy, differential scanning calorimetry, and measurements of water-to-bilayer partition coefficients. 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayers and tripeptides of the form Ala-X-Ala-O-tert-butyl are used as a model system to probe the influence of amino acid side-chain substitution on the insertion of peptides into membranes and the behavior of peptide/bilayer mixtures. Tripeptides with X = Gly, Ala, Phe, and Trp have been examined. All of the tripeptides are water soluble, and all partition into DMPC bilayer vesicles to some extent. The Gly-containing peptide is the least soluble and the Trp-containing peptide the most soluble in the bilayer. The extent of perturbation of the bilayer structure induced by the peptides parallels their bilayer solubility: the Gly and Ala peptides act as simple impurities while peptides containing bulky aromatic rings cause a phase separation. Changes in the fluorescence properties of the Trp analogue upon incorporation into the bilayer indicate that the Trp side chain is probably immersed in the hydrocarbon region of the bilayer. Peptides of this form should serve as easily modifiable model systems with which to examine details of how the bilayer environment affects peptide conformation, as well as how hydrophobic peptides affect the bilayer structure. PMID:3718968

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    PubMed

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

    2015-03-01

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

  5. 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...

  6. An Experimental Investigation of Gas-Phase Combustion Synthesis of SiO2 Nanoparticles Using a Multi-Element

    E-print Network

    Wooldridge, Margaret S.

    An Experimental Investigation of Gas-Phase Combustion Synthesis of SiO2 Nanoparticles Using a Multi of an experimental investigation of gas-phase combustion synthesis of silica (SiO2) particles using a multi of the MEDB in providing a controlled environment for fundamental studies of gas-phase combustion synthesis

  7. Neuroprotective effects of salvianolic acid B on an A?25-35 peptide-induced mouse model of Alzheimer's disease.

    PubMed

    Lee, Young Woo; Kim, Dong Hyun; Jeon, Su Jin; Park, Se Jin; Kim, Jong Min; Jung, Jun Man; Lee, Hyung Eun; Bae, Shin Gil; Oh, Hee Kyong; Son, Kun Ho; Ho Son, Kun Ho; Ryu, Jong Hoon

    2013-03-15

    Salvianolic acid B (SalB) is a polyphenolic compound found in Salvia miltiorrhiza Bunge that has several anti-oxidative and anti-inflammatory effects. In the present study, we investigated whether SalB has neuroprotective effects in an amyloid ? (A?) peptide-induced Alzheimer's disease mouse model. Mice were injected with A?25-35 peptide intracerebroventricularly and were subsequently administered SalB once daily for 7 days. Subchronic SalB administration (10mg/kg) significantly ameliorated the A?25-35 peptide-induced memory impairment in the passive avoidance task (P<0.05). SalB treatment also reduced the number of activated microglia and astrocytes that were observed during the inflammatory reaction after the administration of the A?25-35 peptide. Moreover, SalB markedly reduced inducible nitric oxide synthase and cyclooxygenase-2 expression levels and thiobarbituric acid reactive substances, which were increased by the administration of the A?25-35 peptide. Furthermore, SalB administration significantly rescued the A?25-35 peptide-induced decrease of choline acetyltransferase and brain-derived neurotrophic factor protein levels. These results suggest that SalB exerts neuroprotective activity via anti-inflammatory and anti-oxidative effects and that SalB may be a potential candidate for Alzheimer's disease therapy. PMID:23461850

  8. 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

  9. 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.

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

    PubMed Central

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

    2014-01-01

    The effects of controlled release on immune response to an immunomodulating peptide were evaluated in a murine experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis (MS). The peptide, Ac-PLP-BPI-NH2-2 (Ac-HSLGKWLGHPDKF-(AcpGAcpGAcp)2-ITDGEATDSG-NH2; Ac = acetyl, Acp = aminocaproic acid) was designed to suppress T-cell activation in response to PLP139–151, an antigenic peptide in MS. Poly-lactide-co-glycolide (PLGA) microparticles containing Ac-PLP-BPI-NH2-2 (8±4 ?m, 1.4±0.2% (w/w)) were prepared by a powder-in oil-in water emulsion-solvent evaporation method, sterilized and administered subcutaneously (s.c.) to SJL/J (H-2s) mice in which EAE had been induced by immunization with PLP139–151. Treatment groups received Ac-PLP-BPI-NH2-2: (i) in solution by repeated i.v. or s.c. injection, (ii) in solution co-administered with blank PLGA microparticles, (iii) in solution co-administered with Ac-PLP-BPI-NH2-2 loaded microparticles, and (iv) as Ac-PLP-BPI-NH2-2 loaded microparticles. Administration of Ac-PLP-BPI-NH2-2 as an s.c. solution produced clinical scores and maintenance of body weight comparable to i.v. solution, but with reduced overall survival, presumably due to anaphylaxis. Administration as s.c. microparticles provided a somewhat less effective reduction in symptoms but with no toxicity during treatment. Thus, the results suggest that s.c. administration of Ac-PLP-BPI-NH2-2 microparticles can provide pharmacological efficacy and reduction in dosing frequency without increased toxicity. PMID:19748537

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

    PubMed

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

    2010-01-25

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

  12. Ab initio-based exciton model of amide I vibrations in peptides: definition, conformational dependence, and transferability.

    PubMed

    Gorbunov, Roman D; Kosov, Daniil S; Stock, Gerhard

    2005-06-01

    Various aspects of the ab initio-based parametrization of an exciton model of amide I vibrations in peptides are discussed. Adopting "glycine dipeptide" (Ac-Gly-NHCH3) as a simple building-block model that describes the vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate the effect and importance of the level of theory, the choice of local coordinates, and the localization method. A solvent continuum model description turns out important to obtain planar CONH peptide units when a full geometry optimization (which is necessary to obtain the correct frequencies) is performed. To study the conformational dependence of the amide I vibrations, we calculate (phi,psi) maps of the local-mode frequencies and couplings. Performing conformational averages of the (phi,psi) maps with respect to the most important peptide conformational states in solution (alpha, beta, P(II), and C5), we discuss the relation between these measurable quantities and the corresponding conformation of the peptide. Finally, the transferability of these maps to dipeptides with hydrophilic and hydrophobic side chains as well as to tripeptides with charged end groups is investigated. PMID:15974713

  13. Clear evidence of fluorescence resonance energy transfer in gas-phase ions.

    PubMed

    Dashtiev, Maxim; Azov, Vladimir; Frankevich, Vladimir; Scharfenberg, Ludwig; Zenobi, Renato

    2005-09-01

    Fluorescence resonance energy transfer (FRET) is a distance-sensitive method that correlates changes in fluorescence intensity with conformational changes, for example, of biomolecules in the cellular environment. Applied to the gas phase in combination with Fourier transform ion cyclotron resonance mass spectrometry, it opens up possibilities to define structural/conformational properties of molecular ions, in the absence of solvent, and without the need for purification of the sample. For successfully observing FRET in the gas phase it is important to find suitable fluorophores. In this study several fluorescent dyes were examined, and the correlation between solution-phase and gas-phase fluorescence data were studied. For the first time, FRET in the gas phase is demonstrated unambiguously. PMID:16023366

  14. Structures and Aggregation States of Fluoromethyllithium and Chloromethyllithium Carbenoids in the Gas Phase and in Ethereal

    E-print Network

    Ramachandran, Bala (Ramu)

    in the gas-phase structures. At the most complete level of theory the 173 K standard-state free energy species is the carbenoid, free carbene liberated from the carbenoid, or both. Seebach and co-workers were

  15. Gas Phase Studies of N-Heterocyclic Carbene-Catalyzed Condensation Reactions.

    PubMed

    Tian, Yuan; Lee, Jeehiun K

    2015-07-01

    N-Heterocyclic carbenes (NHCs) catalyze Umpolung condensation reactions of carbonyl compounds, including the Stetter reaction. These types of reactions have not heretofore been examined in the gas phase. Herein, we explore the feasibility of examining these reactions in the absence of solvent. A charge-tagged thiazolylidene catalyst is used to track the reactions by mass spectrometry. We find that the first Umpolung step, the addition of the NHC catalyst to a carbonyl compound to form the "Breslow intermediate", does not readily proceed in the gas phase, contrary to the case in solution. The use of acylsilanes in place of the carbonyl compounds appears to solve this issue, presumably because of a favorable Brook rearrangement. The second addition reaction, with enones, does not occur under our gas phase conditions. These reactions do occur in solution; the differential reactivity between the condensed and gas phases is discussed, and calculations are used to aid in the interpretation of the results. PMID:26066314

  16. Partitioning of formaldehyde between gas phase and particles (PM2.5) in México City

    Microsoft Academic Search

    G. ANDRACA-AYALA; L. G. RUIZ-SUÁREZ

    2005-01-01

    An annular denuder\\/filter-pack sampling technique has been employed to get an insight of the formaldehyde partitioning between gas phase and particles (PM2.5) in México City using short time sampling periods. Formaldehyde was trapped using DNPH derivatives and analyzed by HPLC\\/UV. One annular denuder was used to trap formaldehyde from the gas phase followed by a Teflon filter to trap PM2.5,

  17. The Nuclear Liquid-Gas Phase Transition: Q.E.D

    E-print Network

    V. E. Viola

    2003-11-11

    For the past decade, intense experimental effort has been devoted to the search for a liquid-gas phase transition in highly excited nuclei. Now, synthesis of the large body of existing multifragmentation data provides a strong case for identification of this phenomenon. In this presentation we discuss several salient features of the data that support their interpretation in terms of a spinodal liquid-gas phase transition.

  18. The determination of compressibility factors of gaseous butane-nitrogen mixtures in the gas phase 

    E-print Network

    Evans, Robert Buckner

    1955-01-01

    THE DETERMINATION OF COMPRESSIBILITY FACTORS OF GASEOUS BUTANE-NITROGEN MIXTURES IN THE GAS PHASE A D issertation By Robert Buckner Evans, III Approved as to style and content by: (Chairman of Committee) (Head of^ 'ent Advisor) June 1955... ?-; i'i i ; A R y ? 'A 'Gi- Or- T EX AS THE DETERMINATION OF COMHIESSIBILITI FACTORS OF GASEOUS BUTANE-NITROGEN MIXTURES IN THE GAS PHASE A D issertation By ROBERT BUCKNER EVANS, III Submitted' to the Graduate School of the Agricultural...

  19. 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.

  20. 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.

  1. The determination of compressibility factors of gaseous butane-nitrogen mixtures in the gas phase

    E-print Network

    Evans, Robert Buckner

    1955-01-01

    THE DETERMINATION OF COMPRESSIBILITY FACTORS OF GASEOUS BUTANE-NITROGEN MIXTURES IN THE GAS PHASE A D issertation By Robert Buckner Evans, III Approved as to style and content by: (Chairman of Committee) (Head of^ 'ent Advisor) June 1955... ?-; i'i i ; A R y ? 'A 'Gi- Or- T EX AS THE DETERMINATION OF COMHIESSIBILITI FACTORS OF GASEOUS BUTANE-NITROGEN MIXTURES IN THE GAS PHASE A D issertation By ROBERT BUCKNER EVANS, III Submitted' to the Graduate School of the Agricultural...

  2. Off-gas recycle for long-term low temperature gas phase uranium decontamination

    Microsoft Academic Search

    R. D. Bundy; D. H. Bunch; E. B. Munday; D. W. Simmons

    1994-01-01

    In situ long-term low-temperature (LTLT) gas phase decontamination is being developed and demonstrated at the K-25 site as a technology that has the potential to substantially lower these costs while reducing criticality and safeguards concerns and worker exposure to hazardous and radioactive materials. The objective of gas phase decontamination is to employ a gaseous reagent to fluorinate nonvolatile uranium deposits

  3. 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.

  4. Synthesis and biological applications of collagen-model triple-helical peptides

    PubMed Central

    2013-01-01

    Triple-helical peptides (THPs) have been utilized as collagen models since the 1960s. The original focus for THP-based research was to unravel the structural determinants of collagen. In the last two decades, virtually all aspects of collagen structural biochemistry have been explored with THP models. More specifically, secondary amino acid analogs have been incorporated into THPs to more fully understand the forces that stabilize triple-helical structure. Heterotrimeric THPs have been utilized to better appreciate the contributions of chain sequence diversity on collagen function. The role of collagen as a cell signaling protein has been dissected using THPs that represent ligands for specific receptors. The mechanisms of collagenolysis have been investigated using THP substrates and inhibitors. Finally, THPs have been developed for biomaterial applications. These aspects of THP-based research are overviewed herein. PMID:20204190

  5. Phospholipid-model membrane interactions with branched polypeptide conjugates of a hepatitis A virus peptide epitope.

    PubMed

    Nagy, I B; Alsina, M A; Haro, I; Reig, F; Hudecz, F

    2000-01-01

    To establish correlation between structural properties (charge, composition, and conformation) and membrane penetration capability, the interaction of epitope peptide-carrier constructs with phospholipid model membranes was studied. For this we have conjugated a linear epitope peptide, (110)FWRGDLVFDFQV(121) (110-121), from VP3 capside protein of the Hepatitis A virus with polylysine-based branched polypeptides with different chemical characteristics. The epitope peptide elongated by one Cys residue at the N-terminal [C(110-121)] was attached to poly[Lys-(DL-Ala(m)()-X(i)())] (i < 1, m approximately 3), where x = ø(AK), Ser (SAK), or Glu (EAK) by the amide-thiol heterobifunctional reagent, 3-(2-pyridyldithio)propionic acid N-hydroxy-succinimide ester. The interaction of these polymer-[C(110-121)] conjugates with phospholipid monolayers and bilayers was studied using DPPC and DPPC/PG (95/5 mol/mol) mixture. Changes in the fluidity of liposomes induced by these conjugates were detected by using two fluorescent probes 1,6-diphenyl-1,3, 5-hexatriene (DPH) and sodium anilino naphthalene sulfonate (ANS). The binding of conjugates to the model membranes was compared and the contribution of the polymer component to these interactions were evaluated. We found that conjugates with polyanionic/EAK-[C(110-121)] or polycationic/SAK-[C(110-121)], AK-[C(110-121)]/character were capable to form monomolecular layers at the air/water interface with structure dependent stability in the following order: EAK-[C(110-121)] > SAK-[C(110-121)] > AK-[C(110-121)]. Data obtained from penetration studies into phospholipid monolayers indicated that conjugate insertion is more pronounced for EAK-[C(110-121)] than for AK-[C(110-121)] or SAK-[C(110-121)]. Changes in the fluorescence intensity and in polarization of fluorescent probes either at the polar surface (ANS) or within the hydrophobic core (DPH) of the DPPC/PG liposomes suggested that all three conjugates interact with the outer surface of the bilayer. Marked penetration was documented by a significant increase of the transition temperature only with the polyanionic compound/EAK-[C(110-121)]. Taken together, we found that the binding/penetration of conjugates to phospholipid model membranes is dependent on the charge properties of the constructs. Considering that the orientation and number of VP3 epitope peptides attached to branched polypeptides were almost identical, we can conclude that the structural characteristics (amino acid composition, charge, and surface activity) of the carrier have a pronounced effect on the conjugate-phospholipid membrane interaction. These observations suggest that the selection of polymer carrier for epitope attachment might significantly influence the membrane activity of the conjugate and provide guidelines for adequate presentation of immunogenic peptides to the cells. PMID:10639082

  6. [Hydrolysis by enteropeptidase of nonspecific (model) peptide sequences and possible physiological role of this phenomenon].

    PubMed

    Likhareva, V V; Mikha?lova, A G; Rumsh, L D

    2002-01-01

    Enteropeptidase (enterokinase) (EC 3.4.21.9), a highly specific processing protease, initiating a cascade of reactions activating the digestion enzymes. Catalyzing trypsinogen activation enteropeptidase exhibits unique properties for high efficiency hydrolysis of the polypeptide chain after lysine-15 residue in the -DDDDK15- sequence. In 1998 we found an unusual calcium-dependent autolysis of the enteropeptidase heavy chain leading to the drastic loss of its activity towards trypsinogen: after lysine-360 (-NNYEK360-INCN-), -), arginine-384 (-NEWER384-TQGS-), arginine-422 (-GRRER422-VGLL-) and lysine-465 (-QNMEK465-TIFQ-) residues. We used hepta-nona-peptides as the model substrates for autolysys: human angiotensin II--DRVYIHPF and cattle hemoglobin b-chain fragments: LTAEEKA and MLTAEEKAA. Kinetic parameters of enteropeptidase hydrolysis for these substrates were determined. Recent study demonstrates the ability of enteropeptidase to hydrolyze peptide bonds formed by carboxyl groups of Lys or Arg residues if less than four but at least one negative charged amino acid residue is in any of substrate P2-P5 positions. Ca(2+)-dependent autolysis of enteropeptidase heavy chain and of trypsin were compared; the second one serves as the natural defense mechanism against the undesirable premature proenzymes activation in pancreas leading to pancreatitis. The corresponding enteropeptidase inactivation in low Ca2+ environment ought to be the component of the same protective mechanism. PMID:12698555

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

    PubMed

    Radman, Andreja; Gredi?ak, Matija; Kopriva, Ivica; Jeri?, Ivanka

    2011-01-01

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

  8. What Happens to Hydrophobic Interactions during Transfer from the Solution to the Gas Phase? The Case of Electrospray-Based Soft Ionization Methods

    NASA Astrophysics Data System (ADS)

    Barylyuk, Konstantin; Balabin, Roman M.; Grünstein, Dan; Kikkeri, Raghavendra; Frankevich, Vladimir; Seeberger, Peter H.; Zenobi, Renato

    2011-07-01

    The disappearance of the hydrophobic effect in the gas phase due to the absence of an aqueous surrounding raises a long-standing question: can noncovalent complexes that are exclusively bound by hydrophobic interactions in solution be preserved in the gas phase? Some reports of successful detection by mass spectrometry of complexes largely stabilized by hydrophobic effect are questionable by the presence of electrostatic forces that hold them together in the gas phase. Here, we report on the MS-based analysis of model supramolecular complexes with a purely hydrophobic association in solution, ?-cyclodextrin, and synthetic adamantyl-containing ligands with several binding sites. The stability of these complexes in the gas phase is investigated by quantum chemical methods (DFT-M06). Compared with the free interaction partners, the inclusion complex between ?-cyclodextrin and adamantyl-containing ligand is shown to be stabilized in the gas phase by ? G = 9.6 kcal mol-1. The host-guest association is mainly enthalpy-driven due to strong dispersion interactions caused by a large nonpolar interface and a high steric complementarity of the binding partners. Interference from other types of noncovalent binding forces is virtually absent. The complexes are successfully detected via electrospray ionization mass spectrometry, although a high dissociation yield is also observed. We attribute this pronounced dissociation of the complexes to the collisional activation of ions in the atmospheric interface of mass spectrometer. The comparison of several electrospray-based ionization methods reveals that cold spray ionization provides the softest ion generation conditions for these complexes.

  9. Effect of isothermal dilution on emission factors of organic carbon and n-alkanes in the particle and gas phases of diesel exhaust

    NASA Astrophysics Data System (ADS)

    Fujitani, Yuji; Saitoh, Katsumi; Fushimi, Akihiro; Takahashi, Katsuyuki; Hasegawa, Shuich; Tanabe, Kiyoshi; Kobayashi, Shinji; Furuyama, Akiko; Hirano, Seishiro; Takami, Akinori

    2012-11-01

    To investigate the effect of isothermal dilution (30 °C) on emission factors (EFs) of semivolatile and nonvolatile compounds of heavy-duty diesel exhaust, we measured EFs for particulate matter (PM), organic carbon (OC), and elemental carbon (EC) in the particle phase, and EFs for n-alkanes in both the particle phase and the gas phase of exhaust produced under high-idle engine operating conditions at dilution ratios (DRs) ranging from 8 to 1027. The EC EFs did not vary with DR, whereas the OC EFs in the particle phase determined at DR = 1027 were 13% of the EFs determined at DR = 8, owing to evaporation of organic compounds. Using partitioning theory and n-alkane EFs measured at DR = 14 and 238, we calculated the distributions of compounds between the particle and gas phases at DR = 1760, which corresponds to the DR for tailpipe emissions as they move from the tailpipe to the roadside atmosphere. The gas-phase EF of a compound with a vapor pressure of 10-7 Pa was 0.01 ?g kg-1-fuel at DR = 14, and this value is 1/330 the value derived at DR = 1760. Our results suggest that the EFs of high-volatility compounds in the particle phase will be overestimated and that the EFs of low-volatility compounds in the gas phase will be underestimated if the estimates are derived from data obtained at the low DRs and they are applied to the real world. Therefore, extrapolation from EFs derived at low DR values to EFs at atmospherically relevant DRs will be a source of error in predictions of the concentrations of particulate matter and gas-phase precursors to secondary organic aerosols in air quality models.

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

    SciTech Connect

    Yoshii, Taiki; Niibori, Yuichi; Mimura, Hitoshi [Dept. of Quantum Science and Energy Engineering, Graduate School of Engineering, Tohoku University, 6-6-01-2, Aramaki, Aza-Aoba, Aoba-ku, Sendai 980-8579 (Japan)

    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)

  11. Effects of the non-peptide B 2 receptor antagonist FR173657 in models of visceral and cutaneous inflammation

    Microsoft Academic Search

    T. Griesbacher; F. J. Legat

    2000-01-01

    Objective: The non-peptide B2 receptor antagonist (E)-3-(6-acetamido-3-pyridyl)-N-(N-(2,4-dichloro-3-((2- methyl-8-quinolinyl)oxymethyl)phenyl)-N-methylaminocar- bonylmethyl)acrylamide (FR173657) was compared to the peptide antagonist icatibant in models of visceral and cuta- neous inflammation. Methods: Pancreatitis was induced by caerulein in anaesthe- tized Sprague-Dawley rats. Acute cystitis was induced by intravesical instillation of xylene or i.p. cyclophosphamide injection. Cutaneous inflammation was induced in anaes- thetized guinea-pigs by s.c. injection

  12. 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

  13. 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.

  14. Implicit Solvent Model Studies of the Interactions of the Influenza Hemagglutinin Fusion Peptide with Lipid Bilayers

    Microsoft Academic Search

    Dalit Bechor; Nir Ben-Tal

    2001-01-01

    The “fusion peptide”, a segment of ?20 residues of the influenza hemagglutinin (HA), is necessary and sufficient for HA-induced membrane fusion. We used mean-field calculations of the free energy of peptide-membrane association (?Gtot) to deduce the most probable orientation of the fusion peptide in the membrane. The main contributions to ?Gtot are probably from the electrostatic (?Gel) and nonpolar (?Gnp)

  15. Evaluation of antitumor activity of peptide extracts from medicinal plants on the model of transplanted breast cancer in CBRB-Rb(8.17)1Iem mice.

    PubMed

    Tepkeeva, I I; Moiseeva, E V; Chaadaeva, A V; Zhavoronkova, E V; Kessler, Yu V; Semushina, S G; Demushkin, V P

    2008-04-01

    We studied antitumor effects of peptide extracts from plants on slowly growing mammary adenocarcinoma in CBRB-Rb(8.17)1Iem mice used as a model of breast cancer in humans. The antitumor effect of a single injection of the test peptides was evaluated by the delay of the appearance and growth of palpable breast cancer in mice over 4 weeks. Peptides from Hypericum perforatum and a mixture of Chelidonium majus L., Inula helenium L., Equisetum arvense L., and Inonotus obliquus exhibited maximum activity. Peptide extracts from Frangula alnuc Mill. and Laurus nobilis L. were less active. No antitumor effect of Camelia sinesis Kuntze was detected. PMID:19110595

  16. Toxoplasma gondii: immunogenicity and protection by P30 peptides in a murine model.

    PubMed

    Siachoque, Heber; Guzman, Fanny; Burgos, Javier; Patarroyo, Manuel Elkin; Gomez Marin, Jorge Enrique

    2006-09-01

    Vaccines are promising for the control of toxoplasmosis. Here, we evaluated the immunogenicity of 17 peptides derived from SAG1 surface protein of Toxoplasma gondii in CH3 mice. Only 8 of 16 peptides induced specific antibodies. After a lethal challenge, only the vaccination with 4 of 17 peptides that were from the carboxy terminal end of the protein conferred significant survival. Our work shows that vaccination with peptides from the carboxy-terminal positions of SAG1 major surface protein of Toxoplasma protects mice against a lethal challenge. PMID:16545806

  17. Kinetics and mechanism of the beta-alanine + OH gas phase reaction: a quantum mechanical approach.

    PubMed

    Cruz-Torres, Armando; Galano, Annia; Alvarez-Idaboy, J Raúl

    2006-01-14

    The OH hydrogen abstraction reaction from beta-alanine has been studied using the BHandHLYP hybrid HF-density functional and 6-311G(d,p) basis sets. The energies have been improved by single point calculations at the CCSD(T)/6-311G(d,p) level of theory. The structures of the different stationary points are discussed. Reaction profiles are modeled including the formation of pre-reactive and product complexes. Negative net activation energy is obtained for the overall reaction. A complex mechanism is proposed, and the rate coefficients are calculated using transition state theory over the temperature range of 250-400 K. The rate coefficients are proposed for the first time and it was found that in the gas phase the hydrogen abstraction occurs mainly from the CH(2) group next to the amino end. The following expressions, in cm(3) mol(-1) s(-1), are obtained for the overall rate constants, at 250-400 and 290-310 K, respectively: k(250-400)= 2.36 x 10(-12) exp(340/T), and k(290-310)= 1.296 x 10(-12) exp(743/T). The three parameter expression that best describes the studied reaction is k(250-400)= 1.01 x 10(-21)T(3.09) exp(1374/T). The beta-alanine + OH reaction was found to be 1.5 times faster than the alpha-alanine + OH reaction. PMID:16482271

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

    PubMed

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

    2003-11-15

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

  19. Influence of Benzene on Aerosol- and Gas-Phase Chemistry in Haze Analog Atmospheres

    NASA Astrophysics Data System (ADS)

    Yoon, Y. H.; Horst, S. M.; Li, R.; Barth, E. L.; Trainer, M. G.; De Gouw, J. A.; Tolbert, M. A.

    2012-12-01

    Benzene (C6H6) has been observed in the haze atmospheres of Saturn and Jupiter by the Infrared Space Observatory [1] and in the atmosphere of Titan, most recently during the Cassini mission by the Ion and Neutral Mass Spectrometer [2,3] and the Composite Infrared Spectrometer [4]. Photochemical reactions involving benzene may influence polycyclic aromatic hydrocarbon formation, aerosol formation, and the radiative balance of planetary atmospheres. We measure the influence of benzene on a model system, Titan analog particles, in the laboratory by photolyzing CH4/N2 gas mixtures infused with ppm-levels of C6H6 using a deuterium lamp (115-400 nm). We measure the chemical composition of the aerosol-phase products and gas-phase products using aerosol mass spectrometry and proton-transfer ion-trap mass spectrometry, respectively. We measure the optical properties of the aerosol-phase products at 532 nm using cavity ring-down aerosol extinction spectroscopy. These studies are compared to previous studies [5,6] of Titan analog particles formed by methane photolysis. [1] Bezard B. et al. (2001) Icarus, 154, 492-500. [2] Waite, J. H. et al. (2007) Science, 316, 870-875. [3] Vuitton, V. et al. (2008) JGR, 113, E05007. [4] Coustenis, A. et al. (2007) Icarus, 189, 35-62. [5] Hasenkopf, C.A. et al. (2010) Icarus, 207, 903-913. [6] Trainer, M. G. et al. (2012) Astrobiology, 12, 315-326.

  20. Formation of a submillimeter bubble from an orifice using pulsed acoustic pressure waves in gas phase

    NASA Astrophysics Data System (ADS)

    Shirota, Minori; Sanada, Toshiyuki; Sato, Ayaka; Watanabe, Masao

    2008-04-01

    The mechanism of a bubble production method using pulsed acoustic pressure waves in gas phase is investigated using high-speed photography. The acoustic characteristics of the present bubble generator are also investigated. We found out the optimal acoustic waveform for producing only one bubble per one action; the bubble detachment radius is accurately controlled by first applying the positive onset-assistance acoustic pressure wave and then the negative detachment-assistance acoustic pressure wave with an accurately controlled time lapse. From an orifice with a radius of 0.09mm submerged in water, bubbles with radii in the range of 0.28-0.78mm with an extremely small standard deviation of less than 1?m are obtained. The shrinking and pinch-off motions of a capillary bridge connecting the bubble and orifice at the time of bubble detachment are observed in detail. The balancing force on a growing bubble, which is based on a spherical bubble formation model is also estimated. As a result, we reveal that when the gas pressure is decreased due to a negative pressure wave, the capillary bridge submerges into the orifice and an upward added mass force is applied on the bubble, both of which cause the detachment of the bubble from the orifice.

  1. Development of techniques for measurement of gas-phase hydrogen peroxide

    SciTech Connect

    Shen, J.; Tanner, R.L.; Kelly, T.J.

    1988-02-01

    The techniques of measuring gas-phase hydrogen peroxide by impinger and diffusion scrubber have been extensively investigated. The mass transfer of collected peroxide in a diffusion scrubber is discussed. The equation describing collection of soluble substances by diffusion scrubber is given for low and high gas flow rates. Gaseous hydrogen peroxide in ambient air can be collected by impinger or scrubber without artifact formation of hydrogen peroxide if O/sub 3/ is first removed by gas-phase reaction with nitric oxide. Losses of gas-phase hydrogen peroxide in the sampling tubing and in the scrubber have been quantified. In sampling of gas-phase H/sub 2/O/sub 2/ in ambient air at Brookhaven National Laboratory and in Los Angeles, a total of 180 samples were collected by impinger and 330 by diffusion scrubber. The ambient levels and the diurnal variation of gas-phase H/sub 2/O/sub 2/ are discussed and perhaps indicate the range of observed H/sub 2/O/sub 2/ levels. Data collected simultaneously by impinger and scrubber collection methods are compared, and the causes of lower than predicted recovery efficiency from the scrubber are discussed. 24 refs., 15 figs., 11 tabs.

  2. RgpA-Kgp Peptide-Based Immunogens Provide Protection against Porphyromonas gingivalis Challenge in a Murine Lesion Model

    PubMed Central

    O'Brien-Simpson, Neil M.; Paolini, Rita A.; Reynolds, Eric C.

    2000-01-01

    Porphyromonas gingivalis, a gram-negative bacterium, has been linked to the onset and progression of periodontitis, a chronic inflammatory disease of the supporting tissues of the teeth. A major virulence factor of P. gingivalis is an extracellular complex of Arg- and Lys-specific proteinases and adhesins designated the RgpA-Kgp complex (formerly the PrtR-PrtK complex). In this study we show that the RgpA-Kgp complex, when used as an immunogen with incomplete Freund adjuvant (IFA), protects against challenge with invasive and noninvasive strains of P. gingivalis in the murine lesion model. We identified a variety of peptide vaccine candidates from the RgpA and Kgp polyprotein sequences that involved the putative active site histidine of both proteinases and five repeat motifs in the adhesin domains of both polyproteins implicated in aggregation and binding to host substrates, designated adhesin-binding motif (ABM) peptides. These peptides were synthesized using standard, solid-phase protocols for 9-fluorenylmethoxy carbonyl chemistry with S-acetylmercaptoacetic acid (SAMA) as the N-terminal residue. The SAMA-peptides were then conjugated to diphtheria toxoid and used with IFA to immunize BALB/c mice. Both active-site peptides and three of the five ABM peptides gave protection (P < 0.005) against challenge with P. gingivalis in the murine lesion model. The three ABM peptide sequences that conferred protection exist within a 100-residue span in the RgpA44 and Kgp39 adhesins of the RgpA-Kgp complex. Protective anti-RgpA-Kgp complex mouse antisera recognized the RgpA27, Kgp39, and RgpA44 adhesins in an immunoblot. Epitope mapping of the RgpA27 adhesin using the protective anti-RgpA-Kgp antisera identified a major protective epitope that mapped immediately N terminal to one of the protective ABM peptides in the 100-residue span in RgpA44 and Kgp39. This identified protective epitope contains clusters of basic residues spatially surrounded by hydrophobic amino acids, a finding which is characteristic of a heparin binding motif. PMID:10858222

  3. Infrared reflection absorption spectroscopy of amphipathic model peptides at the air/water interface.

    PubMed

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

    2004-06-01

    The linear sequence KLAL (KLALKLALKALKAALKLA-NH(2)) and its corresponding d,l-isomers k(9)a(10)-KLAL (KLALKLALkaLKAALKLA-NH(2)) and l(11)k(12)-KLAL (KLALKLALKAlkAALKLA-NH(2)) are model compounds for potentially amphipathic alpha-helical peptides which are able to bind to membranes and to increase the membrane permeability in a structure- and target-dependent manner (Dathe and Wieprecht, 1999) We first studied the secondary structure of KLAL and its analogs bound to the air/water using infrared reflection absorption spectroscopy. For the peptide films the shape and position of the amide I and amide II bands indicate that the KLAL adopts at large areas per molecule an alpha-helical secondary structure, whereas at higher surface pressures or smaller areas it converts into a beta-sheet structure. This transition could be observed in the compression isotherm as well as during the adsorption at the air/water interface from the subphase as a function of time. The secondary structures are essentially orientated parallel to the air/water interface. The analogs with d-amino acids in two different positions of the sequence, k(9)a(10)-KLAL and l(11)k(12)-KLAL, form only beta-sheet structures at all surface pressures. The observed results are interpreted using a comparison of hydrophobic moments calculated for alpha-helices and beta-sheets. The differences between the hydrophobic moments calculated using the consensus scale are not large. Using the optimal matching hydrophobicity scale or the whole-residue hydrophobicity scale the beta-sheet even has the larger hydrophobic moment. PMID:15189871

  4. Gas phase precursors to anthropogenic secondary organic aerosol: Using the Master Chemical Mechanism to probe detailed observations of 1,3,5-trimethylbenzene photo-oxidation

    NASA Astrophysics Data System (ADS)

    Rickard, A. R.; Wyche, K. P.; Metzger, A.; Monks, P. S.; Ellis, A. M.; Dommen, J.; Baltensperger, U.; Jenkin, M. E.; Pilling, M. J.

    2010-12-01

    A detailed gas-phase photochemical chamber box model, incorporating the Master Chemical Mechanism (MCMv3.1) degradation scheme for the model anthropogenic aromatic compound 1,3,5-trimethylbenzene, has been used to simulate data measured during a series of aerosol chamber experiments in order to evaluate the mechanism under a variety of VOC/NO x conditions. The chamber model was used in the interpretation of comprehensive high (mass and time) resolution measurements of 1,3,5-trimethylbenzene and its photo-oxidation products recorded by a Chemical Ionisation Reaction Time-of-Flight Mass Spectrometer (CIR-TOF-MS). Supporting gas and aerosol measurements have also enabled us to explore the 'missing link' between the gas and aerosol phases. Model-measurement comparisons have been used to gain insight into the complex array of oxygenated products formed, including the peroxide bicyclic ring opening products (?,?-unsaturated-?-dicarbonyls and furanones) and the O 2-bridged peroxide bicyclic ring-retaining products. To our knowledge this is the first time such high molecular weight species, corresponding to various peroxide bicyclic products represented in the MCMv3.1, have been observed in the gas-phase. The model was also used to give insight into which gas-phase species were participating in SOA formation, with the primary and secondary peroxide products, formed primarily under low NO x conditions, identified as likely candidates.

  5. Evaluation of the Influence of Amino Acid Composition on the Propensity for Collision-Induced Dissociation of Model Peptides Using Molecular Dynamics Simulations

    SciTech Connect

    Cannon, William R.; Taasevigen, Danny J.; Baxter, Douglas J.; Laskin, Julia

    2007-09-01

    The dynamical behavior of model peptides was evaluated with respect to their ability to form internal proton donor-acceptor pairs using molecular dynamics simulations. The proton donor-acceptor pairs are postulated to be prerequisites for peptide bond cleavage resulting in formation of b and y ions during low energy collision-induced dissociation in tandem mass spectrometry (MS/MS). The simulations for the polyalanine pentamer Ala5H+ were compared to experimental data from collision energy-resolved surface induced dissociation (SID) studies. The results of the simulation are insightful into the events that likely lead up to the fragmentation of peptides. 9-mer polyalanine-based model peptides were used to examine the dynamical effect of each of the 20 common amino acids on the probability to form donor-acceptor pairs at labile peptide bonds. A continuous range of probabilities was observed as a function of the substituted amino acid. However, the location of the peptide bond involved in the donor-acceptor pair plays a critical role in the dynamical behavior. This influence of position on the probability of forming a donor-acceptor pair would be hard to predict from statistical analyses on experimental spectra of aggregate, diverse peptides. In addition, the inclusion of basic side chains in the model peptides alters the probability of forming donor-acceptor pairs across the entire backbone. In this case there are still more ionizing protons than basic residues, but the side chains of the basic amino acids form stable hydrogen bond networks with the peptide carbonyl oxygens and thus act to prevent free access of “mobile protons” to labile peptide bonds. It is clear from the work that the identification of peptides from low-energy CID using automated computational methods should consider the location of the fragmenting bond as well as the amino acid composition.

  6. 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

  7. Bombesin-like peptide mediates lung injury in a baboon model of bronchopulmonary dysplasia.

    PubMed Central

    Sunday, M E; Yoder, B A; Cuttitta, F; Haley, K J; Emanuel, R L

    1998-01-01

    The etiology of bronchopulmonary dysplasia (BPD), a chronic lung disease of infants surviving respiratory distress syndrome, remains fundamentally enigmatic. BPD is decreasing in severity but continues to be a major problem in pediatric medicine, being especially prevalent among very premature infants. Increased numbers of pulmonary neuroendocrine cells containing bombesin-like peptide (BLP) have been reported to occur in human infants with BPD. We tested the hypothesis that BLP mediates BPD using the hyperoxic baboon model. Urine BLP levels increased soon after birth only in 100% O2-treated 140-d animals which developed BPD, correlating closely with severity of subsequent chronic lung disease. Similar elevations in urine BLP were observed in the 125-d baboon "interrupted gestation" model of BPD. Postnatal administration of anti-BLP antibody attenuated clinical and pathological evidence of chronic lung disease in the hyperoxic baboon model. Urine BLP could be a biological predictor of infants at risk for BPD, and blocking BLP postnatally could be useful for BPD prevention. PMID:9691095

  8. Free energy of a potassium ion in a model of the channel formed by an amphipathic leucine-serine peptide

    Microsoft Academic Search

    Graham R. Smith; Mark S. P. Sansom

    2002-01-01

    . We use molecular dynamics simulations to investigate the position-dependent free energy of a potassium ion in a model of an ion channel formed by the synthetic amphipathic leucine-serine peptide, LS3. The channel model is a parallel bundle of six LS3 helices around which are packed 146 methane-like spheres in order to mimic a membrane. At either end of and

  9. Formation of 9,10-phenanthrenequinone by atmospheric gas-phase reactions of phenanthrene

    NASA Astrophysics Data System (ADS)

    Wang, Lin; Atkinson, Roger; Arey, Janet

    Phenanthrene is a 3-ring polycyclic aromatic hydrocarbon which exists mainly in the gas-phase in the atmosphere. Recent concern over the presence of 9,10-phenanthrenequinone in ambient particles led us to study the products of the gas-phase reactions of phenanthrene with hydroxyl radicals, nitrate radicals and ozone. The formation yields of 9,10-phenanthrenequinone were measured to be ˜3%, 33±9%, and ˜2% from the OH radical, NO 3 radical and O 3 reactions, respectively. Calculations suggest that daytime OH radical-initiated and nighttime NO 3 radical-initiated reactions of gas-phase phenanthrene may be significant sources of 9,10-phenanthrenequinone in ambient atmospheres. In contrast, the ozone reaction with phenanthrene is unlikely to contribute significantly to ambient 9,10-phenanthrenequinone.

  10. Insights into diastereoisomeric characterization of tetrahydropyridazine amino acid derivatives: crystal structures and gas phase ion chemistry.

    PubMed

    Giorgi, Gianluca; Favi, Gianfranco; Attanasi, Orazio A

    2013-08-14

    Structural, conformational properties, and gas phase reactivity of two representative diastereoisomeric members of a series of ?,?-tetrahydropyridazine amino acid derivatives have been investigated by using X-ray crystallography, tandem mass spectrometry and theoretical calculations. Both diastereoisomers show an unusual screw-boat conformation of the tetrahydropyridazine ring. While protonated molecules mainly decompose in the gas phase by loss of acetamide, the main reactivity of the [M + Na](+) species consists of loss of PhNCO followed by acetamide and it is strictly dependent upon the stereochemistry of the parent compound. The most stable energy minimized structures obtained by theoretical calculations are in full agreement with the experimental data and allowed us to rationalize the gas phase reaction pathways. PMID:23787961

  11. Oxidation of formic acid on the Pt(111) surface in the gas phase.

    PubMed

    Gao, Wang; Keith, John A; Anton, Josef; Jacob, Timo

    2010-09-28

    Formic acid (HCOOH) oxidation on Pt(111) under gas-phase conditions is a benchmark heterogeneous catalysis reaction used to probe electro-catalytic HCOOH conversion in fuel cells, itself an important reaction in energy conversion. We used density functional theory (DFT) calculations to elucidate the fundamental oxidation mechanisms of HCOOH in the gas phase, determining the relative strengths of chemical interactions between HCOOH oxidation intermediates and the Pt(111) surface. We focused on investigating how water and adsorption coverage affects reaction intermediate structures and transition states. Our results show that adsorbed HCOO is a reactive intermediate in gas phase, and co-adsorbed water plays a key role in HCOOH oxidation influencing the structure of reaction intermediates and reaction barriers on Pt(111). The simulations show the preferred catalytic pathway is qualitatively dependent on surface coverage. These results provide a conceptual basis to better interpret its complicated experimental reaction kinetics. PMID:20714626

  12. Gamma-ray spectra of hexane in gas phase and liquid phase

    E-print Network

    Xiaoguang Ma; Feng Wang

    2012-11-01

    Theoretical gamma-ray spectra of molecule hexane have been calculated and compared with the experimental results in both gas (Surko et al, 1997) and liquid (Kerr et al, 1965) phases. The present study reveals that in gas phase not all valence electrons of hexane exhibit the same probability to annihilate a positron. Only the positrophilic electrons in the valence space dominate the gamma-ray spectra, which are in good agreement with the gas phase measurement. When hexane is confined in liquid phase, however, the intermolecular interactions ultimately eliminate the free molecular orientation and selectivity for the positrophilic electrons in the gas phase. As a result, the gamma-ray spectra of hexane become an averaged contribution from all valence electrons, which is again in agreement with liquid phase measurement. The roles of the positrophilic electrons in annihilation process for gas and liquid phases of hexane have been recognized for the first time in the present study.

  13. Formation of secondary aerosols: impact of the gas-phase chemical mechanism

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Sartelet, K.; Seigneur, C.

    2010-08-01

    The impact of two recent gas-phase chemical kinetic mechanisms (CB05 and RACM2) on the formation of secondary inorganic and organic aerosols is compared for simulations of PM2.5 over Europe between 15 July and 15 August 2001. The host chemistry transport model is Polair3D of the Polyphemus air-quality platform. Particulate matter is modeled with SIREAM, which is coupled to the thermodynamic model ISORROPIA and to the secondary organic aerosol module MAEC. Model performance is satisfactory with both mechanisms for speciated PM2.5. The monthly-mean difference of the concentration of PM2.5 is less than 1 ?g/m3 (6%) over the entire domain. Secondary chemical components of PM2.5 include sulfate, nitrate, ammonium and organic aerosols, and the chemical composition of PM2.5 is not significantly different between the two mechanisms. Monthly-mean concentrations of inorganic aerosol are higher with RACM2 than with CB05 (+16% for sulfate, +11% for nitrate, and +12% for ammonium), whereas the concentrations of organic aerosols are slightly higher with CB05 than with RACM2 (+26% for anthropogenic SOA and +1% for biogenic SOA). Differences in the inorganic and organic aerosols result primarily from differences in oxidant concentrations (OH, O3 and NO3). Nitrate formation tends to be HNO3-limited over land and differences in the concentrations of nitrate are due to differences in concentration of HNO3. Differences in aerosols formed from aromatics SVOC are due to different aromatics oxidation between CB05 and RACM2. The aromatics oxidation in CB05 leads to more cresol formation, which then leads to more SOA. Differences in the aromatics aerosols would be significantly reduced with the recent CB05-TU mechanism for toluene oxidation. Differences in the biogenic aerosols are due to different oxidant concentrations (monoterpenes) and different particulate organic mass concentrations affecting the gas-particle partitioning of SOA (isoprene).

  14. Utilizing ESEEM spectroscopy to locate the position of specific regions of membrane-active peptides within model membranes.

    PubMed

    Carmieli, Raanan; Papo, Niv; Zimmermann, Herbert; Potapov, Alexey; Shai, Yechiel; Goldfarb, Daniella

    2006-01-15

    Membrane-active peptides participate in many cellular processes, and therefore knowledge of their mode of interaction with phospholipids is essential for understanding their biological function. Here we present a new methodology based on electron spin-echo envelope modulation to probe, at a relatively high resolution, the location of membrane-bound lytic peptides and to study their effect on the water concentration profile of the membrane. As a first example, we determined the location of the N-terminus of two membrane-active amphipathic peptides, the 26-mer bee venom melittin and a de novo designed 15-mer D,L-amino acid amphipathic peptide (5D-L9K6C), both of which are antimicrobial and bind and act similarly on negatively charged membranes. A nitroxide spin label was introduced to the N-terminus of the peptides and measurements were performed either in H2O solutions with deuterated model membranes or in D2O solutions with nondeuterated model membranes. The lipids used were dipalmitoyl phosphatidylcholine (DPPC) and phosphatidylglycerol (PG), (DPPC/PG (7:3 w/w)), egg phosphatidylcholine (PC) and PG (PC/PG (7:3 w/w)), and phosphatidylethanolamine (PE) and PG (PE/PG, 7:3w/w). The modulation induced by the 2H nuclei was determined and compared with a series of controls that produced a reference "ruler". Actual estimated distances were obtained from a quantitative analysis of the modulation depth based on a simple model of an electron spin situated at a certain distance from the bottom of a layer with homogeneously distributed deuterium nuclei. The N-terminus of both peptides was found to be in the solvent layer in both the DPPC/PG and PC/PG membranes. For PE/PG, a further displacement into the solvent was observed. The addition of the peptides was found to change the water distribution in the membrane, making it "flatter" and increasing the penetration depth into the hydrophobic region. PMID:16258052

  15. Utilizing ESEEM Spectroscopy to Locate the Position of Specific Regions of Membrane-Active Peptides within Model Membranes

    PubMed Central

    Carmieli, Raanan; Papo, Niv; Zimmermann, Herbert; Potapov, Alexey; Shai, Yechiel; Goldfarb, Daniella

    2006-01-01

    Membrane-active peptides participate in many cellular processes, and therefore knowledge of their mode of interaction with phospholipids is essential for understanding their biological function. Here we present a new methodology based on electron spin-echo envelope modulation to probe, at a relatively high resolution, the location of membrane-bound lytic peptides and to study their effect on the water concentration profile of the membrane. As a first example, we determined the location of the N-terminus of two membrane-active amphipathic peptides, the 26-mer bee venom melittin and a de novo designed 15-mer D,L-amino acid amphipathic peptide (5D-L9K6C), both of which are antimicrobial and bind and act similarly on negatively charged membranes. A nitroxide spin label was introduced to the N-terminus of the peptides and measurements were performed either in H2O solutions with deuterated model membranes or in D2O solutions with nondeuterated model membranes. The lipids used were dipalmitoyl phosphatidylcholine (DPPC) and phosphatidylglycerol (PG), (DPPC/PG (7:3 w/w)), egg phosphatidylcholine (PC) and PG (PC/PG (7:3 w/w)), and phosphatidylethanolamine (PE) and PG (PE/PG, 7:3w/w). The modulation induced by the 2H nuclei was determined and compared with a series of controls that produced a reference “ruler”. Actual estimated distances were obtained from a quantitative analysis of the modulation depth based on a simple model of an electron spin situated at a certain distance from the bottom of a layer with homogeneously distributed deuterium nuclei. The N-terminus of both peptides was found to be in the solvent layer in both the DPPC/PG and PC/PG membranes. For PE/PG, a further displacement into the solvent was observed. The addition of the peptides was found to change the water distribution in the membrane, making it “flatter” and increasing the penetration depth into the hydrophobic region. PMID:16258052

  16. Amphipols outperform dodecylmaltoside micelles in stabilizing membrane protein structure in the gas phase.

    PubMed

    Calabrese, Antonio N; Watkinson, Thomas G; Henderson, Peter J F; Radford, Sheena E; Ashcroft, Alison E

    2015-01-20

    Noncovalent mass spectrometry (MS) is emerging as an invaluable technique to probe the structure, interactions, and dynamics of membrane proteins (MPs). However, maintaining native-like MP conformations in the gas phase using detergent solubilized proteins is often challenging and may limit structural analysis. Amphipols, such as the well characterized A8-35, are alternative reagents able to maintain the solubility of MPs in detergent-free solution. In this work, the ability of A8-35 to retain the structural integrity of MPs for interrogation by electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is compared systematically with the commonly used detergent dodecylmaltoside. MPs from the two major structural classes were selected for analysis, including two ?-barrel outer MPs, PagP and OmpT (20.2 and 33.5 kDa, respectively), and two ?-helical proteins, Mhp1 and GalP (54.6 and 51.7 kDa, respectively). Evaluation of the rotationally averaged collision cross sections of the observed ions revealed that the native structures of detergent solubilized MPs were not always retained in the gas phase, with both collapsed and unfolded species being detected. In contrast, ESI-IMS-MS analysis of the amphipol solubilized MPs studied resulted in charge state distributions consistent with less gas phase induced unfolding, and the presence of lowly charged ions which exhibit collision cross sections comparable with those calculated from high resolution structural data. The data demonstrate that A8-35 can be more effective than dodecylmaltoside at maintaining native MP structure and interactions in the gas phase, permitting noncovalent ESI-IMS-MS analysis of MPs from the two major structural classes, while gas phase dissociation from dodecylmaltoside micelles leads to significant gas phase unfolding, especially for the ?-helical MPs studied. PMID:25495802

  17. Measuring Soil-Water Content with Gas-Phase Partitioning Tracers: Mass Transfer Limitations

    NASA Astrophysics Data System (ADS)

    Li, L.; Imhoff, P. T.

    2002-05-01

    Soil-water content is an important parameter for soil scientists, hydrologists, and engineers studying the movement of water, gas, and pollutants in the vadose zone. Traditionally, soil-water content is characterized with point measurements, which include gravimetric analysis of core samples, time domain reflectrometry, and neutron moderation. More recently, the gas-phase partitioning tracer method has been suggested as an in situ tool for obtaining soil water content over large measurement volumes. Here, two tracers move through the gas phase, one that is non-reactive and one that partitions into the bulk water. Chromatographic separation of the tracers occurs that can be related to the soil-water content in the volume traversed by the tracers. Gas-phase partitioning tracers were previously tested under controlled laboratory conditions in homogeneous porous media with reasonably homogeneous distributions of soil-water content. In natural systems, though, soil-water is often heterogeneously distributed and sometimes moving. In this study, we investigated the utility of gas-phase partitioning tracers for these conditions. Laboratory columns were constructed with homogeneous and heterogeneous distributions of sand, which resulted in homogeneous or heterogeneous distributions of soil-water after water addition. In some experiments, the water infiltrated at a steady rate. Carbon dioxide and difluoromethane were selected as bulk-water partitioning tracers, which are tracers whose predominant mechanism of retention is partitioning into water; helium was the conservative tracer. These tracers were flushed through the experimental systems, varying the tracer slug size and gas-phase velocity. Measured soil water contents where compared with known values to infer the conditions under which mass transfer limitations influence gas-phase tracer measurements.

  18. 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.

  19. Direct gas-phase epoxidation of propylene to propylene oxide through radical reactions: A theoretical study

    NASA Astrophysics Data System (ADS)

    Kizilkaya, Ali Can; Fellah, Mehmet Ferdi; Onal, Isik

    2010-03-01

    The gas-phase radical chain reactions which utilize O 2 as the oxidant to produce propylene oxide (PO) are investigated through theoretical calculations. The transition states and energy profiles were obtained for each path. The rate constants were also calculated. The energetics for the competing pathways indicate that PO can be formed selectively due to its relatively low activation barrier (9.3 kcal/mol) which is in a good agreement with the experimental value (11 kcal/mol) of gas-phase propylene epoxidation. The formation of the acrolein and combustion products have relatively high activation barriers and are not favored. These results also support the recent experimental findings.

  20. Atmospheric chemistry of gas-phase polycyclic aromatic hydrocarbons: formation of atmospheric mutagens.

    PubMed Central

    Atkinson, R; Arey, J

    1994-01-01

    The atmospheric chemistry of the 2- to 4-ring polycyclic aromatic hydrocarbons (PAH), which exist mainly in the gas phase in the atmosphere, is discussed. The dominant loss process for the gas-phase PAH is by reaction with the hydroxyl radical, resulting in calculated lifetimes in the atmosphere of generally less than one day. The hydroxyl (OH) radical-initiated reactions and nitrate (NO3) radical-initiated reactions often lead to the formation of mutagenic nitro-PAH and other nitropolycyclic aromatic compounds, including nitrodibenzopyranones. These atmospheric reactions have a significant effect on ambient mutagenic activity, indicating that health risk assessments of combustion emissions should include atmospheric transformation products. PMID:7821285

  1. Application of gamma densitometry and statistical signal analysis to gas phase velocity measurements in pipeline hydrotransport

    NASA Astrophysics Data System (ADS)

    Zych, Marcin; Hanus, Robert; Petryka, Leszek; ?wisulski, Dariusz; Strz?powicz, Anna; Zych, Piotr

    2015-05-01

    The work presents selected methods of signal analysis used in the processing of data obtained from radiometric probes. The used data came from an exemplary study of a two-phase liquid-gas flow at the laboratory installation. In such rigs many possible transport types may be observed, i.e. slug, plug and bubble flow, and each of them gives different signal-to-noise ratio of recorded data. Therefore, available radiometric methods of gas phase velocity measurements give diverse accuracies. Authors consider several improvements of data acquisition and processing which increase possibility of the flow type recognition and higher accuracy of the gas phase velocity estimation.

  2. Control of gas phase nanoparticle shape and its effect on MRI relaxivity

    NASA Astrophysics Data System (ADS)

    Akta?, S?tk?; Thornton, Stuart C.; Binns, Chris; Lari, Leonardo; Pratt, Andrew; Kröger, Roland; Horsfield, Mark A.

    2015-03-01

    We have used a sputtering gas aggregation source to produce Fe@FeO nanoparticles with different shapes, by annealing them at different temperatures in the gas phase. Without annealing, the most common shape found for the nanoparticles is cubic but annealing the nanoparticles at 1129 °C transforms the cubes into cuboctahedra. Measurements of the MRI relaxivity show that the cubic nanoparticles have a higher performance by a factor of two, which is attributed to a higher saturation magnetization for this shape. This indicates that the shape-control enabled by gas-phase synthesis is important for obtaining optimal performance in applications.

  3. A pressure cell for nonresonant inelastic x-ray scattering studies of gas phases

    SciTech Connect

    Minzer, M.; Bradley, J. A.; Musgrave, R.; Seidler, G. T. [Physics Department, University of Washington, Seattle, Washington 98195 (United States); Skilton, A. [Mechanical Engineering Department, University of Washington, Seattle, Washington 98195 (United States)

    2008-08-15

    We report the design and performance of a gas-phase sample cell for measurements of momentum transfer (q) dependent nonresonant inelastic x-ray scattering (NRIXS). NRIXS measurements from He gas at 2 MPa (20 bars) readily demonstrate dipole-allowed and dipole-forbidden final states for two-electron excitations. Direct comparison of gas-phase NRIXS measurements with the corresponding nonresonant electron energy loss spectroscopy results (EELS) will be a valuable method for characterizing systematic errors in either technique for studies that require absolute normalization of the double differential cross section.

  4. 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

    May, Jody C; Goodwin, Cody R; Lareau, Nichole M; Leaptrot, Katrina L; Morris, Caleb B; Kurulugama, Ruwan T; Mordehai, Alex; Klein, Christian; Barry, William; Darland, Ed; Overney, Gregor; Imatani, Kenneth; Stafford, George C; Fjeldsted, John C; McLean, John A

    2014-02-18

    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

  5. 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

  6. Genetic Mechanisms of Coffee Extract Protection in a Caenorhabditis elegans Model of ?-Amyloid Peptide Toxicity

    PubMed Central

    Dostal, Vishantie; Roberts, Christine M.; Link, Christopher D.

    2010-01-01

    Epidemiological studies have reported that coffee and/or caffeine consumption may reduce Alzheimer's disease (AD) risk. We found that coffee extracts can similarly protect against ?-amyloid peptide (A?) toxicity in a transgenic Caenorhabditis elegans Alzheimer's disease model. The primary protective component(s) in this model is not caffeine, although caffeine by itself can show moderate protection. Coffee exposure did not decrease A? transgene expression and did not need to be present during A? induction to convey protection, suggesting that coffee exposure protection might act by activating a protective pathway. By screening the effects of coffee on a series of transgenic C. elegans stress reporter strains, we identified activation of the skn-1 (Nrf2 in mammals) transcription factor as a potential mechanism of coffee extract protection. Inactivation of skn-1 genetically or by RNAi strongly blocked the protective effects of coffee extract, indicating that activation of the skn-1 pathway was the primary mechanism of coffee protection. Coffee also protected against toxicity resulting from an aggregating form of green fluorescent protein (GFP) in a skn-1–dependent manner. These results suggest that the reported protective effects of coffee in multiple neurodegenerative diseases may result from a general activation of the Nrf2 phase II detoxification pathway. PMID:20805557

  7. Sequence Environment of Mutation Affects Stability and Folding in Collagen Model Peptides of Osteogenesis Imperfecta

    PubMed Central

    Bryan, Michael A.; Cheng, Haiming; Brodsky, Barbara

    2010-01-01

    Osteogenesis Imperfecta (OI), a disorder characterized by fragile bones, is often a consequence of missense mutations in type I collagen which change one Gly in the repeating (Gly-Xaaa-Yaa)n sequence to a larger amino acid. The impact of local environment and the identity of the residue replacing Gly was investigated using two sets of triple-helical peptides. Gly mutations in the highly stable (Pro-Hyp-Gly)10 system are compared with mutations in T1-865 peptides where the mutation is located within a less stable natural collagen sequence. Replacement of a Gly residue by Ala, Ser, or Arg leads to significant triple-helical destabilization in both peptide systems. The loss of stability (?Tm) due to a Gly to Ala or Gly to Ser change was greater in the more rigid (Pro-Hyp-Gly)10 peptides than in the T1-865 set, as expected. But the final Tm values, which may be the more biologically meaningful parameters, were higher for the (Pro-Hyp-Gly)10 mutation peptides than for the corresponding T1-865 mutation peptides. In both peptide environments, a Gly to Arg replacement prevented the formation of a fully folded triple-helix. Monitoring of folding by differential scanning calorimetry showed a lower stability species as well as the fully folded triple-helical molecules for T1-865 peptides with Gly to Ala or Ser replacements, and this lower stability species disappears as a function of time. The difficulty in propagation through a mutation site in T1-865 peptides may relate to the delayed folding seen in OI collagens, and indicates a dependence of folding mechanism on the local sequence environment. PMID:20235194

  8. A 3D model of ovarian cancer cell lines on peptide nanofiber scaffold to explore the cell-scaffold interaction and chemotherapeutic resistance of anticancer drugs.

    PubMed

    Yang, Zehong; Zhao, Xiaojun

    2011-01-01

    RADA16-I peptide hydrogel, a type of nanofiber scaffold derived from self-assembling peptide RADA16-I, has been extensively applied to regenerative medicine and tissue repair in order to develop novel nanomedicine systems. In this study, using RADA16-I peptide hydrogel, a three-dimensional (3D) cell culture model was fabricated for in vitro culture of three ovarian cancer cell lines. Firstly, the peptide nanofiber scaffold was evaluated by transmission electron microscopy and atom force microscopy. Using phase contrast microscopy, the appearance of the representative ovarian cancer cells encapsulated in RADA16-I peptide hydrogel on days 1, 3, and 7 in 24-well Petri dishes was illustrated. The cancer cell-nanofiber scaffold construct was cultured for 5 days, and the ovarian cancer cells had actively proliferative potential. The precultured ovarian cancer cells exhibited nearly similar adhesion properties and invasion potentials in vitro between RADA16-I peptide nanofiber and type I collagen, which suggested that RADA16-I peptide hydrogel had some similar characteristics to type I collagen. The precultured ovarian cancer cells had two-fold to five-fold higher anticancer drug resistance than the conventional two-dimensional Petri dish culture. So the 3D cell model on peptide nanofiber scaffold is an optimal type of cell pattern for anticancer drug screening and tumor biology. PMID:21383855

  9. Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy.

    PubMed

    Rezende Valim, Lays; Davies, Julia A; Tveen Jensen, Karina; Guo, Rui; Willison, Keith R; Spickett, Corinne M; Pitt, Andrew R; Klug, David R

    2014-11-13

    Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy. PMID:25347525

  10. Isolation and characterisation of sericin antifreeze peptides and molecular dynamics modelling of their ice-binding interaction.

    PubMed

    Wu, Jinhong; Rong, Yuzhi; Wang, Zhengwu; Zhou, Yanfu; Wang, Shaoyun; Zhao, Bo

    2015-05-01

    This study aimed to isolate and characterise a novel sericin antifreeze peptide and investigate its ice-binding molecular mechanism. The thermal hysteresis activity of ice-binding sericin peptides (I-SP) was measured and their activity reached as high as 0.94 °C. A P4 fraction, with high hypothermia protective activity and inhibition activity of ice recrystallisation, was obtained from I-SP, and a purified sericin peptide, named SM-AFP, with the sequence of TTSPTNVSTT and a molecular weight of 1009.50 Da was then isolated from the P4 fraction. Treatment of Lactobacillus delbrueckii Subsp. bulgaricus LB340 LYO with 100 ?g/ml synthetic SM-AFP led to 1.4-fold increased survival (p < 0.05). Finally, an SM-AFP/ice binding model was constructed and results of molecular dynamics simulation suggested that the binding of SM-AFP with ice and prevention of ice crystal growth could be attributed to hydrogen bond formation, hydrophobic interaction and non-bond interactions. Sericin peptides could be developed into beneficial cryoprotectants and used in frozen food processing. PMID:25529728

  11. 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

  12. Single-Molecule Protein Folding: A Study of the Surface-Mediated Conformational Dynamics of a Model Amphipathic Peptide

    NASA Astrophysics Data System (ADS)

    Cunningham, Joy; English, Douglas

    2004-03-01

    Most surface-active polypeptides, composed of 10-50 amino acids, are devoid of well-defined tertiary structure. The conformation of these proteins is greatly dependent upon their environment and may assume totally different characteristics in an aqueous environment, in a detergent micelle, or in an organic solvent. Most antimicrobial peptides are helix-forming and are activated upon interaction with a membrane-mimicking environment. We are seeking to physically characterize the mechanism of membrane-peptide interaction through studying a simple model peptide, MT-1. MT-1 was designed as a nonhomologous analogue of melittin, the principle component in bee venom. We are using single molecule spectroscopy to examine the induction of secondary structure upon interaction of MT-1 with various membrane-mimicking interfaces. Specifically, we monitor coil-to-helix transition through single molecule fluorescence resonance energy transfer (sm-FRET) to determine conformational distributions of folded and unfolded peptides at an interface. Studies with MT-1 will focus upon the biologically relevant issues of orientation, aggregation, and folding at surfaces using both ensemble and single molecule experiments.

  13. Conditional Solvation Thermodynamics of Isoleucine in Model Peptides and the Limitations of the Group-Transfer Model

    PubMed Central

    2015-01-01

    The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute–solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration and the conflation of background contributions with energetics attributed to the side chain limit the ability of a single scaling factor, such as the fractional solvent exposure of the group in the protein, to map the component energetic contributions of the model-compound data to their value in the protein. But ignoring the origin of cancellations in the underlying components the group-transfer model may appear to provide a reasonable estimate of the free energy for a given error tolerance. PMID:24650057

  14. Analysis of the Gas Phase Kinetics Active during GaN Deposition from NH3 and Ga(CH3)3.

    PubMed

    Ravasio, Stefano; Momose, Takeshi; Fujii, Katsushi; Shimogaki, Yukihiro; Sugiyama, Masakazu; Cavallotti, Carlo

    2015-07-16

    The results of a systematic investigation aimed at determining the dominant gas phase chemistry active during GaN MOVPE are reported and discussed in this work. This study was performed developing a thermodynamic database including the most stable GaN gas phase species and a gas phase mechanism that could efficiently describe their interconversion kinetics. The thermodynamic data and the kinetic mechanism were calculated combining density functional theory and ab initio simulations. Structures and vibrational frequencies of reactants and transition states were determined at the M062X/6-311+G(d,p) level, while energies were computed at the ROCBS-QB3 level. Rate constants were calculated using transition state theory using the rigid rotor - harmonic oscillator approximation and considering the possible degeneration of internal motions in torsional rotations. The thermodynamic analysis indicated that the Ga gas phase species formed in the highest concentration at the standard GaN deposition temperature (1300 K) is GaNH2, followed by GaH and Ga. The diatomic GaN gas phase species, often considered to be the main precursor to the film growth, is predicted to be unstable with respect to GaNH2. Among the gas phase species containing two Ga atoms, the most stable are GaNHGaH(NH2)3, GaNHGaH2(NH2)2, and GaNHGa(NH2)4, thus indicating that the substitution of the methyl groups of the precursor with H or amino groups is thermodynamically favored. Several kinetic routes leading to the formation of these species were examined. It was found that the condensation of Ga(R1)x(R2)3-x species, with R1 and R2 being either CH3, NH2, or H, is a fast process, characterized by the formation of a precursor state whose decomposition to products requires overcoming submerged energy barriers. It is suggested that these species play a key role in the formation of the first GaN nuclei, whose successive growth leads to the formation of GaN powders. A kinetic analysis performed using a fluid dynamic model allowed us to identify the main reactive routes of this complex system. PMID:25919948

  15. Polymerization in the gas phase, in clusters, and on nanoparticle surfaces.

    PubMed

    El-Shall, M Samy

    2008-07-01

    Gas phase and cluster experiments provide unique opportunities to quantitatively study the effects of initiators, solvents, chain transfer agents, and inhibitors on the mechanisms of polymerization. Furthermore, a number of important phenomena, unique structures, and novel properties may exist during gas-phase and cluster polymerization. In this regime, the structure of the growing polymer may change dramatically and the rate coefficient may vary significantly upon the addition of a single molecule of the monomer. These changes would be reflected in the properties of the oligomers deposited from the gas phase. At low pressures, cationic and radical cationic polymerizations may proceed in the gas phase through elimination reactions. In the same systems at high pressure, however, the ionic intermediates may be stabilized, and addition without elimination may occur. In isolated van der Waals clusters of monomer molecules, sequential polymerization with several condensation steps can occur on a time scale of a few microseconds following the ionization of the gas-phase cluster. The cluster reactions, which bridge gas-phase and condensed-phase chemistry, allow examination of the effects of controlled states of aggregation. This Account describes several examples of gas-phase and cluster polymerization studies where the most significant results can be summarized as follows: (1) The carbocation polymerization of isobutene shows slower rates with increasing polymerization steps resulting from entropy barriers, which could explain the need for low temperatures for the efficient propagation of high molecular weight polymers. (2) Radical cation polymerization of propene can be initiated by partial charge transfer from an ionized aromatic molecule such as benzene coupled with covalent condensation of the associated propene molecules. This novel mechanism leads exclusively to the formation of propene oligomer ions and avoids other competitive products. (3) Structural information on the oligomers formed by gas-phase polymerization can be obtained using the mass-selected ion mobility technique where the measured collision cross-sections of the selected oligomer ions and collision-induced dissociation can provide fairly accurate structural identifications. The identification of the structures of the dimers and trimers formed in the gas-phase thermal polymerization of styrene confirms that the polymerization proceeds according to the Mayo mechanism. Similarly, the ion mobility technique has been utilized to confirm the formation of benzene cations by intracluster polymerization following the ionization of acetylene clusters. Finally, it has been shown that polymerization of styrene vapor on the surface of activated nanoparticles can lead to the incorporation of a variety of metal and metal oxide nanoparticles within polystyrene films. The ability to probe the reactivity and structure of the small growing oligomers in the gas phase can provide fundamental insight into mechanisms of polymerization that are difficult to obtain from condensed-phase studies. These experiments are also important for understanding the growth mechanisms of complex organics in flames, combustion processes, interstellar clouds, and solar nebula where gas-phase reactions, cluster polymerization, and surface catalysis on dust nanoparticles represent the major synthetic pathways. This research can lead to the discovery of novel initiation mechanisms and reaction pathways with applications in the synthesis of oligomers and nanocomposites with unique and improved properties. PMID:18557636

  16. Computational peptide vaccinology.

    PubMed

    Söllner, Johannes

    2015-01-01

    Immunoinformatics focuses on modeling immune responses for better understanding of the immune system and in many cases for proposing agents able to modify the immune system. The most classical of these agents are vaccines derived from living organisms such as smallpox or polio. More modern vaccines comprise recombinant proteins, protein domains, and in some cases peptides. Generating a vaccine from peptides however requires technologies and concepts very different from classical vaccinology. Immunoinformatics therefore provides the computational tools to propose peptides suitable for formulation into vaccines. This chapter introduces the essential biological concepts affecting design and efficacy of peptide vaccines and discusses current methods and workflows applied to design successful peptide vaccines using computers. PMID:25555730

  17. 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.

  18. Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

    PubMed

    Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

    2014-10-01

    We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single ?-pair (C2H4) and two ?-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the ?-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the ?-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved. PMID:25296807

  19. 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 ...

  20. 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, ...

  1. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins II reactions at side-chain loci in model systems

    SciTech Connect

    Garrison, W.M.

    1983-11-01

    The major emphasis in radiation biology at the molecular level has been on the nucleic acid component of the nucleic acid-protein complex because of its primary genetic importance. But there is increasing evidence that radiation damage to the protein component also has important biological implications. Damage to capsid protein now appears to be a major factor in the radiation inactivation of phage and other viruses. And, there is increasing evidence that radiation-chemical change in the protein component of chromation leads to changes in the stability of the repressor-operator complexes involved in gene expression. Knowledge of the radiation chemistry of protein is also of importance in other fields such as the application of radiation sterilization to foods and drugs. Recent findings that a class of compounds, the ..cap alpha..,..cap alpha..'-diaminodicarboxylic acids, not normally present in food proteins, are formed in protein radiolysis is of particular significance since certain of their peptide derivatives have been showing to exhibit immunological activity. The purpose of this review is to bring together and to correlate our present knowledge of products and mechanisms in the radiolysis of peptides, polypeptides and proteins both aqueous and solid-state. In part 1 we presented a discussion of the radiation-induced reactions of the peptide main-chain in model peptide and polypeptide systems. Here in part 2 the emphasis is on the competing radiation chemistry at side-chain loci of peptide derivatives of aliphatic, aromatic-unsaturated and sulfur-containing amino acids in similar systems. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis, and ESR spectroscopy are included.

  2. An improved AMBER force field for ?,?-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems.

    PubMed

    Grubiši?, Sonja; Brancato, Giuseppe; Barone, Vincenzo

    2013-10-28

    ?,?-Dialkylated amino acid residues have acquired considerable importance as effective means for introducing backbone conformation constraints in synthetic peptides. The prototype of such a class of residues, namely Aib (?-aminoisobutyric acid), appears to play a dominant role in determining the preferred conformations of host proteins. We have recently introduced into the standard AMBER force field some new parameters, fitted against high-level quantum mechanical (QM) data, for simulating peptides containing ?,?-dialkylated residues with cyclic side chains, such as TOAC (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) and Ac6c (Ac6c = 1-aminocyclohexaneacetic acid). Here, we show that in order to accurately reproduce the observed conformational geometries and structural fluctuations of linear ?,?-dialkylated peptides based on Aib, further improvements of the non-bonding and side chain torsion potential parameters have to be considered, due to the expected larger structural flexibility of linear residues with respect to cyclic ones. To this end, we present an extended set of parameters, which have been optimized by fitting the energies of multiple conformations of the Aib dipeptide analogue to corresponding QM calculations that properly account for dispersion interactions (B3LYP-D3). The quality, transferability and size-consistency of the proposed force field have been assessed both by considering a series of poly-Aib peptides, modeled at the same QM level, and by performing molecular dynamics simulations in solvents with high and low polarity. As a result, the present parameters allow one to reproduce with good reliability the available QM and experimental data, thus representing a notable improvement over current force field especially in the description of the ?/310-helix conformational equilibria of ?,?-dialkylated peptides with linear and cyclic side chains. PMID:24022462

  3. Hemostatic efficacy of biological self-assembling peptide nanofibers in a rat kidney model.

    PubMed

    Song, Hong; Zhang, Lanlan; Zhao, Xiaojun

    2010-01-11

    We evaluated the hemostatic efficacy of a biological self-assembling peptide RADA16-I in a rat kidney injury model. Adult male rats were randomized into five groups: sham operation (no renal excision), no hemostatic agent (control), commercially available gelatin sponge (Gelfoam), 1% RADA16-I, and 2% RADA16-I. After left partial nephrectomy, the anesthetized animal was anticoagulated using 300 IU x kg(-1) heparin, and the topical hemostatic agent was applied to the injury. Blood loss and mean arterial pressure (MAP) were recorded. As was the case for Gelfoam, 2% RADA16-I produced marked hemostasis versus controls (p < 0.01). Blood loss with 1% and 2% RADA16-I was significantly less than controls. The decline in MAP during surgery was less with 2% versus 1% RADA16-I. RADA16-I also resulted in less histological tissue responses than Gelfoam. These data suggest that RADA16-I can stop hemorrhage, with only minimal tissue responses, in experimental renal injury. PMID:19705375

  4. Modulation of A(beta) peptides by estrogen in mouse models.

    PubMed

    Zheng, H; Xu, H; Uljon, S N; Gross, R; Hardy, K; Gaynor, J; Lafrancois, J; Simpkins, J; Refolo, L M; Petanceska, S; Wang, R; Duff, K

    2002-01-01

    Clinical studies have shown that estrogen deprivation through menopause is a risk factor in both the initiation and progression of Alzheimer's disease (AD) and that estrogen replacement therapy may be protective. One of the major pathological features in the human AD brain is the senile plaque, a proteinaceous structure composed mainly of heterogeneous peptides collectively known as A-beta (A(beta)). In vitro studies have linked estrogen with A(beta) modulation, suggesting that one-way that estrogen depletion at menopause may exacerbate the features of AD is through A(beta) accumulation. To test this, two studies were performed on transgenic models of amyloidosis. Firstly, transgenic mice without detectable amyloid aggregates were subjected to ovariectomy and estradiol supplementation, and A(beta) levels were assessed. Secondly, the effects of estrogen modulation were assessed in mice at an age when plaques would be forming initially. Overall, A(beta) levels were higher in estrogen-deprived mice than intact mice, and this effect could be reversed through the administration of estradiol. These data suggest that, in vivo, estrogen depletion leads to the accumulation of A(beta) in the CNS, which can be reversed through replacement of estradiol. These results provide evidence that post-menopausal estrogen depletion may be linked to an increased risk of AD through A(beta) modulation. PMID:11796757

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

    Microsoft Academic Search

    George C. Schatz; Mark D. Moser

    1980-01-01

    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

  6. 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…

  7. Mechanisms for the deposition of thin metallic films by laser driven gas phase reactions

    SciTech Connect

    Jervis, T.R.; Menon, S.K.; Joyce, E.L.; Carroll, D.W.

    1986-01-01

    Gas phase processing makes laser deposition over large areas possible but homogeneous nucleation of large atomic clusters must be avoided if films are to be produced. Clusters can be highly variable in size from a few atoms to significant fractions of a micrometer. If conditions do not allow for complete quenching of the clusters produced in the gas phase, these clusters can arrive at the substrate with sufficient energy to self sinter into homogeneous films which are substantially different from metallic films grown by thermal techniques. Using transmission electron microscopy (TEM), we have characterized the microstructure of thin metallic films deposited by laser breakdown chemical vapor deposition and identified a range of deposition conditions which can lead from powders to homogeneous polycrystalline films and mixed phase materials. Gas phase nucleation is dependent on reactant partial pressures and the gas phase quench rate which can be varied in part by adjusting the H/sub 2/ content of the source gas. Manipulation of these parameters can vary powder size from about one micrometer to less than 2 nanometers. Variation of the quench rate during the deposition of polycrystalline films varies the grain size in the films. Heating the substrate drastically changes the conditions under which the film is formed and as a consequence, can radically alter the microstructure of the film itself. 6 refs., 2 figs.

  8. Gas phase detection of cyclic B3 : 2 2 A1 electronic origin band

    E-print Network

    Maier, John Paul

    Gas phase detection of cyclic B3 : 2 2 E ]X 2 A1 electronic origin band P. Cias, M. Araki, A in the 2 2 E X 2 A1 electronic spectrum of cyclic B3 has been observed by cavity ring down spectroscopy. EXPERIMENT This consists of a standard cavity ring down setup sam- pling a plasma generated in a pulsed

  9. Humidity independent mass spectrometry for gas phase chemical analysis via ambient proton transfer reaction.

    PubMed

    Zhu, Hongying; Huang, Guangming

    2015-03-31

    In this work, a humidity independent mass spectrometric method was developed for rapid analysis of gas phase chemicals. This method is based upon ambient proton transfer reaction between gas phase chemicals and charged water droplets, in a reaction chamber with nearly saturate humidity under atmospheric pressure. The humidity independent nature enables direct and rapid analysis of raw gas phase samples, avoiding time- and sample-consuming sample pretreatments in conventional mass spectrometry methods to control sample humidity. Acetone, benzene, toluene, ethylbenzene and meta-xylene were used to evaluate the analytical performance of present method. The limits of detection for benzene, toluene, ethylbenzene and meta-xylene are in the range of ?0.1 to ?0.3 ppbV; that of benzene is well below the present European Union permissible exposure limit for benzene vapor (5 ?g m(-3), ?1.44 ppbV), with linear ranges of approximately two orders of magnitude. The majority of the homemade device contains a stainless steel tube as reaction chamber and an ultrasonic humidifier as the source of charged water droplets, which makes this cheap device easy to assemble and facile to operate. In addition, potential application of this method was illustrated by the real time identification of raw gas phase chemicals released from plants at different physiological stages. PMID:25813029

  10. 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.

  11. 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/...

  12. Photocatalytic destruction of toluene and xylene at gas phase on a titania based monolithic catalyst

    Microsoft Academic Search

    J. Blanco; P. Avila; A. Bahamonde; E. Alvarez; B. Sánchez; M. Romero

    1996-01-01

    Toluene and xylene were subjected to gas-solid heterogeneous photocatalytic oxidation on a titania based monolithic catalyst, in order to investigate the potential of solar-driven detoxification as a clean and safe method for air purification and gas phase waste destruction. Thus, gaseous streams with toluene or xylene were conducted through a monolithic catalysts based on titania dispersed on a fibrous silicate

  13. Gas-phase photoemission with soft x-rays: cross sections and angular distributions

    SciTech Connect

    Shirley, D.A.; Kobrin, P.H.; Truesdale, C.M.; Lindle, D.W.; Ferrett, T.A.; Heimann, P.A.; Becker, U.; Kerkhoff, H.G.; Southworth, S.H.

    1983-09-01

    A summary is presented of typical gas-phase photoemission studies based on synchrotron radiation in the 50-5000 eV range, using beam lines at the Stanford Synchrotron Radiation Laboratory. Three topics are addressed: atomic inner-shell photoelectron cross sections and asymmetries, correlation peaks in rare gases, and core-level shape resonances in molecules.

  14. Surface Induced Dissociation: Dissecting Noncovalent Protein Complexes in the Gas phase

    E-print Network

    Wysocki, Vicki H.

    with the native quaternary structure of several protein systems studied, even for a large chaperone protein, GroSurface Induced Dissociation: Dissecting Noncovalent Protein Complexes in the Gas phase Mowei Zhou Avenue, Columbus, Ohio 43210, United States CONSPECTUS: The quaternary structures of proteins are both

  15. APPLICATIONS ANALYSIS REPORT: ECO LOGIC INTERNATIONAL GAS-PHASE CHEMICAL REDUCTION PROCESS - THE REACTOR SYSTEM

    EPA Science Inventory

    This report details the Superfund Innovative Technology Evaluation of Eco Logic International's gas-phase chemical reduction process, with an emphasis on their Reactor System. he Eco Logic process employees a high temperature reactor filled with hydrogen gas as the means to destr...

  16. Research Paper Sugar Synthesis from a Gas-Phase Formose Reaction

    Microsoft Academic Search

    ABRAHAM F. JALBOUT; LEIF ABRELL; LUDWIK ADAMOWICZ; ROBIN POLT; A. J. APPONI; L. M. ZIURYS

    Prebiotic possibilities for the synthesis of interstellar ribose through a protic variant of the formose reaction under gas-phase conditions were studied in the absence of any known cat- alyst. The ion-molecule reaction products, diose and triose, were sought by mass spectrome- try, and relevant masses were observed. Ab initio calculations were used to evaluate protic formose mechanism possibilities. A bilateral

  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. The isomeric ions produced by the gas phase protonation of HNCO and HCNO

    NASA Astrophysics Data System (ADS)

    Hop, C. E. C. A.; Holmes, J. L.; Ruttink, P. J. A.; Schaftenaar, G.; Terlouw, J. K.

    1989-03-01

    Ab initio molecular orbital theory calculations combined with mass spectrometric experiments show that the gas phase protonation of HNCO yields [H 2NCO] + (? Hf0=672 kJ mol -1), whereas HCNO produces [HCNOH] + (? Hf0=990 kJ mol -1). The proton affinity of fulminic acid, HCNO, is estimated to be 758 kJ mol -1.

  19. 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

  20. 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 structure, formation mechanism, chemical reactivity, and so on. To examine these question, chemical reaction clusters. In order to observe the chemical reaction product on a clean baseline, all clusters except for C

  1. Magnetizabilities and Nuclear Shielding Constants of the Fluoromethanes in the Gas Phase and Solution

    E-print Network

    Helgaker, Trygve

    Magnetizabilities and Nuclear Shielding Constants of the Fluoromethanes in the Gas Phase and Solution Per-Olof A° strand,*,, Kurt V. Mikkelsen,, Kenneth Ruud,§ and Trygve Helgaker§ Department are discussed, and it is demonstrated that they must be included in order to reproduce the experimental gas

  2. SELECTIVE OXIDATION OF ALCOHOLS IN GAS PHASE USING LIGHT-ACTIVATED TITANIUM DIOXIDE

    EPA Science Inventory

    Selective oxidations of various primary and secondary alcohols were studied in a gas phase photochemical reactor using immobilized TiO2 catalyst. An annular photoreactor was used at 463K with an average contact time of 32sec. The system was found to be specifically suited for the...

  3. A Lithium Amide Protected Against Protonation in the Gas Phase: Unexpected Effect of LiCl.

    PubMed

    Lesage, Denis; Barozzino-Consiglio, Gabriella; Duwald, Romain; Fressigné, Catherine; Harrison-Marchand, Anne; Faull, Kym F; Maddaluno, Jacques; Gimbert, Yves

    2015-06-19

    In cold THF and in the presence of LiCl, a lithium pyrrolidinylamide forms a 1:1 mixed aggregate, which is observed directly by ESI-MS. Gas-phase protonation of this species leads to selective transfer of H(+) to the chlorine, suggesting that LiCl shields the amide nitrogen and prevents its direct protonation. PMID:25997158

  4. Molecular Orbital Studies of Zinc Oxide Chemical Vapor Deposition: Gas-Phase Radical Reactions

    E-print Network

    Schlegel, H. Bernhard

    Molecular Orbital Studies of Zinc Oxide Chemical Vapor Deposition: Gas-Phase Radical Reactions-phase reactions involved in the radical mechanism for zinc oxide chemical vapor deposition have been examined in the radical and closed shell mechanisms for zinc oxide chemical vapor deposition shows that the barrier

  5. ORIGINAL PAPER Gas-Phase Hydroformylation of Propene over Silica-Supported

    E-print Network

    Iglesia, Enrique

    ORIGINAL PAPER Gas-Phase Hydroformylation of Propene over Silica-Supported PPh3-Modified Rhodium Hydroformylation Á Butanal Á Heterogeneous Á Rhodium Á Silica Á Supported 1 Introduction Aldehydes are produced industrially by hydroformylation of olefins with synthesis gas. Homogeneous complexes of Rh and Co

  6. The ozonizer discharge as a gas-phase advanced oxidation process

    Microsoft Academic Search

    Rosocha

    1997-01-01

    In the past several years, there has been increased interest in gas-phase pollution control arising from a larger body of environmental regulations and a greater respect for the environment. One promising class of pollution-control technologies is that called advanced oxidation processes (AOPs). Ozonizers have been used for over a century in water treatment and for about two decades in advanced

  7. EFFECTS OF RING STRAIN ON GAS-PHASE RATE CONSTANTS. 2. OH RADICAL REACTIONS WITH CYCLOALKENES

    EPA Science Inventory

    Relative rate constants for the gas phase reactions of OH radicals with a series of cycloalkenes have been determined at 298 + or - 2 K, using methyl nitrite photolysis in air as a source of OH radicals. The data show that the rate constants for the nonconjugated cycloalkenes stu...

  8. Photodissociation and spectroscopy of gas phase bimetallic clusters. Progress report for 1990--1991

    Microsoft Academic Search

    1991-01-01

    The general goals of this research project are (1) to synthesize novel bimetallic clusters in the gas phase; (2) to characterize their geometry, electronic structure, and chemical bonding; and (3) to compare these heterogeneous systems to corresponding pure component clusters. Clusters are synthesized by pulsed laser vaporization of solid metal rods coincident with laser photolysis of volatile metal complexes (e.g.,

  9. Photoelectron spectroscopy and photochemistry of tetracyanoethylene radical anion in the gas phase

    E-print Network

    Sanov, Andrei

    Photoelectron spectroscopy and photochemistry of tetracyanoethylene radical anion in the gas phase photochemistry. Ó 2012 Elsevier B.V. All rights reserved. 1. Introduction In the past decades, a considerable and photochemistry using photoelectron imaging and photofragment mass-spectros- copy. We report the first direct

  10. Gas phase hydrogenation of acetonitrile on Raney nickel catalysts: reactive hydrogen

    Microsoft Academic Search

    F. Hochard; H. Jobic; J. Massardier; A. J. Renouprez

    1995-01-01

    Catalytic hydrogenation of acetonitrile on Raney nickel has been studied in gas phase. The chemisorption of hydrogen has been followed by TPD and inelastic neutron scattering; these techniques indicate the presence of both weakly and strongly adsorbed hydrogen. Kinetic studies and pulse experiments show that only weakly adsorbed hydrogen, localised on top of the nickel atoms and on C3v symmetry

  11. Detection of apoptosis in a rat model of focal cerebral ischemia using a homing peptide selected from in vivo phage display.

    PubMed

    Hong, Hai-Yan; Choi, Jung Sook; Kim, Yoon Jung; Lee, Hwa Young; Kwak, Wonjung; Yoo, Jeongsoo; Lee, Jae-Tae; Kwon, Tae-Hwan; Kim, In-San; Han, Hyung-Soo; Lee, Byung-Heon

    2008-11-12

    Focal cerebral ischemia, known as stroke, is caused by a sudden interruption in the blood supply to the brain. We attempted to identify peptides that can home to ischemic stroke tissue and detect the apoptosis of cells. A phage library displaying random peptides was screened for homing peptides to ischemic stroke tissue in a rat transient middle cerebral artery (MCA) occlusion model. After three rounds of in vivo screening, a phage clone displaying the most frequently occurring CLEVSRKNC sequence was selected. The CLEVSRKNC-phage preferentially homed to ischemic stroke tissue after intravenous administration into the MCA occlusion rats. The fluorescein-labeled synthetic CLEVSRKNC peptide, but not a scrambled control peptide, homed to ischemic stroke tissue with a lack of homing to non-ischemic brain tissue. The CLEVSRKNC peptide co-localized with a portion of neuronal cells, rather than with astrocytes, undergoing apoptosis at the penumbra region of stroke lesions. In autoradiographic studies, the uptake of the (131)I-labeled CLEVSRKNC peptide into an ischemic lesion increased at the first day and peaked at the third day after the injury. These results demonstrate that the CLEVSRKNC peptide can home to ischemic stroke tissue, while detecting apoptotic neuronal cells, and suggest it has applications as a targeting moiety for molecular imaging and selective drug delivery to stroke tissue. PMID:18692101

  12. Transferred NOESY NMR studies of biotin mimetic peptide (FSHPQNT) bound to streptavidin: A structural model for studies of peptide-protein interactions

    PubMed Central

    Gizachew, Dawit; Dratz, Edward

    2011-01-01

    Protein-protein interactions control signaling, specific adhesion and many other biological functions. The three dimensional structures of the interfaces and bound ligand can be approached with Tr-NOESY NMR, which can be applied to much larger proteins than conventional NMR and requires less concentrated protein. However, it is not clear how accurately the structures of protein-bound peptides can be determined by Tr-NOESY. We studied the structure of a biotin-mimetic peptide (FSHPQNT) bound to streptavidin, since the x-ray structure of the complex is available to 1.74Å resolution and we found that conditions could be adjusted so that the off-rates were fast enough for Tr-NOESY NMR. The off-rate was determined with 19F NMR, using a para-fluoro-phenylalanine analog of the peptide. A new criterion for a lower limit on kinetic off-rate was found, which allowed accurate structure determination at a slower off-rate. Non-specific binding of the peptide to streptavidin was not significant, since biotin blocked the peptide Tr-NOESY. Protein mediation for the long range peptide Tr-NOESY cross-peaks was corrected by a Tr-NOESY/ROESY averaging procedure. The protein-bound structure of the peptide was determined by Tr-NOESY constrained and simulated annealing. The structure deduced from the NMR was close to the x-ray structure. PMID:21294848

  13. Combination of Markov State Models and Kinetic Networks for the Analysis of Molecular Dynamics Simulations of Peptide Folding

    PubMed Central

    2011-01-01

    Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed. PMID:21553833

  14. 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

  15. 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 IN, 47405 An ion trap/ion mobility/quadrupole/time-of-flight mass spectrometer has been developed tube where ions separate ac- cording to differences in gas-phase ion mobilities. Upon exiting the drift

  16. 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.

  17. The Stability of CI02 as a Product of Gas Phase Decontamination Treatments

    SciTech Connect

    D. W. Simmons

    1994-09-01

    The gas phase decontamination project is investigating the use of chlorine trifluoride (ClF{sub 3}) to fluorinate nonvolatile uranium deposits to produce uranium hexafluoride (UF{sub 6}) gas. The potential existence of chlorine dioxide (ClO{sub 2}) during gas phase decontamination with ClF{sub 3} has been the subject of recent safety discussions. Some of the laboratory data collected during feasibility studies of the gas phase process has been evaluated for the presence of ClO{sub 2} in the product gas stream. The preliminary evidence to date can be summarized as follows: (1) ClO{sub 2} was not detected in the flow loop in the absence of ClF{sub 3}; (2) ClO{sub 2} was not detected in the static reactors in the absence of both ClF{sub 3} and ClF; and (3) ClO{sub 2} was detected in a static reactor in the absence of all fluorinating gases. The experimental evidence suggests that ClO{sub 2} will not exist in the presence of ClF{sub 3}, ClF, or UF{sub 6}. The data analyzed to date is insufficient to determine the stability of ClO{sub 2} in the presence of ClO{sub 2}F. Thermodynamic calculations of the ClF{sub 3} + H{sub 2}O system support the experimental evidence, and suggest that ClO{sub 2} will not exist in the presence of ClO{sub 2}F. Additional experimental efforts are needed to provide a better understanding of the gas phase ClF{sub 3} treatments and the product gases. However, preliminary evidence to date suggests that ClO{sub 2} should not be present as a product during the normal operations of the gas phase decontamination project.

  18. Disulfide-Intact and -Reduced Lysozyme in the Gas Phase: Conformations and Pathways of Folding and Unfolding

    E-print Network

    Clemmer, David E.

    have been studied in the gas phase using ion mobility mass spectrometry techniques. When solutions-intact and disulfide-reduced lysozyme ions in the gas phase using ion-mobility techniques.11-14 Lysozyme is made up, 1997X The conformations of gaseous lysozyme ions (+5 through +18) produced by electrospray ionization

  19. Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides Iwona Anusiewicz,,, Joanna Berdys-Kochanska,, Cezary Czaplewski, Monika Sobczyk,,

    E-print Network

    Simons, Jack

    Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides Iwona Anusiewicz,,,§ Joanna. Introduction A. Review of Experimental Findings on Negative Oli- goucleotides. In recent gas-phase experiments1 on small mul- tiply charged single-strand oligonucleotides,2 the Parks group has observed very slow (e

  20. The mid-IR absorption spectrum of gas-phase clusters of the nucleobases guanine and cytosine

    E-print Network

    de Vries, Mattanjah S.

    The mid-IR absorption spectrum of gas-phase clusters of the nucleobases guanine and cytosine Joost pairs that cross-link the two strands, (ii) the interaction between the nucleobases on one strand the factors that play a role, which can be achieved by studying isolated molecules in the gas phase

  1. Proceedings of the Symposium on Fundamental Gas-Phase and Surface Chemistry of Vapor-Phase Materials Synthesis,

    E-print Network

    Taylor, James H.

    Proceedings of the Symposium on Fundamental Gas-Phase and Surface Chemistry of Vapor-Phase Materials Synthesis, PV98-28, p. 153,The Electrochemical Society, 1998. IN SITU STUDIES OF TEOS/OZONE CVD, gas chromatographic and other evidence (5-9) supports the participation of transient gas phase

  2. Peptides modeled on the RGG domain of AUF1/hnRNP-D regulate 3?UTR-dependent gene expression

    PubMed Central

    Fellows, Abigail; Deng, Bin; Mierke, Dale; Robey, R. Brooks; Nichols, Ralph C.

    2013-01-01

    Messenger RNA binding proteins control post-transcriptional gene expression of targeted mRNA’s. The RGG (arginine-glycine-glycine) domain of the AUF1/hnRNP-D mRNA binding protein is a regulatory region that is essential for protein function and is the focus of this report. Previously, we have established that AUF1-RGG peptides, modeled on the RGG domain of AUF1, repress expression of the macrophage cytokine, VEGF. This report expands studies on AUF1-RGG peptides and evaluates the role of post-translational modifications of the AUF1 protein. Tandem to the RGG domain in AUF1-RGG peptides are a poly-glutamine motif and a nuclear localization signal (NLS). This report shows that a minimal 31-amino acid AUF1-RGG peptide that lacks the poly-glutamine and NLS motifs retains activity on a VEGF-3?UTR reporter. In addition, studies have shown that arginines in RGG motifs of mRNA binding proteins may be methylated with resulting changes in protein function. To determine if the RGG motif in AUF1 is affected by cell activation, mass spectroscopy analysis was performed on AUF1 expressed in RAW-264.7 cells. In resting cells, arginines in the first and second RGG motifs are monomethylated. When RAW-264.7 cells are activated with lipopolysaccharide, the arginines are dimethylated. To evaluate if the arginine residues are essential for AUF1-RGG activity, the methylatable arginines in the AUF1-3RGG peptide were mutated to lysine or alanine. The R?K and R?A mutants lack activity. These results support the hypothesis that the RGG domain of AUF1 is a regulatory motif. We also demonstrate that PI3K/AKT inhibitors reduce VEGF gene expression. Although immunoscreening of AUF1 suggests that LPS and PI3K inhibitors alter the phosphorylation status of AUF1-p37, mass spectroscopy results show that the p37 AUF1 isoform is not phosphorylated with or without lipopolysaccharide stimulation. In summary, arginines in the RGG domain of AUF1 are methylated, and AUF1-RGG peptides modeled on the RGG domain may be novel reagents that reduce macrophage activation in inflammation. PMID:23747316

  3. Safety evaluation of the antimicrobial peptide bovicin HC5 orally administered to a murine model

    PubMed Central

    2013-01-01

    Background Bovicin HC5 is an antimicrobial peptide that shows a broad spectrum of activity and potential for biotechnological and therapeutic applications. To gain insight about the safety of bovicin HC5 application, the histological and immunostimulatory effects of orally administrated bovicin HC5 to BALB/c mice were evaluated. BALB/c mice were divided into three groups: negative control (NC group); mice given purified bovicin HC5 (Bov group); mice given ovalbumin (positive control, PC group; a murine model of enteropathy). The mice were initially pre-sensitized, and PBS, bovicin HC5 or ovalbumin were administered for 30 days by daily gavages. Histological and morphometric analysis were performed and the relative expression of cytokines was analyzed by real-time RT-PCR. Results The oral administration of bovicin HC5 to BALB/c mice reduced weight gain and caused alterations in the small intestine, although absorptive changes have not been detected. The number of total goblet cells and the mucopolysaccharides production were not affected by bovicin HC5 administration. A hypertrophy of Paneth cells and an increase in the number of mitotic cells were observed in Bov group, while the number of mast cells remained unaltered. Increased expression of TNF-?, INF-? and IL-12 was observed in the small intestine upon bovicin HC5 administration. Conclusion Bovicin HC5 has only minor effects on intestinal permeability and did not elicit an allergenic response upon oral administration to animal models. Considering the low in vivo toxicity of bovicin HC5, it might be a good candidate for enteral applications. PMID:23537130

  4. A study on the atomic hydrophobicity of peptides in aqueous solutions using molecular dynamics modeling methods

    NASA Astrophysics Data System (ADS)

    Nguyen, Myhuong T.; Chaffee, Alan L.; Held, Marie; Boysen, Reinhard I.; Nicolau, Dan V.; Hearn, Milton T. W.

    2008-12-01

    Accurate quantification of the hydrophobic/hydrophilic properties of protein surfaces requires detailed knowledge of the hydrophobicity of amino acids at the atomic level. As discussed previously in various published papers, molecular modeling can be used with effect to acquire such knowledge. In this study, molecular dynamics methods have been employed to examine the role of the distance between an amino acid atom and its nearest water molecule in relation to its intrinsic atom hydrophobicity. This distance is the radius of the water-excluding-region around the atom; therefore, it can provide information on the solvent accessibility and steric hindrance that may influence the atom hydrophobicity. Molecular models of tripeptide in the form of GXG, and pentapeptides in the form of AcWLXLL-NH2 and AcGGXGGNH2 for 20 natural amino acids in the X position were constructed and allowed to dynamically interact with surrounding water for a sufficient period of time. The distance value for each atom in all natural amino acids were calculated and analyzed against the atom/amino acid's other parameters such as radial distribution function, solvent-accessible surface area, and hydrogen bonding. It was observed that, when the dynamic factor is taken into account, peptide molecular conformation is modified noticeably with residue type. For protein surface identification purposes, preliminary results are consistent with those reported in the literature on the need to include the amino acid structural properties as well as the effects of its neighboring residues. Further investigation is envisaged in order to verify these observations.

  5. Generation and mid-IR measurement of a gas-phase to predict security parameters of aviation jet fuel.

    PubMed

    Gómez-Carracedo, M P; Andrade, J M; Calviño, M A; Prada, D; Fernández, E; Muniategui, S

    2003-07-27

    The worldwide use of kerosene as aviation jet fuel makes its safety considerations of most importance not only for aircraft security but for the workers' health (chronic and/or acute exposure). As most kerosene risks come from its vapours, this work focuses on predicting seven characteristics (flash point, freezing point, % of aromatics and four distillation points) which assess its potential hazards. Two experimental devices were implemented in order to, first, generate a kerosene vapour phase and, then, to measure its mid-IR spectrum. All the working conditions required to generate the gas phase were optimised either in a univariate or a multivariate (SIMPLEX) approach. Next, multivariate prediction models were deployed using partial least squares regression and it was found that both the average prediction errors and precision parameters were satisfactory, almost always well below the reference figures. PMID:18969130

  6. 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).

  7. Hydration studies of electrospray ions from amino acids and small peptides

    NASA Astrophysics Data System (ADS)

    Nguyen, Chuong (Steve)

    This project was undertaken to gain a better understanding of the hydration behaviors of gas phase ions from solutions containing amino acids and peptides. In order to characterize their hydration behavior, the molecules of interest in solutions were first converted into gas phase ions by electrospray ionization (ESI). The completely desolvated ions were then deliberately dispersed into an inert bath gas, usually nitrogen, containing accurately known concentrations of solvent vapor. The resulting mixtures of ions and bath gas were subsequently passed into a vacuum chamber by way of an adiabatic supersonic free jet expansion. The cooling during that expansion caused solvation of the ions, the extent of which was determined by a quadrupole mass analyzer. Mass analysis of the solute ions in the absence of vapor showed peaks with the mass to charge ratios corresponding to the desolvated ions. On the other hand, mass spectrometric analyses of ions in the presence of solvent vapor showed sequences of peaks corresponding to the solvated ions with varying numbers of water molecules. The extent of the ion solvation was controlled by varying the concentration of solvent vapor in the bath gas. Two different scales were proposed for the evaluation of the relative affinities of amino acids for water molecules. One was based primarily on the assumption that the affinities of amino acids for water molecules are directly proportional to their gas phase solvation rate constants ( k). An alternative approach produced an affinity scale based on the extent of ion hydration occurred during the free jet expansion. It was found that the addition of a polar solvent vapor to the bath gas at low concentrations substantially enhanced the production of the bare solute ions from the evaporating charged droplets. This remarkable result not only provided a means to increase the ion production and thus detection sensitivity of mass spectrometric analyses, but also yielded important information regarding the ion formation mechanism of ESI. Additional studies revealed that the extent of the increase in ion yield was directly related to the charge state and molecular weight of the solute ions. In sum, this evidence strongly indicated that gas phase ions produced from charged droplets, as in electrospray ionization, must proceed by the sequence of events assumed in the Ion Evaporation Model proposed by Iribarne and Thomson rather than in the Charged Residue Model originally proposed by Malcolm Dole and coworkers. The hydration behaviors of electrospray ions from peptides with similar primary amino acid sequences and capable of forming ions with more than one charge state were also investigated. In a study with dipeptides, the extent of hydration was found to vary widely and to depend not only on the chemical composition of the ions but also on their configurations and charge states. The results obtained with lysine oligomers clearly indicated that the number of charges on an ion played an important role in the solvation process. An exception to this generalization was found in an experiment with multiply protonated pentalysine ions. For example, the quadruply protonated monomers of that species were found to undergo charge reduction via proton exchange with the surrounding water molecules in such a way as to maximize the distance between charges on the molecule, thereby reducing the internal repulsive forces. The hydration study of angiotensin II and III showed that while the former has an additional hydrophilic amino acid on the N-terminus, the latter peptide was more hydrophilic. This result suggests that the hydrophilicities of peptides are not a simple sum of the hydrophilicities of the individual amino acid components. As further evidence of interaction complexity, the Magic Number Clusters containing 21 water molecules were obtained with the doubly protonated angiotensin III, but not with the doubly protonated angiotensin II. Taken together, these observations seem to indicate that the multiply charged ions of angiotensin II and III had different str

  8. Summarization vs Peptide-Based Models in Label-Free Quantitative Proteomics: Performance, Pitfalls, and Data Analysis Guidelines.

    PubMed

    Goeminne, Ludger J E; Argentini, Andrea; Martens, Lennart; Clement, Lieven

    2015-06-01

    Quantitative label-free mass spectrometry is increasingly used to analyze the proteomes of complex biological samples. However, the choice of appropriate data analysis methods remains a major challenge. We therefore provide a rigorous comparison between peptide-based models and peptide-summarization-based pipelines. We show that peptide-based models outperform summarization-based pipelines in terms of sensitivity, specificity, accuracy, and precision. We also demonstrate that the predefined FDR cutoffs for the detection of differentially regulated proteins can become problematic when differentially expressed (DE) proteins are highly abundant in one or more samples. Care should therefore be taken when data are interpreted from samples with spiked-in internal controls and from samples that contain a few very highly abundant proteins. We do, however, show that specific diagnostic plots can be used for assessing differentially expressed proteins and the overall quality of the obtained fold change estimates. Finally, our study also illustrates that imputation under the "missing by low abundance" assumption is beneficial for the detection of differential expression in proteins with low abundance, but it negatively affects moderately to highly abundant proteins. Hence, imputation strategies that are commonly implemented in standard proteomics software should be used with care. PMID:25827922

  9. [Antitumor activity of the plant remedy peptide extract PE-PM in a new mouse T-lymphoma/eukemia model].

    PubMed

    Chaadaeva, A V; Tenkeeva, I I; Moiseeva, E V; Svirshchevskaia, E V; Demushkin, V P

    2009-01-01

    A new mouse ASF-LL model of adult T-lymphoma/leukemia (ATLL) in humans was characterized by cytological, histopathological, and flow cytometry analyses. Encouraging similarities of morphological, pathological, and clinical signs were found. These included characteristic flower appearance of leukemic cells, lymphadenopathy and hepatosplenomegaly, multiple growths in the skin, urogenital tissues, lungs and pituitary gland, CD4+CD25+ phenotype of the majority of tumor cells that were selectin-L positive, a rapid clinical course, and poor response to standard chemotherapy. Plant peptides obtained from the traditional Russian herbal medicine have gradually gained considerable attention as a new source of anticancer drugs. We have tested antitumor activity of a peptide extract PE-PM obtained from a mixture of Chelidonium majus L., Inula helenium L., Equisetum arvense L. and Inonotus obliquus in new mouse T-lymphoma/leukemia model ASF-LL. Distinct antitumor activity of two local injections of the peptide extract PE-PM was detected by tumor growth inhibition and survival improvement of 33% of recipients bearing intraperitoneal form of ASF-LL. PMID:19351037

  10. A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization

    PubMed Central

    Goldstein, Leonard D.; Howarth, Mark; Cardelli, Luca; Emmott, Stephen; Elliott, Tim; Werner, Joern M.

    2011-01-01

    Major Histocompatibility Complex (MHC) class I molecules enable cytotoxic T lymphocytes to destroy virus-infected or cancerous cells, thereby preventing disease progression. MHC class I molecules provide a snapshot of the contents of a cell by binding to protein fragments arising from intracellular protein turnover and presenting these fragments at the cell surface. Competing fragments (peptides) are selected for cell-surface presentation on the basis of their ability to form a stable complex with MHC class I, by a process known as peptide optimization. A better understanding of the optimization process is important for our understanding of immunodominance, the predominance of some T lymphocyte specificities over others, which can determine the efficacy of an immune response, the danger of immune evasion, and the success of vaccination strategies. In this paper we present a dynamical systems model of peptide optimization by MHC class I. We incorporate the chaperone molecule tapasin, which has been shown to enhance peptide optimization to different extents for different MHC class I alleles. Using a combination of published and novel experimental data to parameterize the model, we arrive at a relation of peptide filtering, which quantifies peptide optimization as a function of peptide supply and peptide unbinding rates. From this relation, we find that tapasin enhances peptide unbinding to improve peptide optimization without significantly delaying the transit of MHC to the cell surface, and differences in peptide optimization across MHC class I alleles can be explained by allele-specific differences in peptide binding. Importantly, our filtering relation may be used to dynamically predict the cell surface abundance of any number of competing peptides by MHC class I alleles, providing a quantitative basis to investigate viral infection or disease at the cellular level. We exemplify this by simulating optimization of the distribution of peptides derived from Human Immunodeficiency Virus Gag-Pol polyprotein. PMID:22022238

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

    SciTech Connect

    Goldsborough, S.S. [Department of Mechanical Engineering, Marquette University, Milwaukee, WI (United States); Johnson, M.V. [Energy Systems Division, Argonne National Laboratory, IL (United States); Zhu, G.S. [HDEP Performance and Emissions, DTNA - Detroit Diesel Corporation, Detroit, MI (United States); Aggarwal, S.K. [Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, 1030 Engineering Research Facility, Chicago, IL (United States)

    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)

  12. Synthesis, decomposition, and structural studies in the gas phase and solid state of N,N-dimethylaminoxygermane.

    PubMed

    Mitzel, N W; Losehand, U; Hinchley, S L; Rankin, D W

    2001-02-12

    N,N-Dimethylaminoxygermane, H3GeONMe2, was prepared by the reaction of H3GeBr with LiONMe2 in dimethyl ether at -96 degrees C. The identity of H3GeONMe2 was proven by gas-phase IR and solution NMR spectroscopy (1H, 13C, 15N, 17O). It is an unstable volatile liquid compound. It decomposes by cleavage of a Ge-O and a Ge-H bond giving HONMe2 and an insoluble germanium hydride polymer (GeH2)n. This decomposition reaction has been modeled at the MP2/6-311G(d,p) level of theory by the homodesmotic reaction H3GeONMe2 + Ge2H6-->Ge3H8 + HONMe2, which is predicted slightly exothermic by 14 kJ mol-1. The molecular structure of H3GeONMe2 was determined by gas-phase electron diffraction supported by an ab initio geometry [MP2/6-311G(d,p)] and a force field [MP2/6-31G(d)]. The structure of the compound in the crystal lattice was determined by low-temperature crystallography using a single crystal of H3GeONMe2 grown in situ [C2H9NOGe, orthorhombic, Pnma, Z = 4, a = 8.1280(12) A, b = 9.7037(15) A, c = 7.0722(12) A]. Important bond lengths and angles (gas phase/solid state, A/deg) are Ge-O 1.785(2)/1.815(1), O-N 1.462(7)/1.460(2), N-C 1.460(4)/1.453(2), Ge-O-N 105.2(5)/104.6(1), O-N-C 105.8(5)/105.8(1), C-N-C 110.8(9)/111.2(2), Ge...N 2.587(6)/2.601(1). In the solid state the compound forms infinite chains by intermolecular Ge...O contacts of 2.808 A. The question of the attraction between Ge and N atoms is discussed with respect to reference Ge/O and N/O compounds, which have wider angles at oxygen than H3GeONMe2. For comparison the structures of the compounds H3CONMe2, H3SiONMe2, and H3SnONMe2 were also calculated to reflect the influence of the group 14 atom on the structure and to discuss the occurrence of weak E...N interactions in the compounds H3EONMe2. PMID:11225108

  13. Charge loss in gas-phase multiply negatively charged oligonucleotides.

    PubMed

    Anusiewicz, Iwona; Berdys-Kochanska, Joanna; Czaplewski, Cezary; Sobczyk, Monika; Daranowski, Emma M; Skurski, Piotr; Simons, Jack

    2005-01-13

    In an attempt to shed light on the mechanism by which gaseous samples of negatively charged oligonucleotides undergo extremely slow (i.e., over 1-1000 s) charge loss, we have carried out molecular dynamics simulations on an oligonucleotide anion, T(5)(3-), containing five thymine, deoxyribose, and phosphate units in which the first, third, and fifth phosphates are negatively charged. The study is aimed at determining the rate at which an electron is detached from such a trianion by way of an internal Coulomb repulsion induced event. In this process, the intrinsic 5.0-5.1 eV electron binding strength of each phosphate site is reduced by the repulsive Coulomb potentials of the other two negative sites. As geometrical fluctuations cause the distances among the three negative phosphate sites to change, this causes the Coulomb repulsion energies at these sites to fluctuate. Once the Coulomb potential at any phosphate site exceeds ca. 5 eV, the electron on that site is able to undergo autodetachment. Although such an electron must tunnel through a barrier to escape, it is shown that the tunneling rate is not the rate-limiting step in electron loss; instead, it is the rate at which geometrical fluctuations cause the Coulomb potentials to exceed 5 eV that determines the rate of electron loss. Because these rates are extremely slow, special techniques had to be introduced to allow results of dynamics simulations on more flexible models of T(5)(3-) to be extrapolated to predict the behavior of the actual T(5)(3-). PMID:16839113

  14. Diagnostic model of saliva peptide finger print analysis of primary Sjögren's syndrome patients by using weak cation exchange magnetic beads.

    PubMed

    Wei, Pan; Kuo, Winston Patrick; Chen, Feng; Hua, Hong

    2013-01-01

    Saliva diagnostics has become an attractive field utilizing nanotechnology and molecular technologies for pSS (primary Sjögren's syndrome). However, no specific methods have been established. To refine the diagnostic power of the saliva peptide finger print for the early detection of pSS, we screened the expression spectrum of salivary peptides in pSS patients by using mass spectrometry MALDI-TOF-MS (matrix-assisted laser-desorption ionization-time-of-flight MS) combined with magnetic bead. The present study was comprised 12 pSS patients and 13 healthy controls and broken down to two different phases. In the initial 'exploratory phase', we enrolled seven pSS patients with eight age- and sex-matched healthy volunteers. Proteomics analysis of the unstimulated salivary samples was conducted to generate proportional peptide mass fingerprints. A diagnostic model was established. The testing cohort of the second 'validation phase' was represented by five pSS patients and five age- and sex-matched healthy controls. The diagnostic power of this diagnostic panel was then validated. The results showed seven m/z (mass-to-charge) ratio peaks with significant differences. Five peptides were up-regulated and two down-regulated in the pSS patients compared with matched healthy subjects. In the validation phase, four out of five pSS patients were diagnosed as pSS, and four of the five healthy controls were diagnosed as healthy controls, respectively. Potential biomarkers were also primarily predicted. The novel diagnostic proteomic model with m/z peaks 1068.1 Da, 1196.2 Da, 1738.4 Da, 3375.3 Da, 3429.3 Da, 3449.7 Da and 3490.6 Da is of certain value for early diagnosis of pSS. PMID:23682999

  15. Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study.

    PubMed

    Bharadwaj, Vivek S; Vyas, Shubham; Villano, Stephanie M; Maupin, C Mark; Dean, Anthony M

    2015-02-14

    The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ?100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter-molecular non-covalent interactions. PMID:25566585

  16. Identification of multiple antimicrobial peptides from the skin of fine-spined frog, Hylarana spinulosa (Ranidae).

    PubMed

    Yang, Xiaolong; Hu, Yuhong; Xu, Shiqi; Hu, Yonghong; Meng, Hao; Guo, Chao; Liu, Yuliang; Liu, Jingze; Yu, Zhijun; Wang, Hui

    2013-12-01

    In this study, peptidomics and genomics analyses were used to study antimicrobial peptides from the skin of Hylarana spinulosa. Twenty-nine different antimicrobial peptide precursors were characterized from the skin of H. spinulosa, which produce 23 mature antimicrobial peptides belonging to 12 different families. To confirm the actual presence and characteristics of these antimicrobial peptides in the skin tissue extractions from H. spinulosa, we used two distinct methods, one was peptide purification method that combined gel filtration chromatography and reversed-phase high performance liquid chromatography (RP-HPLC), and the other was peptidomics approach based on liquid chromatography in conjunction with tandem mass spectrometry (LC-MS/MS). In the peptidomics approach, incomplete tryptic digestion and gas-phase fractionation (GPF) analysis were used to increase peptidome coverage and reproducibility of peptide ion selection. Multiple species of microorganisms were chosen to test and analyze the antimicrobial activities and spectrum of these antimicrobial peptides. PMID:24055160

  17. DFT study on foscarnet as an antiviral drug: Conformer analysis, gas phase acidity, metal ion affinity and influence of metal complexation on gas phase acidity

    NASA Astrophysics Data System (ADS)

    Khalili, Behzad; Rimaz, Mehdi; Tondro, Tahereh

    2015-01-01

    This work presents a density functional theory study of Foscarnet (FOS), an anti-viral drug. In this study conformational analysis, gas phase acidity and metal ion affinity (MIA) of foscarnet with selected cations from alkalis (Li+, Na+, and K+) and alkaline earths (Ca2+ and Mg2+) were calculated. All of the structure optimizations and frequency calculations were performed at the B3LYP level of theory with 6-311++G(d,p) basis set. The calculations showed the MIA order to be K+ < Na+ < Li+ < Ca2+ < Mg2+, in agreement with increasing gas phase acidity of the foscarnet molecule during complexation. Natural bond orbital theory (NBO) and quantum theory of atoms in molecules (QTAIM) were used to investigate the charge transfer process and the nature of interactions in the formed complexes. The results of the NBO analysis revealed that Mn+ acts as charge acceptor and the amount of charge transfer is in agreement with MIA. The QTAIM analysis shows that (Msbnd O) coordinations are electrostatic in nature, and their strengths are in agreement with electron densities at their bond critical points (BCP).

  18. Radiolytic Modification of Sulfur Containing Acidic Amino Residues in Model Peptides: Fundamental Studies for Protein Footprinting

    SciTech Connect

    Xu,G.; Chance, M.

    2005-01-01

    Protein footprinting based on hydroxyl radical-mediated modification and quantitative mass spectroscopic analysis is a proven technique for examining protein structure, protein-ligand interactions, and structural allostery upon protein complex formation. The reactive and solvent-accessible amino acid side chains function as structural probes; however, correct structural analysis depends on the identification and quantification of all the relevant oxidative modifications within the protein sequence. Sulfur-containing amino acids are oxidized readily and the mechanisms of oxidation are particularly complex, although they have been extensively investigated by EPR and other spectroscopic methods. Here we have undertaken a detailed mass spectrometry study (using electrospray ionization mass spectrometry and tandem mass spectrometry) of model peptides containing cysteine (Cys-SH), cystine (disulfide bonded Cys), and methionine after oxidation using {gamma}-rays or synchrotron X-rays and have compared these results to those expected from oxidation mechanisms proposed in the literature. Radiolysis of cysteine leads to cysteine sulfonic acid (+48 Da mass shift) and cystine as the major products; other minor products including cysteine sulfinic acid (+32 Da mass shift) and serine (-16 Da mass shift) are observed. Radiolysis of cystine results in the oxidative opening of the disulfide bond and generation of cysteine sulfonic acid and sulfinic acid; however, the rate of oxidation is significantly less than that for cysteine. Radiolysis of methionine gives rise primarily to methionine sulfoxide (+16 Da mass shift); this can be further oxidized to methionine sulfone (+32 Da mass shift) or another product with a -32 Da mass shift likely due to aldehyde formation at the {gamma}-carbon. Due to the high reactivity of sulfur-containing amino acids, the extent of oxidation is easily influenced by secondary oxidation events or the presence of redox reagents used in standard proteolytic digestions; when these are accounted for, a reactivity order of cysteine > methionine {approx} tryptophan > cystine is observed.

  19. 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. 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).

  20. Efficacy and safety profile of the novel antimicrobial peptide PXL150 in a mouse model of infected burn wounds.

    PubMed

    Björn, Camilla; Noppa, Laila; Näslund Salomonsson, Emelie; Johansson, Anna-Lena; Nilsson, Elin; Mahlapuu, Margit; Håkansson, Joakim

    2015-05-01

    The urgent need to develop novel antimicrobial therapies has stimulated interest in antimicrobial peptides as therapeutic candidates for the treatment of infectious diseases. The aim of this study was to evaluate the anti-infectious effect of the synthetic antimicrobial peptide PXL150, formulated in hydroxypropyl cellulose (HPC) gel, on Pseudomonas aeruginosa in vitro and in an in vivo mouse model of infected burn wounds as well as to assess the in vivo safety profile of PXL150 in rats and rabbits. Minimal microbicidal concentration analysis showed prominent efficacy of PXL150 against P. aeruginosa in vitro, which was further enhanced in formulating the peptide in HPC gel. Application of 1.25, 2.5, 5, 10 and 20mg/g PXL150 in HPC gel twice daily for four consecutive days significantly reduced bacterial counts in the burn wounds compared with non-treated or placebo-treated controls. Continuous bioluminescence measurements of the bacteria revealed a pronounced anti-infective effect already at the first day post infection by PXL150 in concentrations of ?2.5mg/g. In the non-clinical safety studies, PXL150 showed a favourable safety profile following repeated administration systemically and locally in rats and rabbits, respectively. In conclusion, these data support that PXL150 has the potential to be an effective and safe drug candidate for the treatment of infected burn wounds. The findings encourage the progression of PXL150 as a novel topical treatment of microbial infections. PMID:25649371

  1. Symbiotic Plant Peptides Eliminate Candida albicans Both In Vitro and in an Epithelial Infection Model and Inhibit the Proliferation of Immortalized Human Cells

    PubMed Central

    Ördögh, Lilla; Vörös, Andrea; Nagy, István; Kondorosi, Éva

    2014-01-01

    The increasing number of multidrug-resistant microbes now emerging necessitates the identification of novel antimicrobial agents. Plants produce a great variety of antimicrobial peptides including hundreds of small, nodule-specific cysteine-rich NCR peptides that, in the legume Medicago truncatula, govern the differentiation of endosymbiotic nitrogen fixing bacteria and, in vitro, can display potent antibacterial activities. In this study, the potential candidacidal activity of 19 NCR peptides was investigated. Cationic NCR peptides having an isoelectric point above 9 were efficient in killing Candida albicans, one of the most common fungal pathogens of humans. None of the tested NCR peptides were toxic for immortalized human epithelial cells at concentrations that effectively killed the fungus; however, at higher concentrations, some of them inhibited the division of the cells. Furthermore, the cationic peptides successfully inhibited C. albicans induced human epithelial cell death in an in vitro coculture model. These results highlight the therapeutic potential of cationic NCR peptides in the treatment of candidiasis. PMID:25243129

  2. Symbiotic plant peptides eliminate Candida albicans both in vitro and in an epithelial infection model and inhibit the proliferation of immortalized human cells.

    PubMed

    Ordögh, Lilla; Vörös, Andrea; Nagy, István; Kondorosi, Eva; Kereszt, Attila

    2014-01-01

    The increasing number of multidrug-resistant microbes now emerging necessitates the identification of novel antimicrobial agents. Plants produce a great variety of antimicrobial peptides including hundreds of small, nodule-specific cysteine-rich NCR peptides that, in the legume Medicago truncatula, govern the differentiation of endosymbiotic nitrogen fixing bacteria and, in vitro, can display potent antibacterial activities. In this study, the potential candidacidal activity of 19 NCR peptides was investigated. Cationic NCR peptides having an isoelectric point above 9 were efficient in killing Candida albicans, one of the most common fungal pathogens of humans. None of the tested NCR peptides were toxic for immortalized human epithelial cells at concentrations that effectively killed the fungus; however, at higher concentrations, some of them inhibited the division of the cells. Furthermore, the cationic peptides successfully inhibited C. albicans induced human epithelial cell death in an in vitro coculture model. These results highlight the therapeutic potential of cationic NCR peptides in the treatment of candidiasis. PMID:25243129

  3. Uptake of gas-phase ammonia. 1. Uptake by aqueous surfaces as a function of pH

    SciTech Connect

    Shi, Q.; Davidovits, P.; Jayne, J.T.; Worsnop, D.R.; Kolb, C.E.

    1999-11-04

    Ammonia in the atmosphere originates primarily from ground sources including decaying organic matter and chemical fertilizers. Significant amounts of NH{sub 3} (0.1--100 ppbv) are found in both clean and polluted atmospheres as well as in cloud and fog droplets. Since ammonia is the only soluble base found in the atmosphere in significant quantities, it plays a principal role in neutralizing acidic aerosols (H{sub 2}SO{sub 4}, HNO{sub 3}, and HCl) converting them to new nonvolatile or semivolatile components; (NH{sub 4}){sub 2}SO{sub 4}, NH{sub 4}HSO{sub 4}, NH{sub 4}NO{sub 3}, NH{sub 4}Cl. The process of neutralization influences the aqueous oxidation rates of S(IV) species. The uptake of gas-phase ammonia by aqueous surfaces was measured as a function of temperature, gas liquid interaction time, and pH in the range 0--13. Uptake measurements at low pH yielded values of the mass accommodation coefficient ({alpha}) as a function of temperature. The mass accommodation coefficient increases as the temperature decreases, from 0.08 at 290 K to 0.35 at 260 K. Time dependence of the uptake yielded values for the Henry's law constant. Uptake measurements at high pH indicate that an ammonia surface complex is formed at the interface. Codeposition studies in which an aqueous surface, initially at pH = 4, was simultaneously exposed to both gas-phase ammonia and SO{sub 2} were also performed. In such a codeposition experiment, the species entering the liquid neutralize each other and as a result the uptake of each species is enhanced. Modeling calculations indicate that the uptake of each species is in accord with bulk liquid-phase kinetics.

  4. 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.

  5. Kinetics of the gas phase reaction of SnO with O2

    NASA Astrophysics Data System (ADS)

    Herzler, J.; Kennedy, M.; Kruis, F. E.; Roth, P.

    The gas phase reaction of SnOg with O2 was studied behind reflected shock waves at temperatures between 1700 and 2300 K and pressures around 100 kPa by applying atomic resonance absorption spectroscopy for time-resolved measurements of O atoms at 130.6 nm. The source of gas phase SnOg were SnO nanoparticles which rapidly evaporate behind the reflected shock wave in a few microseconds. For the reaction SnOg+O2?SnO2,g+O a rate coefficient of k 1=1014.78±0.19 × exp(-23530±840K/T)cm 3 mol -1 s -1 was determined for the temperature range of the present experiments.

  6. Properties of clusters in the gas phase. V - Complexes of neutral molecules onto negative ions

    NASA Technical Reports Server (NTRS)

    Keesee, R. G.; Lee, N.; Castleman, A. W., Jr.

    1980-01-01

    Ion-molecules association reactions of the form A(-)(B)n-1 + B = A(-)(B)n were studied over a range of temperatures in the gas phase using high pressure mass spectrometry. Enthalpy and entropy changes were determined for the stepwise clustering reactions of (1) sulfur dioxide onto Cl(-), I(-), and NO2(-) with n ranging from one to three or four, and onto SO2(-) and SO3(-) with n equal to one; and (2) carbon dioxide onto Cl(-), I(-), NO2(-), CO3(-), and SO3(-) with n equal to one. From these data and earlier hydration results, the order of the magnitude of the enthalpy changes on the association of the first neutral for a series of negative ions was found to parallel the gas-phase basicity of those anions.

  7. Accumulation of polycyclic aromatic hydrocarbons by lichen transplants: Comparison with gas-phase passive air samplers.

    PubMed

    Loppi, S; Pozo, K; Estellano, V H; Corsolini, S; Sardella, G; Paoli, L

    2015-09-01

    This study compared the accumulation of 16 polycyclic aromatic hydrocarbons (PAHs) in samples of the lichen Evernia prunastri exposed for 3months in and around an industrial area of S Italy with that in co-located passive gas-phase air samplers. The results showed a strong linear correlations (R=0.96, P<0.05) between total PAHs in lichens and in passive samplers, clearly indicating that lichen transplants may provide direct quantitative information on the atmospheric load by total PAHs, allowing translation of lichen values into atmospheric concentrations. To the best of our knowledge this is the first study reporting such a correlation with gas-phase passive air samplers. PMID:25911045

  8. Fragmentation of deprotonated glycolaldehyde in the gas phase and relevance to the formose reaction.

    PubMed

    Sekiguchi, Osamu; Uggerud, Einar

    2013-11-01

    From gas phase reactivity studies employing tandem mass spectrometry, the unimolecular dissociation of the corresponding base of glycolaldehyde has been probed under conditions of collisional activation. Three reactions were observed (in order of decreasing abundance): loss of CO, CH2O, and loss of H2. Detailed reaction mechanisms for each of the three reactions were obtained by quantum chemical calculations, and the reaction characteristics and energetics were found to be in good agreement with experimental observations. The relevance of these findings to the formose reaction and possible interstellar formation of carbohydrates from formaldehyde is discussed. It is concluded that the critical C-C bond forming reaction between two formaldehyde molecules to give the glycoladehyde is unlikely to occur in the gas phase via a route involving the free formyl anion, thereby precluding a key pathway for interstellar formation of carbohydrates. However, an alternative formation reaction is suggested. PMID:24102334

  9. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    PubMed

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments. PMID:25290160

  10. Ability of Innate Defence Regulator Peptides IDR-1002, IDR-HH2 and IDR-1018 to Protect against Mycobacterium tuberculosis Infections in Animal Models

    PubMed Central

    Rivas-Santiago, Bruno; Castañeda-Delgado, Julio E.; Rivas Santiago, Cesar E.; Waldbrook, Matt; González-Curiel, Irma; León–Contreras, Juan C.; Enciso-Moreno, Jose Antonio; del Villar, Victor; Mendez-Ramos, Jazmin; Hancock, Robert E. W.; Hernandez-Pando, Rogelio

    2013-01-01

    Tuberculosis is an ongoing threat to global health, especially with the emergence of multi drug-resistant (MDR) and extremely drug-resistant strains that are motivating the search for new treatment strategies. One potential strategy is immunotherapy using Innate Defence Regulator (IDR) peptides that selectively modulate innate immunity, enhancing chemokine induction and cell recruitment while suppressing potentially harmful inflammatory responses. IDR peptides possess only modest antimicrobial activity but have profound immunomodulatory functions that appear to be influential in resolving animal model infections. The IDR peptides HH2, 1018 and 1002 were tested for their activity against two M. tuberculosis strains, one drug-sensitive and the other MDR in both in vitro and in vivo models. All peptides showed no cytotoxic activity and only modest direct antimicrobial activity versus M. tuberculosis (MIC of 15–30 µg/ml). Nevertheless peptides HH2 and 1018 reduced bacillary loads in animal models with both the virulent drug susceptible H37Rv strain and an MDR isolate and, especially 1018 led to a considerable reduction in lung inflammation as revealed by decreased pneumonia. These results indicate that IDR peptides have potential as a novel immunotherapy against TB. PMID:23555622

  11. Modeling the interaction of dodecylphosphocholine micelles with the anticoccidial peptide PW2 guided by NMR data.

    PubMed

    Gomes-Neto, Francisco; Valente, Ana Paula; Almeida, Fabio C L

    2013-01-01

    Antimicrobial peptides are highly dynamic entities that acquire structure upon binding to a membrane interface. To better understand the structure and the mechanism for the molecular recognition of dodecylphosphocholine (DPC) micelles by the anticoccidial peptide PW2, we performed molecular dynamics (MD) simulations guided by NMR experimental data, focusing on strategies to explore the transient nature of micelles, which rearrange on a millisecond to second timescale. We simulated the association of PW2 with a pre-built DPC micelle and with free-DPC molecules that spontaneously forms micelles in the presence of the peptide along the simulation. The simulation with spontaneous micelle formation provided the adequate environment which replicated the experimental data. The unrestrained MD simulations reproduced the NMR structure for the entire 100 ns MD simulation time. Hidden discrete conformational states could be described. Coulomb interactions are important for initial approximation and hydrogen bonds for anchoring the aromatic region at the interface, being essential for the stabilization of the interaction. Arg9 is strongly attached with phosphate. We observed a helix elongation process stabilized by the intermolecular peptide-micelle association. Full association that mimics the experimental data only happens after complete micelle re-association. Fast micelle dynamics without dissociation of surfactants leads to only superficial binding. PMID:23966088

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

    E-print Network

    Radivojac, Predrag

    chromatography-ion trap mass spectrometry and compared to a tryptic digest of Deinococcus radiodurans. Similar in favor of longer sequence identification was observed. Peptide identification as a function of site characterization. Furthermore, they are uniquely suited to delineate the physical properties that influence

  13. Intra-and Intermolecular Effects on 1 H Chemical Shifts in a Silk Model Peptide

    E-print Network

    Williamson, Mike P.

    of calculations of the ring current effect, magnetic anisotropy effect and electric field effect, and so on.11 peptide (Ala-Gly)15 for the crystalline domain of Bombyx mori silk fibroin in silk I and silk II observed for the amide protons of (AG)15 in silk I, whereas only one broad peak was observed for silk II

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

    E-print Network

    Funk, Geoffrey Alexander

    2013-02-22

    into the phospholipid bilayer of the cell. To this end, we have been working on the synthesis of a group of peptides with the general sequence +H3N-Ala2-Leu3-Ala7-Trp-Ala-X-Ala10-Lys6-COOH, where we will substitute all twenty naturally occurring amino acids...

  15. Importance of the Peptide Backbone Description in Modeling the Selectivity Filter in Potassium Channels

    Microsoft Academic Search

    Turgut Bastug; Serdar Kuyucak

    2009-01-01

    A dihedral energy correction (CMAP) term has been recently included in the CHARMM force field to obtain a more accurate description of the peptide backbone. Its importance in improving dynamical properties of proteins and preserving their stability in long molecular-dynamics simulations has been established for several globular proteins. Here we investigate its role in maintaining the structure and function of

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

    E-print Network

    Pompeu Fabra, Universitat

    Torrent1,2 *, David Andreu2 , Victo` ria M. Nogue´s1 , Ester Boix1 1 Department of Biochemistry that sequence derived parameters are enough to characterize antimicrobial peptides. Citation: Torrent M, Andreu; Published February 9, 2011 Copyright: ß 2011 Torrent et al. This is an open-access article distributed under

  17. 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.

  18. Clear evidence of fluorescence resonance energy transfer in gas-phase ions

    Microsoft Academic Search

    Maxim Dashtiev; Vladimir Azov; Vladimir Frankevich; Ludwig Scharfenberg; Renato Zenobi

    2005-01-01

    Fluorescence resonance energy transfer (FRET) is a distance-sensitive method that correlates changes in fluorescence intensity\\u000a with conformational changes, for example, of biomolecules in the cellular environment. Applied to the gas phase in combination\\u000a with Fourier transform ion cyclotron resonance mass spectrometry, it opens up possibilities to define structural\\/conformational\\u000a properties of molecular ions, in the absence of solvent, and without the

  19. 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.

  20. Synthesis of ? - and ? Rhombohedral Boron Powders via Gas Phase Thermal Dissociation of Boron Trichloride by Hydrogen

    Microsoft Academic Search

    Duygu A?ao?ullar?; Özge Balc?; ?sma?l Duman; M. Lütf? Öveço?lu

    2011-01-01

    The ?-rhombohedral and ?-rhombohedral crystal structures of pure elemental boron powders have been synthesized via gas phase thermal dissociation\\u000a of BCl3 by H2 on a quartz substrate. The parameters affecting the crystal structures of the final products and the process efficiency,\\u000a such as BCl3\\/H2 molar ratio (1\\/2 and 1\\/4) and reaction temperature (1173 K to 1373 K [900 °C to 1100 °C]), have been examined.

  1. Sequence dependent conformations of glycidyl methacrylate\\/butyl methacrylate copolymers in the gas phase

    Microsoft Academic Search

    Erin Shammel Baker; Jennifer Gidden; William J. Simonsick; Michael C. Grady; Michael T. Bowers

    2004-01-01

    Sequence dependent conformations of a series of glycidyl methacrylate\\/butyl methacrylate (GMA\\/BMA) copolymers cationized by sodium were analyzed in the gas phase using ion mobility methods. GMA and BMA have the same nominal mass but vary in exact mass by 0.036Da (CH4 versus O). Matrix assisted laser desorption\\/ionization (MALDI) was used to form Na+(GMA\\/BMA) copolymer ions and their collision cross-sections were

  2. Gas-phase ion-molecule reactions of doubly charged fullerenes with oxygen

    Microsoft Academic Search

    James J. Stry; James F. Garvey

    1993-01-01

    The gas-phase ion-molecule chemistry of doubly charged fullerene cations (C[sub n][sup 2+] where n = 46, 48, ..., 60 and 70) with neutral oxygen molecules were investigated using a triple quadrupole mass spectrometer. In this paper, we report additions to the fullerene cage structure which result in the formation of C[sub n]O[sup 2+], C[sub n]O[sub 2][sup 2+], and C[sub n]O[sub

  3. Conformational composition, molecular structure and decomposition of difluorophosphoryl azide in the gas phase.

    PubMed

    Wu, Zhuang; Li, Hongmin; Zhu, Bifeng; Zeng, Xiaoqing; Hayes, Stuart A; Mitzel, Norbert W; Beckers, Helmut; Berger, Raphael J F

    2015-04-14

    The conformational composition, molecular structure and decomposition of difluorophosphoryl azide F2P(O)N3 in the gas phase were studied using gas electron diffraction (GED), matrix isolation IR spectroscopy, and quantum-chemical calculations, respectively. While computational methods predict only minor differences in the total energy between the two possible conformers (syn and anti), the analysis of electron diffraction data reveals the dominating abundance of the syn conformer in the gas phase at room temperature. Ab initio frequency analyses suggest that a low-frequency large-amplitude motion of the N3 group with respect to the P-N-N-N torsion is to be expected for the syn conformer. The large amplitude motion was included explicitly into the GED structure refinement procedure. It presumably contributes to a thermodynamic stabilization of the syn-conformer with respect to the anti-conformer in the gas phase at ambient temperature. Upon flash vacuum pyrolysis, this syn conformer undergoes a stepwise decomposition via the difluorophosphoryl nitrene, F2P(O)N, which features as the first experimentally observed phosphoryl nitrene that can be thermally produced in the gas phase. To reveal the reaction mechanism, quantum-chemical calculations on the potential energy surface (PES) of F2P(O)N3 were performed. Both B3LYP/6-311+G(3df) and CBS-QB3 calculation results strongly support a stepwise decomposition into the singlet F2P(O)N, which prefers intersystem crossing to the thermally persistent triplet ground state instead of a Curtius rearrangement into FP(O)NF. PMID:25740559

  4. Missing gas-phase source of HONO inferred from Zeppelin measurements in the troposphere

    NASA Astrophysics Data System (ADS)

    Li, Xin; Rohrer, Franz; Hofzumahaus, Andreas; Brauers, Theo; Häseler, Rolf; Bohn, Birger; Broch, Sebastian; Fuchs, Hendrik; Gomm, Sebastian; Holland, Frank; Jäger, Julia; Kaiser, Jennifer; Keutsch, Frank N.; Lohse, Insa; Tillmann, Ralf; Wegener, Robert; Wolfe, Glenn M.; Mentel, Thomas F.; Kiendler-Scharr, Astrid; Wahner, Andreas

    2014-05-01

    Nitrous acid (HONO) is an important trace gas in the atmosphere due to its contribution to the cycles of nitrogen oxides (NOX) and hydrogen oxides (HOX). In the past decades, ground-based observations of HONO around the world showed much higher daytime concentrations than can be explained by the known gas-phase chemistry (i.e., HONO + h? ? OH + NO, HONO + OH ? NO2 + H2O, OH + NO + M ? HONO + M). Different light-dependent reactions on ground surfaces have been proposed as additional daytime HONO sources. However, due to lack of measurements, little is known about the concentrations of HONO and its sources in the planetary boundary layer (PBL) at higher altitudes above the earth's surface. The airship Zeppelin NT is an ideal platform to investigate the chemistry and dynamics of the PBL. During the PEGASOS field campaigns in 2012 and 2013, HONO and its gas-phase sources and sinks were measured simultaneously on-board the airship Zeppelin NT, for the lowest 1 km of the PBL. In the upper part of the altitude range during morning hours, when the airmass is still isolated from processes at the earth's surface by the remaining nocturnal boundary layer, we find unexpectedly large concentrations of HONO which can neither be explained by heterogeneous reactions on aerosol and ground surfaces, nor by known gas-phase reactions. Our observations show evidence for an unknown gas-phase light-dependent HONO production which dominates the overall HONO formation in the lower troposphere. This new HONO source requires NOX and possibly OH or HO2 radicals. As a result, the general impact of HONO on the OH formation is likely overestimated.

  5. Control of particle size distribution of ultrafine iron particles in the gas phase reaction

    Microsoft Academic Search

    Hee Dong Jang; Kyun Young Park; Cheong Song Choi

    1996-01-01

    Experiments on the synthesis of ultrafine iron particles have been made for the control of particle size distribution using\\u000a the gas phase reduction of ferrous chloride with hydrogen. The previous studies were focused on the control of particle size\\u000a of ultrafine particles with the variation of the partial pressure of reactants, residence time of feed, and reaction temperature.\\u000a However, it

  6. Theoretical study of the uncatalyzed hydration of carbon dioxide in the gas phase

    Microsoft Academic Search

    Jiin Yun. Liang; William N. Lipscomb

    1986-01-01

    The reaction energy surface and pathway of the reversible gas-phase reaction of COâ with HâO and OH⁻ have been evaluated with PRDDO and 4-31G SCF-MO methods, including one MP2 correlation calculation. In the most favorable pathway, H and O of water approach respectively O and C of COâ simultaneously, and after the transition state is passed the new OH bond

  7. Initial Commercial Experience with Gas-Phase Brominated Mercury Sorbents and Injection System Hardware

    Microsoft Academic Search

    Ronald R. Landreth; Sid Nelson; Xin Liu; Jon E. Miller; Chris Nagel; Fred Allard; Charles Ash

    Sorbent Technologies Corporation (STC) is now in full production of its family of gas- phase brominated mercury sorbents: B-PACTM, C-PACTM, and H-PACTM, for coal-fired power plants. These sorbents have now been tested in over 30 field trials, including five conducted by STC which were partially funded by the United States Department of Energy. While full-scale trials continue, the use of

  8. Excimer laser photolysis of group 6 metal carbonyls in the gas phase

    SciTech Connect

    Ishikawa, Yoichi; Brown, C.E.; Hackett, P.A.; Rayner, D.M. (National Research Council of Canada, Ottawa, Ontario (Canada))

    1990-03-22

    The excimer laser photolysis of Mo(CO){sub 6} in the gas phase has been studied at 351, 308, 248, and 222 nm with laser-based, time-resolved infrared absorption spectroscopy. Results have also been obtained on the 308- and 222-nm photolysis of Cr(CO){sub 6} and on the 222-nm photolysis of W(CO){sub 6}, complementing earlier studies and presenting a complete picture of group 6 metal carbonyl ultraviolet photodecomposition.

  9. Sustainable production of acrolein: Gas-phase dehydration of glycerol over Nb 2O 5 catalyst

    Microsoft Academic Search

    Song-Hai Chai; Hao-Peng Wang; Yu Liang; Bo-Qing Xu

    2007-01-01

    Gas-phase dehydration of glycerol to produce acrolein was investigated at 315?°C over Nb2O5 catalysts calcined in the temperature range of 350–700?°C. The catalysts were characterized by nitrogen physisorption, TG-DTA, XRD, and n-butylamine titration using Hammett indicators to gain insight into the effect of calcination temperature on catalyst texture, crystal structure, and acidity. Calcination at 350 and 400?°C produced amorphous Nb2O5

  10. Gas phase proton transfer reaction of nitric acid-ammonia and the role of water

    Microsoft Academic Search

    Fu-Ming Tao

    1998-01-01

    The gas-phase proton transfer reaction of nitric acid-ammonia and the effect of the first three water molecules are investigated by high level ab initio calculations on the molecular clusters HNO3-NH3-(H2O)n, n=0,1,2,3. The equilibrium structures, binding energies, and harmonic frequencies of the clusters as well as the potential energy surfaces along the proton transfer pathway of nitric acid-ammonia are calculated at

  11. Photocatalytic oxidation of gas-phase methyl tert-butyl ether and tert-butyl alcohol

    Microsoft Academic Search

    Sergei Preis; John L. Falconer; Raquel del Prado Asensio; Nuria Capdet Santiago; Anna Kachina; Juha Kallas

    2006-01-01

    Adsorbed methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) were oxidized at room temperature by transient photocatalytic oxidation (PCO) on TiO2 and Pt-TiO2 catalysts; carbon dioxide, water, and acetone were the main gas-phase products. TBA oxidized faster than MTBE. Reaction products such as formic acid, which remained on the surface, were characterized by temperature-programmed desorption (TPD) and oxidation (TPO). The

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

    E-print Network

    Maier, John Paul

    quantum behavior [1]. One-dimensional carbon-based materials like nanotubes [2], Pt-containing polyyne [3, the gas phase electronic spectra of hydrogen terminated carbon nano- molecular wires such as HC2nH [4,5] and HC2nþ1H [6] were studied by a mass selective resonant two-color two- photon ionization (R2C2PI

  13. Hydrothermal transformation of Chinese privet seed biomass to gas-phase and semi-volatile products

    Microsoft Academic Search

    Thomas L. Eberhardt; W. James Catallo; Todd F. Shupe

    2010-01-01

    Hydrothermal (HT) treatment of seeds from Chinese privet (Ligustrum sinense), a non-native and invasive species in the southeastern United States, was examined with respect to the generation of gas-phase and semi-volatile organic chemicals of industrial importance from a lipid-rich biomass resource. Aqueous seed slurries were transformed into biphasic liquid systems comprised of a milky aqueous phase overlain by a black

  14. Method and apparatus for selective capture of gas phase analytes using metal .beta.-diketonate polymers

    DOEpatents

    Harvey, Scott D [Kennewick, WA

    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.

  15. Uptake of Gas-Phase Nitric Acid by Water-Ice Surfaces

    Microsoft Academic Search

    M. Ullerstam; J. P. Abbatt

    2004-01-01

    Nitric acid is a widespread molecule found in the atmosphere. It is mainly removed from the troposphere by wet or dry deposition. In colder regions such as the upper troposphere and tropopause where cirrus clouds are formed nitric acid can also be scavenged by cirrus ice particles. The uptake of gas-phase nitric acid by water-ice films has been re-examined with

  16. Determination of gas-phase ligand binding energies to Mg\\/sup +\\/ by FTMS techniques

    Microsoft Academic Search

    Lorenza. Operti; Edward C. Tews; Ben S. Freiser

    1988-01-01

    Relative and absolute gas-phase binding energies of 12 organic molecules to Mg\\/sup +\\/ have been determined by four different methods involving Fourier transform mass spectrometry (FTMS). Mg\\/sup +\\/ is generated in the FTMS cell by pulsed laser ionization and reacts with the organic compounds to give MgL\\/sup +\\/ either by direct condensation or by a fast two-step displacement reaction. The

  17. Surface modification of superaustenitic and maraging stainless steels by low-temperature gas-phase carburization

    Microsoft Academic Search

    Johannes Gentil

    2008-01-01

    Low-temperature gas-phase carburization of 316L austenitic stainless steel was developed in recent years by the Swagelok company. This process generates great mechanical and electrochemical surface properties. Hardness, wear resistance, fatigue behavior, and corrosion resistance are dramatically improved, while the formation of carbides is effectively suppressed. This new technique is of technical, economical, but especially of scientific interest because the surface

  18. Interaction of Electrons with Indole, Tryptophan, and their Derivatives in the Gas Phase

    Microsoft Academic Search

    N. A. Borisevich; A. L. Ivanov; S. M. Kazakov; D. V. Murtazaliev; V. A. Povedailo; O. V. Khristoforov

    2005-01-01

    The electron energy loss spectra (EELS) of indole, 3-indolyl propionic acid, 3-indolealdehyde, 3-dimethylaminomethylindole, tryptophan, and N-acetyl-L-tryptophan in the gas phase upon excitation by monokinetic electrons with an energy of E0 = 11–50 eV are obtained. The structure of EELS is determined in the main by the indole chromophore; the side groups, except for the C=O group of 3-indolealdehyde, exert an

  19. Thickness uniformity of gas-phase coatings in narrow channels: II. One-side confined channels

    Microsoft Academic Search

    E M Tolstopyatov; S H Yang; M C Kim

    2002-01-01

    The process of the coating profile formation in one-side confined narrow channels in the course of the gas-phase deposition was theoretically investigated for the aspect ratio exceeding 20. The coating thickness distribution along a channel was shown to be described analytically only for the first-order deposition process. The correlation in an analytic form was established between the conformity parameters for

  20. Physicochemical properties and structural evolutions of gas-phase carbonization chars at high temperatures

    Microsoft Academic Search

    Youqing Wu; Shiyong Wu; Sheng Huang; Jinsheng Gao

    2010-01-01

    The gas-phase carbonization chars from hydrocarbons with low molecular weight (anthracene oil and petroleum ether) were prepared using a drop tube reactor at 1000–1200°C, and their physicochemical properties and structural evolutions (elemental composition, carbon crystallite structure, surface morphology, pore structure and chemical composition of volatile matters) were mainly investigated. The chars obtained in the high temperature region, which appeared with

  1. Gas-phase hydrogenation of acetonitrile on zirconium-doped mesoporous silica-supported nickel catalysts

    Microsoft Academic Search

    P Braos-Garc??a; P Maireles-Torres; E Rodr??guez-Castellón; A Jiménez-López

    2003-01-01

    Nickel supported on zirconium-doped mesoporous silica catalysts, with varying nickel loadings (4–26wt.%), were evaluated in the gas-phase hydrogenation of acetonitrile. Prior to the catalytic study, the catalysts were characterised by using XRD, XPS, HREM, H2-TPR, N2 adsorption–desorption at 77K, H2 and O2 chemisorption and NH3-TPD. The catalytic activity, at 408K, was shown to be influenced by the incorporation procedure of

  2. The gas phase hydrogenation of 2-butanone over supported nickel catalysts: introduction of enantioselectivity

    Microsoft Academic Search

    Amalia López-Mart??nez; Mark A Keane

    2000-01-01

    The gas phase hydrogenation of 2-butanone to 2-butanol at 343 K promoted using a Y zeolite-supported nickel catalyst (2.2% w\\/w Ni) prepared by ion exchange and a range of Ni\\/SiO2 catalysts (1.5–20.3% w\\/w Ni) prepared by precipitation\\/deposition and impregnation has been studied. The freshly activated catalysts generated racemic products and enantioselectivity was introduced to a negligible degree by in situ

  3. Gas-phase hydrogenation\\/hydrogenolysis of phenol over supported nickel catalysts

    Microsoft Academic Search

    Eun-Jae Shin; Mark A. Keane

    2000-01-01

    The gas-phase hydrogenation\\/hydrogenolysis of alcoholic solutions of phenol between 423 and 573 K has been studied using a Y zeolite-supported nickel catalyst (2.2% w\\/w Ni) and Ni\\/SiOâ catalysts (1.5--20.3% w\\/w Ni). This is a viable means of treating concentrated phenol streams to generate recyclable raw material. Phenol hydrogenation proceeded in a stepwise fashion with cyclohexanone as a reactive intermediate while

  4. {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

  5. 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

  6. 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

  7. 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

  8. Movable fiber probe for gas-phase laser-induced breakdown spectroscopy

    SciTech Connect

    Dumitrescu, Cosmin E.; Puzinauskas, Paulius V.; Olcmen, Semih

    2008-11-01

    A movable probe that fiber couples both the beam delivery and the signal collection functions of gas-phase laser-induced breakdown spectroscopy (LIBS) measurements was evaluated. The adjustable probe was used to investigate the effect of delivery fiber curvature on plasma characteristics and the associated effect on LIBS spectra and to further identify issues remaining to facilitate fully fiber-coupled gas-phase LIBS measurements. LIBS data were collected from lean methane-air mixtures of various equivalence ratios and spectroscopically analyzed to establish the ability to determine relative fuel-air ratio. Measurements with straight delivery fiber were compared to those with the fiber curved at specific radii. Decreasing fiber radius of curvature decreased fiber transmission efficiency and reduced the spark formation probability by almost a factor of 2. For constant fiber input energy, this decreased transmission increased the percentage of failed spark formations and influenced the LIBS elemental ratio calculations. However, minimal difference was found between LIBS measurements with straight or curved fiber as long as the output energy and a constant laser beam spot diameter were maintained on the exit beam focusing lens. A significant reduction in data scatter and improved linearity were achieved by using the Balmer series H{alpha} and H{beta} hydrogen emission line ratio as a data selection criterion. Observed linear variation of H/N elemental ratio with equivalence ratio confirmed the possibility of a flexible, light-contained, fully fiber-coupled probe for remote gas-phase LIBS analysis.

  9. The use of gas-phase substrates to study enzyme catalysis at low hydration.

    PubMed Central

    Dunn, Rachel V; Daniel, Roy M

    2004-01-01

    Although there are varying estimates as to the degree of enzyme hydration required for activity, a threshold value of ca. 0.2 g of water per gram of protein has been widely accepted. The evidence upon which this is based is reviewed here. In particular, results from the use of gas-phase substrates are discussed. Results using solid-phase enzyme-substrate mixtures are not altogether in accord with those obtained using gas-phase substrates. The use of gaseous substrates and products provides an experimental system in which the hydration of the enzyme can be easily controlled, but which is not limited by diffusion. All the results show that increasing hydration enhances activity. The results using gas-phase substrates do not support the existence of a critical hydration value below which enzymatic activity is absent, and suggest that enzyme activity is possible at much lower hydrations than previously thought; they do not support the notion that significant hydration of the surface polar groups is required for activity. However, the marked improvement of activity as hydration is increased suggests that water does play a role, perhaps in optimizing the structure or facilitating the flexibility required for maximal activity. PMID:15306385

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

    E-print Network

    Clemmer, David E.

    mobility spectrometry has been com- bined with time-of-flight mass spectrometry for analysis by electrospray ionization. Ion mobility/time-of-flight dis- tributions have been recorded for all ions using. Mass spectrometry (MS)-based methods can be used to rapidly assess abundance information for ions

  11. 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

    Ion mobility spectrometry (IMS) separates ions on the basis of ion-neutral collision cross-sections (CCS, [omega]), which are determined by the geometry or conformation of the ions. The size-based IM separation can be ...

  12. 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

    dimer is investigated using a combination of mass spectrometry techniques, viz. ESI-IM-MS and hydrogen/deuterium exchange (HDX)-MS, and MDS. The IM experiments reveal three distinct gramicidin A species, detected as the sodium ion adduct ions, [2GA + 2Na...

  13. Establishment and Characterization of an Omasal Epithelial Cell Model Derived from Dairy Calves for the Study of Small Peptide Absorption

    PubMed Central

    Xu, Qingbiao; Wu, Yueming; Liu, Hongyun; Xie, Yingming; Huang, Xinbei; Liu, Jianxin

    2014-01-01

    The objective of this study was to establish a primary culture of omasal epithelial cells (OECs) derived from dairy calves and to characterize its function in small peptide absorption. Bovine omasal tissues were obtained from newborn Chinese Holstein calves and digested with a 2.5% trypsin solution to obtain OECs. The isolated cells were later cultured in DMEM containing 10% fetal bovine serum, 5 ?g/ml insulin, 10 ng/ml epidermal growth factor, 100 U/ml penicillin, 100 ?g/ml streptomycin, 50 ?g/ml gentamycin and 2.5 ?g/ml amphotericin B. Hematoxylin and eosin staining of omasal tissue after digestion indicated that the cultured cells originated from the epithelial strata. Pure epithelial cells displayed an epithelial cell-like morphology, similar to cobblestone, with few visible fibroblasts and were cytokeratin 18-positive according to immunocytochemical analyses. The OECs were morphologically characterized with desmosomes, tight junctions and microvilli. These cells exhibited normal growth properties, as assessed using a cell growth curve, and were stably cultured for 10 passages. The OECs expressed the peptide transporter 1 (PEPT1) mRNA and absorbed intact glycylsarcosine (Gly-Sar). The uptake of Gly-Sar by OECs was pH-dependent with an optimal pH of 5.5–6.5. Furthermore, the uptake of Gly-Sar was also time-dependent, concentration-dependent and temperature-dependent. Moreover, PEPT1 was saturated with Gly-Sar at a concentration of 2.5 mM. The uptake via PEPT1 was higher compared with that via passive route at low substrate concentrations (<1.5 mM). This result suggested that PEPT1 contributed more to total small peptide absorption at low concentrations. In addition, this uptake could be competitively inhibited by methionine-glycine. Taken together, these data suggested that PEPT1 contributes to small peptide absorption in OECs. Thus, OECs may serve as a useful culture model for the study of the absorption of small peptides in bovine omasum. PMID:24633419

  14. 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 ...

  15. 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

  16. MEPE-derived ASARM peptide inhibits odontogenic differentiation of dental pulp stem cells and impairs mineralization in tooth models of X-linked hypophosphatemia.

    PubMed

    Salmon, Benjamin; Bardet, Claire; 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

  17. Combined use of ion mobility and collision-induced dissociation to investigate the opening of disulfide bridges by electron-transfer dissociation in peptides bearing two disulfide bonds.

    PubMed

    Massonnet, Philippe; Upert, Gregory; Smargiasso, Nicolas; Gilles, Nicolas; Quinton, Loïc; De Pauw, Edwin

    2015-05-19

    Disulfide bonds are post-translational modifications (PTMs) often found in peptides and proteins. They increase their stability toward enzymatic degradations and provide the structure and (consequently) the activity of such folded proteins. The characterization of disulfide patterns, i.e., the cysteine connectivity, is crucial to achieve a global picture of the active conformation of the protein of interest. Electron-transfer dissociation (ETD) constitutes a valuable tool to cleave the disulfide bonds in the gas phase, avoiding chemical reduction/alkylation in solution. To characterize the cysteine pairing, the present work proposes (i) to reduce by ETD one of the two disulfide bridges of model peptides, resulting in the opening of the cyclic structures, (ii) to separate the generated species by ion mobility, and (iii) to characterize the species using collision-induced dissociation (CID). Results of this strategy applied to several peptides show different behaviors depending on the connectivity. The loss of SH· radical species, observed for all the peptides, confirms the cleavage of the disulfides during the ETD process. PMID:25915795

  18. Synthetic antimicrobial peptide design.

    PubMed

    Powell, W A; Catranis, C M; Maynard, C A

    1995-01-01

    To guide the design of potential plant pathogen-resistance genes, synthetic variants of naturally occurring antimicrobial gene products were evaluated. Five 20-amino acid (ESF1, ESF4, ESF5, ESF6, ESF13), one 18-amino acid (ESF12), and one 17-amino acid (ESF17) amphipathic peptide sequences were designed, synthesized, and tested with in vitro bioassays. Positive charges on the hydrophilic side of the peptide were shown to be essential for antifungal activity, yet the number of positive charges could be varied with little or no change in activity. The size could be reduced to 18 amino acids, but at 17 amino acids a significant reduction in activity was observed. ESF1, 5, 6, and 12 peptides were inhibitory to the germination of conidia from Cryphonectria parasitica, Fusarium oxysporum f. sp. lycopersici, and Septoria musiva but did not inhibit the germination of pollen from Castanea mollissima and Salix lucida. ESF12 also had no effect on the germination of Malus sylvestris and Lycopersicon esculentum pollen, but inhibited the growth of the bacteria Agrobacterium tumefaciens, Erwinia amylovora, and Pseudomonas syringae. The minimal inhibitory concentrations of the active ESF peptides were similar to those of the naturally occurring control peptides, magainin II and cecropin B. The significant differential in sensitivity between the microbes and plant cells indicated that the active ESF peptides are potentially useful models for designing plant pathogen-resistance genes. PMID:7579625

  19. Designed peptides as model self-assembling nanosystems: characterization and potential biomedical applications.

    PubMed

    Panda, Jiban J; Kaul, Ankur; Alam, Shadab; Babbar, Anil K; Mishra, Anil K; Chauhan, Virander S

    2011-02-01

    Synthesis of nanomaterials via 'molecular self-assembly' allows one to define the properties of the nanomaterial by rational design of the individual constituents. Use of peptides for self-assembly offers the ease of design and synthesis, and provides higher biofunctionality and biocompatibility to nanomaterials. Our work focused on the synthesis, characterization and potential biomedical applications of small self-assembled peptide-based nanosystems. We demonstrated that dipeptides containing the conformational restricting residue alpha,beta-dehydrophenylalanine, self-assembled into nanovesicular and nanotubular structures. The nanosystems could encapsulate and release anticancer drugs, showed enhanced stability to proteinase K degradation, a property crucial for them to have a high in vivo half-life, and exhibited no cytotoxicity towards cultured mammalian cells. The dipeptide nanostructures were easily taken up by cells and could evade uptake by reticuloendothelial systems when injected into healthy laboratory animals. Thus, small self-assembling peptides may offer novel scaffolds for the future design of nanostructures with potential applications in the field of drug delivery. PMID:22833945

  20. 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