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1

Modelling of the gas-phase phosphate group loss and rearrangement in phosphorylated peptides.  

PubMed

The gas-phase dissociation of phosphorylated peptides was modelled using a combination of quantum mechanics and the Rice-Ramsperger-Kassel-Marcus theory. Potential energy surfaces and unimolecular reaction rates for several low-energy fragmentation and rearrangement pathways were estimated, and a general mechanism was proposed. The neutral loss of the phosphoric acid was mainly an outcome of the intramolecular nucleophilic substitution mechanism. The mechanism involves a nucleophilic attack of the phosphorylated amino acid N-terminal carbonyl oxygen on ?-carbon, yielding a cyclic five-membered oxazoline product ion. Regardless of the proton mobility, the pathway was charge directed either by a mobile proton or by a positively charged side chain of some basic residue. Although the mechanistic aspects of the phosphate loss are not influenced by the proton mobility environment, it does affect ion abundances. Results suggest that under the mobile proton environment, the interplay between phosphoric acid neutral loss product ion and backbone cleavage fragments should occur. On the other hand, when proton mobility is limited, neutral loss product ion may predominate. The fragmentation dynamics of phosphoserine versus phosphothreonine containing peptides suggests that H(3)PO(4) neutral loss from phosphothreonine containing peptides is less abundant than that from their phosphoserine containing analogs. During the low-energy CID of phosphorylated peptides in the millisecond time range, typical for ion trap instruments, a phosphate group rearrangement may happen, resulting in an interchange between the phosphorylated and the hydroxylated residues. Unimolecular dissociation rate constants imply the low abundance of such scrambled product ions. PMID:21915960

Rožman, Marko

2011-09-01

2

Gas Phase Dissociation Behavior of Acyl-Arginine Peptides  

PubMed Central

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

McGee, William M.; McLuckey, Scott A.

2013-01-01

3

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

E-print Network

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

Clemmer, David E.

4

Cold core gas-phase chemical model  

NASA Astrophysics Data System (ADS)

This model written in Fortran77 can be used to compute the gas-phase chemical evolution of a dense molecular cloud at a fixed temperature and density. The model is adapted for the osu.2005 (https://www.physics.ohio-state.edu/~eric/research.html) chemical database of Eric Herbst (Ohio State University, USA) but can be modified to read any network. The model contains an option to compute the uncertainties of the modeled abundances. The method for the uncertainty calculation is explained in Wakelam et al. (2005).

Wakelam, V.

2006-11-01

5

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

PubMed Central

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

McGee, William M.; McLuckey, Scott A.

2014-01-01

6

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

PubMed Central

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

Tao, Yuanqi; Julian, Ryan R.

2013-01-01

7

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

PubMed

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

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

2015-02-01

8

Reagent Cluster Anions for Multiple Gas-phase Covalent Modifications of Peptide and Protein Cations  

PubMed Central

Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated here using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used here to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the ‘cost’ of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K10+3H]3+ and the reagent cluster [5R5Na-Na]?). This type of gas phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anions which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included here as illustrative of the results obtained for the clusters comprised of 2–6 reagent molecules. PMID:23702708

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

2013-01-01

9

Multiscale Aspects of Modeling Gas-Phase Nanoparticle Synthesis  

PubMed Central

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

Buesser, B.; Gröhn, A.J.

2013-01-01

10

Factors that Influence Helical Preferences for Singly-Charged Gas-Phase Peptide Ions: The Effects of Multiple Potential Charge-Carrying Sites  

PubMed Central

Ion mobility-mass spectrometry is used to investigate the structure(s) of a series of model peptide [M + H]+ ions to better understand how intrinsic properties affect structure in low dielectric environments. The influence of peptide length, amino acid sequence and composition on gas-phase structure is examined for a series of model peptides that have been previously studied in solution. Collision cross-sections for the [M + H]+ ions of Ac-(AAKAA)nY-NH2 (n = 3 – 6) and Ac-Y(AEAAKA)nF-NH2 (n = 2 – 5) are reported and correlated with candidate structures generated obtained using molecular modeling techniques. The [M + H]+ ions of the AAKAA peptide series each exhibit a single, dominant ion mobility arrival time distribution (ATD) which correlates to partial helical structures, whereas the [M + H]+ ions of the AEAAKA ion series are composed of ATDs which correlate to charge-solvated globules (i.e. the charge is coordinated or solvated by polar peptide functional groups). These data raise numerous questions concerning intrinsic properties (amino acid sequence and composition as well as charge location) that dictate gas-phase peptide ion structure, which may reflect trends for peptide ion structure in low dielectric environments, such as transmembrane segments. PMID:20000372

McLean, Janel R.; McLean, John A.; Wu, Zhaoxiang; Becker, Christopher; Pérez, Lisa M; Pace, C. Nick; Scholtz, J. Martin; Russell, David H.

2009-01-01

11

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

NASA Astrophysics Data System (ADS)

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

Markovi?, V. Lj.; Petrovi?, Z. Lj.; Pejovi?, M. M.

1996-07-01

12

Nahoon: Time-dependent gas-phase chemical model  

NASA Astrophysics Data System (ADS)

Nahoon is a gas-phase chemical model that computes the chemical evolution in a 1D temperature and density structure. It uses chemical networks downloaded from the KInetic Database for Astrochemistry (KIDA) but the model can be adapted to any network. The program is written in Fortran 90 and uses the DLSODES (double precision) solver from the ODEPACK package to solve the coupled stiff differential equations. The solver computes the chemical evolution of gas-phase species at a fixed temperature and density and can be used in one dimension (1D) if a grid of temperature, density, and visual extinction is provided. Grains, both neutral and negatively charged, and electrons are considered as chemical species and their concentrations are computed at the same time as those of the other species. Nahoon contains a test to check the temperature range of the validity of the rate coefficients and avoid extrapolations outside this range. A test is also included to check for duplication of chemical reactions, defined over complementary ranges of temperature.

Wakelam, V.

2014-09-01

13

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

PubMed Central

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

Prentice, Boone M.

2013-01-01

14

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)

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.

Gaigeot, Marie-Pierre

2009-03-01

15

Energetics and dynamics of electron transfer and proton transfer in dissociation of metal(III)(salen)-peptide complexes in the gas phase.  

PubMed

Time- and collision energy-resolved surface-induced dissociation (SID) of ternary complexes of Co(III)(salen)+, Fe(III)(salen)+, and Mn(III)(salen)+ with several angiotensin peptide analogues was studied using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Time-resolved fragmentation efficiency curves (TFECs) were modeled using an RRKM-based approach developed in our laboratory. The approach utilizes a very flexible analytical expression for the internal energy deposition function that is capable of reproducing both single-collision and multiple-collision activation in the gas phase and excitation by collisions with a surface. The energetics and dynamics of competing dissociation pathways obtained from the modeling provides important insight on the competition between proton transfer, electron transfer, loss of neutral peptide ligand, and other processes that determine gas-phase fragmentation of these model systems. Similar fragmentation behavior was obtained for various Co(III)(salen)-peptide systems of different angiotensin analogues. In contrast, dissociation pathways and relative stabilities of the complexes changed dramatically when cobalt was replaced with trivalent iron or manganese. We demonstrate that the electron-transfer efficiency is correlated with redox properties of the metal(III)(salen) complexes (Co > Fe > Mn), while differences in the types of fragments formed from the complexes reflect differences in the modes of binding between the metal-salen complex and the peptide ligand. RRKM modeling of time- and collision-energy-resolved SID data suggests that the competition between proton transfer and electron transfer during dissociation of Co(III)(salen)-peptide complexes is mainly determined by differences in entropy effects while the energetics of these two pathways are very similar. PMID:18266367

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

2008-03-12

16

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

SciTech Connect

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

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

2008-03-12

17

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

E-print Network

- ated with full models of gas phase RDX combustion, and thus significantly improve computational a wide variety of thermochemical phenomena, the effects of detailed finite rate chemistry must link between traditional collision-based gas phase chemistry and fundamental fluid mechanics. However

18

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

PubMed

Insights on mechanisms for the generation of gas-phase peptide ions and their dissociation in matrix-assisted laser desorption ionization (MALDI) gained from the kinetic and ion yield studies are presented. Even though the time-resolved photodissociation technique was initially used to determine the dissociation kinetics of peptide ions and their effective temperature, it was replaced by a simpler method utilizing dissociation yields from in-source decay (ISD) and post-source decay (PSD). The ion yields for a matrix and a peptide were measured by repeatedly irradiating a region on a sample and collecting ion signals until the sample in the region was completely depleted. Matrix- and peptide-derived gas-phase cations were found to be generated by pre-formed ion emission or by ion-pair emission followed by anion loss, but not by laser-induced ionization. The total number of ions, that is, matrix plus peptide, was found to be equal to the number of ions emitted from a pure matrix. A matrix plume was found to cool as it expanded, from around 800-1,000?K to 400-500?K. Dissociation of peptide ions along b/y channels was found to occur statistically, that is, following RRKM behavior. Small critical energy (E0 ?=?0.6-0.7?eV) and highly negative critical entropy (?S(‡) ?=?-30 to -25?eu) suggested that the transition structure was stabilized by multiple intramolecular interactions. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 94-115, 2015. PMID:24863621

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

2015-04-01

19

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

PubMed Central

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

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

2005-01-01

20

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

SciTech Connect

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.

Malandra, J.

1993-05-01

21

The Role of Acidic Residues and of Sodium Ion Adduction on the Gas-Phase H/D Exchange of Peptides and Peptide Dimers  

PubMed Central

Gas-phase H/D exchange is widely used for characterizing the structure of ions. However, many structural parameters that affect the rate of H/D exchange are poorly understood, which complicates the interpretation of experimental data. Here, the effects of sodium ion adduction on the rate of H/D exchange with D2O for a series of peptides and peptide dimers with varying numbers of acidic residues are described. The maximum number of sodium ion adducts that can be accommodated by the peptides and peptide dimers in this study is N + 1, where N is the number of free carboxylic acid groups. The formation of methyl-esters at all carboxylic acid groups, or the replacement of all the acidic hydrogens with sodium ions, effectively shuts down H/D exchange with D2O. In contrast, both the rate and the extent of H/D exchange with D2O are increased for most of the peptides and peptide dimers by the adduction of an intermediate number of sodium ions. These results are consistent with the H/D exchange occurring via a salt-bridge mechanism and show that the presence of two carboxylic acid groups is much better than one. The results with peptide dimers also indicate that surface accessibility may not be a dominant factor in the extent of H/D exchange for these ions. PMID:14652194

Jurchen, John C.; Cooper, Russell E.; Williams, Evan R.

2005-01-01

22

Fragmentation mechanism of UV-excited peptides in the gas phase  

NASA Astrophysics Data System (ADS)

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.

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

2014-10-01

23

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

24

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

NASA Astrophysics Data System (ADS)

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.

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

25

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

PubMed

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

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

26

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

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

27

Gas-Phase Fragmentation Characteristics of Benzyl-Aminated Lysyl-Containing Tryptic Peptides  

PubMed Central

The fragmentation characteristics of peptides derivatized at the side chain ?-amino group of lysyl residues via reductive amination with benzaldehyde have been examined using collision-induced dissociation (CID) tandem mass spectrometry. The resulting MS/MS spectra exhibit peaks representing product ions formed from two independent fragmentation pathways. One pathway results in backbone fragmentation and commonly observed sequence ion peaks. The other pathway corresponds to the unsymmetrical, heterolytic cleavage of the C?-N? bond that links the benzyl derivative to the side chain lysyl residue. This results in the elimination of the derivative as a benzylic or tropylium carbocation and a (n-1)+-charged peptide product (where n is the precursor ion charge state). The frequency of occurrence of the elimination pathway increases with increasing charge of the precursor ion. For the benzyl-modified tryptic peptides analyzed in this study, peaks representing products from both of these pathways are observed in the MS/MS spectra of doubly-charged precursor ions, but the carbocation elimination pathway occurs almost exclusively for triply-charged precursor ions. The experimental evidence presented herein, combined with molecular orbital calculations, suggests that the elimination pathway is a charge-directed reaction contingent upon protonation of the secondary ?-amino group of the benzyl-derivatized lysyl side chain. If the secondary ?-amine is protonated, then the elimination of the carbocation is observed. If the precursor is not protonated at the secondary ?-amine then backbone fragmentation persists. The application of appropriately substituted benzyl analogs may allow for selective control over the relative abundance of product ions generated from the two pathways. PMID:20471281

Simon, E.S.; Papoulias, P.G.; Andrews, P.C.

2010-01-01

28

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

NASA Astrophysics Data System (ADS)

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

Pluha?ová, Eva; Marsalek, Ondrej; Schmidt, Burkhard; Jungwirth, Pavel

2012-11-01

29

METHODS FOR SIMULATING GAS PHASE SO2 OXIDATION IN ATMOSPHERIC MODELS  

EPA Science Inventory

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

30

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

E-print Network

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

Matthewson, M. John

31

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

PubMed

The effect of the basic residue on the energetics, dynamics, and mechanisms of backbone fragmentation of protonated peptides was investigated. Time-resolved and collision energy-resolved surface-induced dissociation (SID) of singly protonated peptides with the N-terminal arginine residue and their analogues, in which arginine is replaced with less basic lysine and histidine residues, was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). SID experiments demonstrated different kinetics of formation of several primary product ions of peptides with and without arginine residue. The energetics and dynamics of these pathways were determined from Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental data. Comparison between the kinetics and energetics of fragmentation of arginine-containing peptides and the corresponding methyl ester derivatives provides important information on the effect of dissociation pathways involving salt bridge (SB) intermediates on the observed fragmentation behavior. Because pathways involving SB intermediates are characterized by low threshold energies, they efficiently compete with classical oxazolone and imine/enol pathways of arginine-containing peptides on a long time scale of the FTICR instrument. In contrast, fragmentation of histidine- and lysine-containing peptides is largely determined by canonical pathways. Because SB pathways are characterized by negative activation entropies, fragmentation of arginine-containing peptides is kinetically hindered and observed at higher collision energies as compared to their lysine- and histidine-containing analogues. PMID:20977217

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

2010-11-17

32

Modeling of the all-gas-phase iodine laser (AGIL)  

NASA Astrophysics Data System (ADS)

This work revisits the finite-rate chemistry mechanism for AGIL in light of recent rate measurements for kinetic processes. The effect of temperature dependence of kinetic processes measured only at room temperature conditions is explored by assuming a square-root dependence upon temperature in line with kinetic theory. A sensitivity study is performed to elucidate the relative impact of each chemical kinetic process modeled with respect to the larger set of modeled chemical kinetic processes. And reactant mixing is examined, with documentation of the effects of the reactant mixing predictions upon recent multi-watt power extraction experiments.

Madden, Timothy J.; Manke, Gerald C., II; Hager, Gordon D.

2005-03-01

33

Gas-phase peptide structures unraveled by far-IR spectroscopy: combining IR-UV ion-dip experiments with Born-Oppenheimer molecular dynamics simulations.  

PubMed

Vibrational spectroscopy provides an important probe of the three-dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides. Although the far-IR region (<500?cm(-1)) may contain a wealth of structural information, as recognized in condensed phase studies, DFT often performs poorly in predicting the far-IR spectra of peptides. Here, Born-Oppenheimer molecular dynamics (BOMD) is applied to predict the far-IR signatures of two ?-turn peptides. Combining experiments and simulations, far-IR spectra can provide structural information on gas-phase peptides superior to that extracted from mid-IR and amide?A features. PMID:24574197

Jaeqx, Sander; Oomens, Jos; Cimas, Alvaro; Gaigeot, Marie-Pierre; Rijs, Anouk M

2014-04-01

34

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

SciTech Connect

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

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

1992-06-01

35

Assigning structures to gas-phase peptide cations and cation-radicals. An infrared multiphoton dissociation, ion mobility, electron transfer, and computational study of a histidine peptide ion.  

PubMed

Infrared multiphoton dissociation (IRMPD) spectroscopy, using a free-electron laser, and ion mobility measurements, using both drift-cell and traveling-wave instruments, were used to investigate the structure of gas-phase peptide (AAHAL + 2H)(2+) ions produced by electrospray ionization. The experimental data from the IRMPD spectra and collisional cross section (?) measurements were consistent with the respective infrared spectra and ? calculated for the lowest-energy peptide ion conformer obtained by extensive molecular dynamics searches and combined density functional theory and ab initio geometry optimizations and energy calculations. Traveling-wave ion mobility measurements were employed to obtain the ? of charge-reduced peptide cation-radicals, (AAHAL + 2H)(+?), and the c(3), c(4), z(3), and z(4) fragments from electron-transfer dissociation (ETD) of (AAHAL + 2H)(2+). The experimental ? for the ETD charge-reduced and fragment ions were consistent with the values calculated for fully optimized ion structures and indicated that the ions retained specific hydrogen bonding motifs from the precursor ion. In particular, the ? for the doubly protonated ions and charge-reduced cation-radicals were nearly identical, indicating negligible unfolding and small secondary structure changes upon electron transfer. The experimental ? for the (AAHAL + 2H)(+?) cation-radicals were compatible with both zwitterionic and histidine radical structures formed by electron attachment to different sites in the precursor ion, but did not allow their distinction. The best agreement with the experimental ? was found for ion structures fully optimized with M06-2X/6-31+G(d,p) and using both projection approximation and trajectory methods to calculate the theoretical ? values. PMID:22364440

Moss, Christopher L; Chamot-Rooke, Julia; Nicol, Edith; Brown, Jeffery; Campuzano, Iain; Richardson, Keith; Williams, Jonathan P; Bush, Matthew F; Bythell, Benjamin; Paizs, Bela; Turecek, Frantisek

2012-03-15

36

Action-FRET: probing the molecular conformation of mass-selected gas-phase peptides with Förster resonance energy transfer detected by acceptor-specific fragmentation.  

PubMed

The use of Förster resonance energy transfer (FRET) as a probe of the structure of biological molecules through fluorescence measurements in solution is well-attested. The transposition of this technique to the gas phase is appealing since it opens the perspective of combining the structural accuracy of FRET with the specificity and selectivity of mass spectrometry (MS). Here, we report FRET results on gas-phase polyalanine ions obtained by measuring FRET efficiency through specific photofragmentation rather than fluorescence. The structural sensitivity of the method was tested using commercially available chromophores (QSY 7 and carboxyrhodamine 575) grafted on a series of small, alanine-based peptides of differing sizes. The photofragmentation of these systems was investigated through action spectroscopy, and their conformations were probed using ion mobility spectrometry (IMS) and Monte Carlo minimization (MCM) simulations. We show that specific excitation of the donor chromophore results in the observation of fragments that are specific to the electronic excitation of the acceptor chromophore. This shows that energy transfer took place between the two chromophores and hence that the action-FRET technique can be used as a new and sensitive probe of the structure of gas-phase biomolecules, which opens perspectives as a new tool in structural biology. PMID:25073016

Daly, Steven; Poussigue, Frédéric; Simon, Anne-Laure; MacAleese, Luke; Bertorelle, Franck; Chirot, Fabien; Antoine, Rodolphe; Dugourd, Philippe

2014-09-01

37

The Gas-Phase Absorption Spectrum of a Neutral GFP Model Chromophore  

PubMed Central

We have studied the gas-phase absorption properties of the green fluorescent protein (GFP) chromophore in its neutral (protonated) charge state in a heavy-ion storage ring. To accomplish this we synthesized a new molecular chromophore with a charged NH3 group attached to a neutral model chromophore of GFP. The gas-phase absorption cross section of this chromophore molecule as a function of the wavelength is compared to the well-known absorption profile of GFP. The chromophore has a maximum absorption at 415 ± 5 nm. When corrected for the presence of the charged group attached to the GFP model chromophore, the unperturbed neutral chromophore is predicted to have an absorption maximum at 399 nm in vacuum. This is very close to the corresponding absorption peak of the protein at 397 nm. Together with previous data obtained with an anionic GFP model chromophore, the present data show that the absorption of GFP is primarily determined by intrinsic chromophore properties. In other words, there is strong experimental evidence that, in terms of absorption, the conditions in the hydrophobic interior of this protein are very close to those in vacuum. PMID:17040991

Lammich, L.; Petersen, M. Åxman; Nielsen, M. Brøndsted; Andersen, L. H.

2007-01-01

38

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

SciTech Connect

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

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

1993-02-01

39

The modeling of gas phase permeation through iron and nickel membranes  

NASA Technical Reports Server (NTRS)

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

Kuhn, David K.; Shanabarger, Mickey R.

1989-01-01

40

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

SciTech Connect

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)

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

41

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

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

42

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

NASA Astrophysics Data System (ADS)

The aim of this work was to develop a model ideally suited for detailed studies on aerosol dynamics, gas and particle phase chemistry within urban plumes, from local scale (1×1 km2) to regional or global scale. This article describes and evaluates the trajectory model for Aerosol Dynamics, gas and particle phase CHEMistry and radiative transfer (ADCHEM), which has been developed and used at Lund University since 2007. The model treats both vertical and horizontal dispersion perpendicular to an air mass trajectory (2-space dimensions), which is not treated in Lagrangian box-models (0-space dimensions). The Lagrangian approach enables a more detailed representation of the aerosol dynamics, gas and particle phase chemistry and a finer spatial and temporal resolution compared to that of available regional 3D-CTMs. These features make it among others ideally suited for urban plume studies. The aerosol dynamics model includes Brownian coagulation, dry deposition, wet deposition, in-cloud processing, condensation, evaporation, primary particle emissions and homogeneous nucleation. The gas phase chemistry model calculates the gas phase concentrations of 63 different species, using 119 different chemical reactions. Daily isoprene and monoterpene emissions from European forests were simulated separately with the vegetation model LPJ-GUESS, and included as input to ADCHEM. ADCHEM was used to simulate the ageing of the urban plumes from the city of Malmö in Southern Sweden (280 000 inhabitants). Several sensitivity tests were performed concerning the number of size bins, size structure method, coupled or uncoupled condensation, the volatility basis set (VBS) or traditional 2-product model for secondary organic aerosol formation, different aerosol dynamic processes and vertical and horizontal mixing. The simulations show that the full-stationary size structure gives accurate results with little numerical diffusion when more than 50 size bins are used between 1.5 and 2500 nm, while the moving-center method is preferable when only a few size bins are selected. The particle number size distribution in the center of the urban plume from Malmö is mainly affected by dry deposition, coagulation and condensation, and is relatively insensitive to moderate variations in the vertical and horizontal mixing, as long as the mixing height is relatively uniform. The modeled PM2.5 was dominated by organics, nitrate, sulfate and ammonium. If treating the condensation of HNO3 and NH3 as a coupled process (pH independent) the model gave lower nitrate PM2.5 values than if considering uncoupled condensation. However, both methods gave similar and significant temporal variation in the particulate nitrate content, primarily due to fluctuation in the relative humidity.

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

2010-08-01

43

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

NASA Astrophysics Data System (ADS)

A theoretical study of the reactions of NH_4^+ with formaldehyde and CH_5^+ with formamide is carried out. The viability of these gas-phase ion-molecule reactions as possible sources of formamide and acetamide under the conditions of interstellar medium is evaluated. We report a theoretical estimation of the reaction enthalpies and an analysis of their potential energy surfaces. Formation of protonated formamide from the reaction between ammonium cation and formaldehyde is an exothermic process, but all the channels located on the potential energy surface leading to this product present net activation energies. For the reaction between methanium and formamide, different products are possible from a thermodynamic point of view. An analysis of its potential energy surface showed that formation of protonated acetamide and amino acetaldehyde takes place through barrier-free paths. Therefore, this reaction could be a feasible source of acetamide and amino acetaldehyde in space.

Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

2014-09-01

44

The Q-K model for gas-phase chemical reaction rates  

NASA Astrophysics Data System (ADS)

The quantum-kinetic, or Q-K, model is based on the quantum vibration model that is employed in the computation of gas flows at the molecular level by the direct simulation Monte Carlo (DSMC) method. The Q-K procedure for dissociation is physically realistic within the context of the vibration model in that the reaction occurs upon the selection of the vibrational level that corresponds to dissociation. An analogous, but entirely phenomenological, procedure has been presented for endothermic exchange and chain reactions. These procedures for the endothermic reactions have been well validated, but the existing procedures for the corresponding exothermic reactions have proved to be problematic. This paper presents new procedures for the exothermic reactions that are computationally efficient and provide a near exact match with the equilibrium constant of statistical mechanics. The Q-K model does not depend on the availability of continuum rate coefficients. Instead, the simplicity of the new DSMC procedures allows analytical expressions to be written down for the corresponding rate coefficients in an equilibrium gas. These are used to validate the Q-K model for reactions in high temperature air and in hydrogen-oxygen combustion. The development of the Q-K model has been driven by the need for efficient reaction procedures in DSMC applications that often involve the computation of billions of simulated collisions. It is not intended to compete with the modern theories for gas-phase chemical reactions that employ more accurate physical representations of real reactions. At the same time, the degree of validation of the model is such that the analytical expressions for the rate coefficients that correspond to the model should be useful in their own right.

Bird, G. A.

2011-10-01

45

N-terminal derivatization and fragmentation of neutral peptides via ion--molecule reactions with acylium ions: toward gas-phase Edman degradation?  

PubMed

The gas-phase ion-molecule reactions of neutral alanylglycine have been examined with various mass-selected acylium ions RCO(+) (R= CH(3), CD(3), C(6)H(5), C(6)F(5) and (CH(3))( 2)N), as well as the transacylation reagent O-benzoylbenzophenone in a Fourier transform ion cyclotron resonance mass spectrometer. Reactions of the gaseous dipeptide with acylium ions trapped in the ICR cell result in the formation of energized [M + RCO](+) adduct ions that fragment to yield N-terminal b-type and C-terminal y-type product ions, including a modified b(1) ion which is typically not observed in the fragmentation of protonated peptides. Judicious choice of the acylium ion employed allows some control over the product ion types that are observed (i.e., b versus y ions). The product ion distributions from these ion--molecule reactions are similar to those obtained by collision-activated dissociation in a triple quadrupole mass spectrometer of the authentic N-acylated alanylglycine derivatives. These data indicate that derivatization of the peptide in the gas-phase occurs at the N-terminal amine. Ab initio molecular orbital calculations, performed to estimate the thermochemistry of the steps associated with adduct formation as well as product ion formation, indicate that (i) the initially formed adduct is energized and hence likely to rapidly undergo fragmentation, and (ii) the likelihood for the formation of modified b(1) ions in preference to y(1) ions is dependent on the R substituent of the acylium ion. The reaction of the tetrapeptide valine--alanine--alanine--phenylalanine with the benzoyl cation was also found to yield a number of product ions, including a modified b(1) ion. This result suggests that the new experimental approach described here may provide a tool to address one of the major limitations associated with traditional mass spectrometric peptide sequencing approaches, that is, determination of the identity and order of the two N-terminal amino acids. Analogies are made between the reactions observed here and the derivatization and N-terminal cleavage reactions employed in the condensed-phase Edman degradation method. PMID:11456672

Reid, G E; Tichy, S E; Pérez, J; O'Hair, R A; Simpson, R J; Kenttämaa, H I

2001-02-14

46

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...

47

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

PubMed Central

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

Flicker, T M; Green, S A

2001-01-01

48

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

PubMed Central

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

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

2012-01-01

49

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 ...

50

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

E-print Network

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

Millar, Tom

51

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

SciTech Connect

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

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

1993-09-01

52

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

SciTech Connect

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

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

1992-06-01

53

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

SciTech Connect

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

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

1993-02-01

54

A global model for C4F8 plasmas coupling gas phase and wall surface reaction kinetics  

NASA Astrophysics Data System (ADS)

A global or zero-dimensional model for C4F8 plasmas is formulated by coupling gas phase and wall surface reaction kinetics. A set of surface reactions implements experimental findings and quantifies the effect of the fluorocarbon film formed on the reactor walls on the densities of species in the gas phase. The model allows the calculation of the pressure change after the ignition of the discharge and the effective sticking (surface loss) coefficients of the neutral species on the wall surface. The model is validated by comparison with experimental measurements, i.e. pressure rise and densities of F atoms, CF2 and CF radicals, in an inductively coupled plasma reactor. It is predicted that C4F8 is vastly dissociated and CF4 becomes the dominant species even at low power conditions. A net production of CF3 radical and a net consumption of CF2 radical at the reactor walls are predicted. A study on the contribution of each reaction to the production and consumption of the species shows that at least one surface reaction is among the major sinks or sources of CF4, CFx radicals and F.

Kokkoris, George; Goodyear, Andy; Cooke, Mike; Gogolides, Evangelos

2008-10-01

55

SHORT COMMUNICATION Gas-Phase Separations of Protease Digests  

E-print Network

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

Clemmer, David E.

56

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

Microsoft Academic Search

Time- and collision energy-resolved surface-induced dissociation (SID) of ternary complexes of CoIII(salen)+, FeIII(salen)+, and MnIII(salen)+ with several angiotensin peptide analogs was studied using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Time-resolved fragmentation efficiency curves (TFECs) were modeled using an RRKM-based approach developed in our laboratory. The approach utilizes a very flexible

Julia Laskin; Zhibo Yang; Ivan K. Chu

2008-01-01

57

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

NASA Technical Reports Server (NTRS)

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.

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

1988-01-01

58

Development and application of a new air pollution modeling system-part I: Gas-phase simulations  

NASA Astrophysics Data System (ADS)

A new air pollution modeling system is discussed and applied. The system consists of GATOR, a gas, aerosol, transport, and radiation air quality model and MMTD, a mesoscale meteorological and tracer dispersion model. The gas-phase processes treated by GATOR include photochemistry, deposition, emissions, and gas-to-particle conversion. To solve stiff chemical rate equations, a sparse-matrix, vectorized Gear-type code (SMVGEAR) was used. The aerosol processes in GATOR include coagulation, aqueous chemistry, chemical equilibrium, condensational growth, dissolutional growth, evaporation, nucleation, emissions, deposition, and sedimentation. The transport processes include horizontal advection and diffusion and vertical convection and diffusion. Finally, the radiation algorithm calculates ultraviolet, visible, and infrared optical depths, mean intensities for photodissociation rates, and radiative heat fluxes for temperature calculations. The MMTD predicts winds, diffusion, temperature, pressure, humidity, soil moisture, and rainfall. These variables are fed to GATOR and radiative heating rates from GATOR are fed back to the MMTD. With the GATOR/MMTD system, gas-phase pollution was simulated for the Southern California Air Quality Study (SCAQ) days of 26-28 August 1987. Results were compared to surface measurements for many parameters. The model predicted normalized gross errors for ozone of 17.6% and 23.4% at 2:30 p.m. on the first and second days of simulation, respectively. Also, the normalized gross error during the first 12 h of simulation was 22%. Correct emissions and initial mixing ratios appear to be necessary for obtaining good results. Initial conditions outside the basin seem to affect results by the second and third days. Time-series plots, statistics, and a sensitivity test are discussed. Aerosol simulation results will be shown in a later work.

Jacobson, Mark Z.; Lu, Rong; Turco, Richard P.; Toon, Owen B.

59

Modeling the maximum charge state of arginine-containing Peptide ions formed by electrospray ionization.  

PubMed

A model for the gas-phase proton transfer reactivity of multiply protonated molecules is used to quantitatively account for the maximum charge states of a series of arginine-containing peptide ions measured by Downard and Biemann (Int. J. Mass Spectrom. Ion Processes 1995, 148, 191-202). We find that our calculations account exactly for the maximum charge state for 7 of the 10 peptides and are off by one charge for the remaining 3. These calculations clearly predict the trend in maximum charge states for these peptides and provide further evidence that the maximum charge state of ions formed by electrospray ionization is determined by their gas-phase proton transfer reactivity. PMID:16467911

Schnier, P D; Price, W D; Williams, E R

1996-09-01

60

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

SciTech Connect

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

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

2012-05-22

61

Integrated pressure-dependence in automated mechanism generation : a new tool for building gas-phase kinetic models  

E-print Network

A host of vital, current, and developing technologies, such as pyrolysis, thermal cracking, partial oxidation, and high-efficiency combustion engines, involve complex, gas-phase chemical mechanisms with hundreds of species ...

Matheu, David M. (David Michael), 1974-

2003-01-01

62

The Q-K model for gas-phase chemical reaction rates  

Microsoft Academic Search

The quantum-kinetic, or Q-K, model is based on the quantum vibration model that is employed in the computation of gas flows at the molecular level by the direct simulation Monte Carlo (DSMC) method. The Q-K procedure for dissociation is physically realistic within the context of the vibration model in that the reaction occurs upon the selection of the vibrational level

G. A. Bird

2011-01-01

63

Development of gas-phase chemistry, secondary organic aerosol, and aqueous-phase chemistry modules for PM modeling. Final report  

SciTech Connect

The Coordinating Research Council (CRC) is sponsoring a multi-phase study to develop improved air quality models for particulate matter (PM). Improved urban and regional scale PM air quality models are needed to develop reliable emission control strategies for areas that exceed the National Ambient Air Quality Standards (NAAQS) for PM-2.5 and PM-10, and for National Parks and other Class 1 areas with impaired visibility. This report describes the development and implementation of two process modules for PM models. These particular process modules are needed to simulate secondary aerosol species, which are often the dominate portion of PM-2.5 mass. The first module simulates the gas-phase atmospheric chemistry of the VOC/NO{sub x}/SO{sub 2}/ozone system and the formation of secondary organic aerosols. The module also simulates the formation of inorganic species, including sulfuric acid and nitric acid, that form important aerosol species: sulfate and nitrate; The second module simulates the aqueous-phase chemistry in fogs and clouds. This chemistry primarily enhances SO{sub 2} oxidation rates and leads to enhanced sulfate aerosol concentrations.

Strader, R.; Gurciullo, C.S.; Pandis, S.N.; Kumar, N.; Lurmann, F.W.

1998-10-30

64

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

NASA Astrophysics Data System (ADS)

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.

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

2011-11-01

65

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

NASA Astrophysics Data System (ADS)

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

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

66

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

NASA Astrophysics Data System (ADS)

We propose a new formulation of the statistical multifragmentation model based on the analysis of the virial expansion for a system of the nuclear fragments of all sizes. The developed model not only allows us to account for short-range repulsion, but also to calculate the surface free energy which is induced by the interaction between the fragments. Also we propose a new parameterization for the liquid phase pressure which allows us to introduce a compressible nuclear liquid into the statistical multifragmentation model. The resulting model is exactly solvable and has no irregular behavior of the isotherms in the mixed phase region that is typical for mean-field models. The general conditions for the 1-st and 2-nd (or higher) order phase transitions are formulated. It is shown that all endpoints of the present model phase diagram are the tricritical points, if the Fisher exponent ? is in the range 32???2. The treatment of nuclear liquid compressibility allows us to reduce the tricritical endpoint density of the statistical multifragmentation model to one third of the normal nuclear density. A specific attention is paid to the fragment size distributions in the region of a negative surface tension at supercritical temperatures.

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

2014-04-01

67

Aerosol formation from the reaction of αpinene and ozone using a gas-phase kinetics-aerosol partitioning model  

Microsoft Academic Search

As a result of new aerosol compositional information, the authors have implemented an exploratory model for predicting aerosol yields from the reaction of α-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

Richard Kamens; Myoseon Jang; Chao-Jung Chien; Keri Leach

1999-01-01

68

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

E-print Network

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

Dabdub, Donald

69

Peptide models for membrane channels.  

PubMed Central

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

Marsh, D

1996-01-01

70

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

NASA Astrophysics Data System (ADS)

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

Buendía, G. M.; Rikvold, P. A.

2012-03-01

71

A global model for SF6 plasmas coupling reaction kinetics in the gas phase and on the surface of the reactor walls  

NASA Astrophysics Data System (ADS)

Gas phase and reactor wall-surface kinetics are coupled in a global model for SF6 plasmas. A complete set of gas phase and surface reactions is formulated. The rate coefficients of the electron impact reactions are based on pertinent cross section data from the literature, which are integrated over a Druyvesteyn electron energy distribution function. The rate coefficients of the surface reactions are adjustable parameters and are calculated by fitting the model to experimental data from an inductively coupled plasma reactor, i.e. F atom density and pressure change after the ignition of the discharge. The model predicts that SF6, F, F2 and SF4 are the dominant neutral species while SF_5^+ and F- are the dominant ions. The fit sheds light on the interaction between the gas phase and the reactor walls. A loss mechanism for SFx radicals by deposition of a fluoro-sulfur film on the reactor walls is needed to predict the experimental data. It is found that there is a net production of SF5, F2 and SF6, and a net consumption of F, SF3 and SF4 on the reactor walls. Surface reactions as well as reactions between neutral species in the gas phase are found to be important sources and sinks of the neutral species.

Kokkoris, George; Panagiotopoulos, Apostolos; Goodyear, Andy; Cooke, Mike; Gogolides, Evangelos

2009-03-01

72

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

Microsoft Academic Search

Copper complexes with a cyclic D-His-beta-Ala-L-His-L-Lys and all-L-His-beta-Ala-His-Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D-His and L-His complexes. All complexes underwent peptide cross-ring cleavages upon electron capture. The

C. Afonso; J. C. Tabet; G. Giorgi; F. Turecek

2012-01-01

73

Molecular Dynamics Modeling of Hypersonic Gas-Phase and Gas-Surface Reactions  

NASA Astrophysics Data System (ADS)

Efforts to use molecular dynamics (MD) to develop both non-equilibrium dissociation models required in the shock layer as well as gas-surface interaction models specifically for surface catalysis will be summarized. First, an accelerated MD algorithm for dilute gases is presented, called the Event-Driven/Time-Driven (ED/TD) MD method. The method detects and moves molecules directly to their impending collision while still integrating each collision, including multi-body collisions, using conventional Time-Driven (TD) MD with an arbitrary inter-atomic potential. The simulation thus proceeds at time steps approaching the mean-collision-time. Preliminary nonequilibrium relaxation and normal shock wave simulations are in excellent agreement with direct simulation Monte Carlo (DSMC) results with large speedups over conventional TD MD, especially at low densities. Second, an MD simulation technique to study surface catalysis employing the ReaxFF inter-atomic potential is detailed. SiO2 surfaces are equilibrated with a dissociated gas mixture at various temperatures and pressures, establishing surface coverage. Rates of dominant reaction mechanisms, including adsorption, desorption, and E-R/L-H recombination, are then determined by counting individual events. The experimentally measured exponential dependence of recombination coefficient on temperature is well predicted by the MD simulations.

Schwartzentruber, T. E.; Norman, P.; Valentini, P.

2011-05-01

74

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

75

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

NASA Astrophysics Data System (ADS)

Organic aerosol (OA) as one of a major fine particulate matter in the atmosphere plays an important role in air pollution, human health, and climate forcing. OA is composed of directly emitted primary organic aerosol and chemically produced secondary organic aerosols (SOA). Despite much recent progress in understanding SOA formation, current air quality models cannot explain the magnitude and growth of atmospheric SOA, due to high uncertainties in sources, properties, and chemical reactions of precursors and formation pathways of SOA. Recent laboratory and modeling studies showed that glyoxal may serve as an important SOA precursor in the condensed solution of inorganic or organic aerosol particles (e.g., ammonium sulfate, fulvic acid, and amino acids). In this study, the Weather Research and Forecasting model with chemistry (WRF/Chem) is modified to account for the latest observed gas-phase yields of glyoxal from various volatile organic compounds (VOCs) and the associated SOA formation in the aqueous aerosol phase. The SOA formation in the aqueous aerosol phase is implemented using two approaches. In the first approach, two simplified parameterizations are used to represent the lumped particle-phase chemical processes under dark conditions and photochemical surface uptake. In the second approach, more detailed kinetic glyoxal reactions such as reversible glyoxal uptake, dimer formation of glyoxal, and oligomerization are treated and resolved explicitly. The updated WRF/Chem is assessed over the Mexico City and the surrounding region during March 2006 using the MILAGRO campaign data. Various observations such as organic matter from Aerodyne Aerosol Mass Spectrometer and VOCs from Proton-transfer Ion Trap Mass Spectrometry were compared. The preliminary results showed that the addition of the SOA formation from glyoxal in aqueous particles brings SOA predictions into a better agreement with field observations, in particular in presence of high relative humidity. The simulation with updated glyoxal yields gives a factor of 2 higher mixing ratio of glyoxal. The uncertainties in the model treatments as well as future work will also be discussed.

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

2011-12-01

76

Gas Phase Nanoparticle Integration  

Microsoft Academic Search

We report on two gas phase nanoparticle integration processes to assemble nanomaterials onto desired areas on a substrate. We expect these processes to work with any material that can be charged. The processes offer self- aligned integration and could be applied to any nanomaterial device requiring site specific assembly. The Coulomb force process directs the assembly of nanoparticles onto charged

Chad R. Barry; Heiko O. Jacobs

2007-01-01

77

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

PubMed

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

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

2011-09-01

78

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

PubMed

Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here a methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte's surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte's unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma. PMID:25371986

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

2014-12-01

79

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

SciTech Connect

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

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

1993-06-01

80

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)

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.

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

2014-11-01

81

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

PubMed

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

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

2012-06-01

82

GEM-AC, a stratospheric-tropospheric global and regional model for air quality and climate change: evaluation of gas phase properties  

NASA Astrophysics Data System (ADS)

The Global Environmental Multiscale model for Air Quality and climate change (GEM-AC) is a global general circulation model based on the GEM model developed by the Meteorological Service of Canada for operational weather forecasting. It can be run with a global uniform (GU) grid or a global variable (GV) grid where the core has uniform grid spacing and the exterior grid expands. With a GV grid high resolution regional runs can be accomplished without a concern for boundary conditions. The work described here uses GEM version 3.3.2. The gas-phase chemistry consists in detailed reactions of Ox, NOx, HOx, CO, CH4, NMVOCs, halocarbons, ClOx and BrO. We have recently added elements of the Global Modal-aerosol eXtension (GMXe) scheme to address aerosol microphysics and gas-aerosol partitioning. The evaluation of the MESSY GMXe aerosol scheme is addressed in another poster. The Canadian aerosol module (CAM) is also available. Tracers are advected using the semi-Lagrangian scheme native to GEM. The vertical transport includes parameterized subgrid scale turbulence and large scale convection. Dry deposition is implemented as a flux boundary condition in the vertical diffusion equation. For climate runs the GHGs CO2, CH4, N2O, CFCs in the radiation scheme are adjusted to the scenario considered. In GV regional mode at high resolutions a lake model, FLAKE is also included. Wet removal comprises both in-cloud and below-cloud scavenging. With the gas phase chemistry the model has been run for a series of ten year time slices on a 3°×3° global grid with 77 hybrid levels from the surface to 0.15 hPa. The tropospheric and stratospheric gas phase results are compared with satellite measurements including, ACE, MIPAS, MOPITT, and OSIRIS. Current evaluations of the ozone field and other stratospheric fields are encouraging and tropospheric lifetimes for CH4 and CH3CCl3 are in reasonable accord with tropospheric models. We will present results for current and future climate conditions forced by SST for 2050.

Kaminski, J. W.; Semeniuk, K.; McConnell, J. C.; Lupu, A.; Mamun, A.

2012-12-01

83

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

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

84

EPA GAS PHASE CHEMISTRY CHAMBER STUDIES  

EPA Science Inventory

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

85

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

EPA Science Inventory

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

86

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

EPA Science Inventory

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

87

Gas-phase chemical dynamics  

SciTech Connect

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

Weston, R.E. Jr.; Sears, T.J.; Preses, J.M. [Brookhaven National Laboratory, Upton, NY (United States)

1993-12-01

88

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

PubMed

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 (S(N)2) 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

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

2009-01-01

89

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

NASA Astrophysics Data System (ADS)

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

Bhaskaran, Renjith; Sarma, Manabendra

2013-07-01

90

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

.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

Millar, Tom

91

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

PubMed Central

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

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

2009-01-01

92

Gas Phase Reactivity of Carboxylates with N-Hydroxysuccinimide Esters  

NASA Astrophysics Data System (ADS)

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.

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

2015-01-01

93

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)

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.

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

2011-03-01

94

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

E-print Network

Multiphysics modeling of carbon gasification processes in a well-stirred reactor with detailed gas: Coal gasification Carbon gasification Detailed chemistry Heterogeneous surface reactions Radiation Multi-physics numerical modeling a b s t r a c t Fuel synthesis through coal and biomass gasification

Qiao, Li

95

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

PubMed

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

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

2014-03-30

96

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

PubMed Central

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

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

2013-01-01

97

Gas phase catalysis by zeolites  

Microsoft Academic Search

This paper provides an overview about today’s use of zeolites and related microporous materials as catalysts within the fields of refining, petrochemistry and commodity chemicals. The content of this presentation is devoted to gas phase catalysis—with focus on acid catalysis, hydrocarbon conversion and formation, oil and natural gas upgrading as well as catalytic probe reactions for the characterisation of zeolites

Michael Stöcker

2005-01-01

98

Gas phase atmospheric bromine photochemistry  

Microsoft Academic Search

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.

D. J. Lary

1996-01-01

99

In Silico Models for Designing and Discovering Novel Anticancer Peptides  

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

100

Modeling of the dynamics of a gas phase evaporating from the surface of a condensed phase under the effect of concentrated radiation pulses  

Microsoft Academic Search

An algorithm is developed which describes changes with time of the gas phase pressure near the condensate-gas interface due to the effect of concentrated radiation pulses. In the simplest case of a gas transparent to radiation, theoretical results are shown to be in qualitative agreement with experimental data.

P. V. Gerasimenko; V. A. Mazarchenkov; A. D. Suprun; A. M. Fedorchenko

1986-01-01

101

Gas-Phase Reactivity of Carboxylic Acid Functional Groups with Carbodiimides  

NASA Astrophysics Data System (ADS)

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.

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

2013-01-01

102

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

SciTech Connect

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

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

1995-12-01

103

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

E-print Network

therapeutic agents in fighting a wide range of microorganisms. Some antimicro- bial peptides (AMPs) have beenPeptides 26 (2005) 197­206 Protegrin structure­activity relationships: using homology models The protegrin family of antimicrobial peptides is among the shortest in sequence length while remaining very

Minnesota, University of

104

Action of Antimicrobial Peptides:  Two-State Model  

Microsoft Academic Search

The argument and experimental evidence are presented for a two-state model that explains the action of both helical and ‚-sheet antimicrobial peptides after they bind to the plasma membranes of cells. Each peptide has two distinct physical states of binding to lipid bilayers. At low peptide-to-lipid ratios (P\\/L), the peptide tends to adsorb in the lipid headgroup region in a

Huey W. Huang

2000-01-01

105

Computational modeling of Peptide-aptamer binding.  

PubMed

Evolution is the progressive process that holds each living creature in its grasp. From strands of DNA evolution shapes life with response to our ever-changing environment and time. It is the continued study of this most primitive process that has led to the advancement of modern biology. The success and failure in the reading, processing, replication, and expression of genetic code and its resulting biomolecules keep the delicate balance of life. Investigations into these fundamental processes continue to make headlines as science continues to explore smaller scale interactions with increasing complexity. New applications and advanced understanding of DNA, RNA, peptides, and proteins are pushing technology and science forward and together. Today the addition of computers and advances in science has led to the fields of computational biology and chemistry. Through these computational advances it is now possible not only to quantify the end results but also visualize, analyze, and fully understand mechanisms by gaining deeper insights. The biomolecular motion that exists governing the physical and chemical phenomena can now be analyzed with the advent of computational modeling. Ever-increasing computational power combined with efficient algorithms and components are further expanding the fidelity and scope of such modeling and simulations. This chapter discusses computational methods that apply biological processes, in particular computational modeling of peptide-aptamer binding. PMID:25555731

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

2015-01-01

106

Strategies for the Gas Phase Modification of Cationized Arginine via Ion/ion Reactions  

PubMed Central

The gas phase acetylation of cationized arginine residues is demonstrated here using ion/ion reactions with sulfosuccinimidyl acetate (sulfo-NHS acetate) anions. Previous reports have demonstrated the gas phase modification of uncharged primary amine (the N-terminus and ?-amino side chain of lysine) and uncharged guanidine (the arginine side chain) functionalities via sulfo-NHS ester chemistry. Herein, charge-saturated arginine-containing peptides that contain sodium ions as the charge carriers, such as [ac-ARAAARA+2Na]2+, are shown to exhibit strong reactivity towards sulfo-NHS acetate whereas the protonated peptide analogues exhibit no such reactivity. This difference in reactivity is attributed to the lower sodium ion (as compared to proton) affinity of the arginine, which results in increased nucleophilicity of the cationized arginine guanidinium functionality. This increased nucleophilicity improves the arginine residue's reactivity towards sulfo-NHS esters and enhances the gas phase covalent modification pathway. No such dramatic increase in reactivity towards sulfo-NHS acetate has been observed upon sodium cationization of lysine amino acid residues, indicating that this behavior appears to be unique to arginine. The sodium cationization process is demonstrated in the condensed phase by simply spiking sodium chloride into the peptide sample solution and in the gas phase by a peptide-sodium cation exchange process with a sulfo-NHS acetate sodium-bound dimer cluster reagent. This methodology demonstrates several ways by which arginine can be covalently modified in the gas phase even when it is charged. Collisional activation of an acetylated arginine product can result in deguanidination of the residue, generating an ornithine. This gas phase ornithination exhibits similar site-specific fragmentation behavior to that observed with peptides ornithinated in solution and may represent a useful approach for inducing selective peptide cleavages. PMID:24273437

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

2013-01-01

107

SVOC partitioning between the gas phase and settled dust indoors  

NASA Astrophysics Data System (ADS)

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.

Weschler, Charles J.; Nazaroff, William W.

2010-09-01

108

Isotropic and anisotropic dipeptide films based on gas phase deposition  

NASA Astrophysics Data System (ADS)

We demonstrated the fabrication and application of well-ordered and vertically aligned dipeptide nanostructures based on a simple gas phase deposition. Deposited nanostructures exhibited the superhydrophobic property with a very low sliding angle. Highly reproducible SERS data have also been obtained after combining deposited films with a thin layer of gold. In addition to these, directional peptide films were, for the first time, successfully fabricated based on the oblique angle deposition technique. We believe that such bio-inspired materials would have a great impact in several technological applications involving catalysis, tissue engineering and biosensors.

Demirel, Gokhan; Tamer, Ugur

2012-06-01

109

Yingjie Li, Barbara Brodsky and Jean Baum model peptide  

E-print Network

Yingjie Li, Barbara Brodsky and Jean Baum model peptide in an osteogenesis imperfecta collagen TO SER SUBSTITUTION IN AN OSTEOGENESIS IMPERFECTA COLLAGEN MODEL PEPTIDE* Yingjie Li , Barbara Brodsky Running Title: NMR studies on an osteogenesis imperfecta mutation in collagen disease Address

Lawson, Catherine L.

110

Analysis of the gas phase reactivity of chlorosilanes.  

PubMed

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

Ravasio, Stefano; Masi, Maurizio; Cavallotti, Carlo

2013-06-27

111

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.

112

Group 3 LEA protein model peptides protect liposomes during desiccation.  

PubMed

We investigated whether a model peptide for group 3 LEA (G3LEA) proteins we developed in previous studies can protect liposomes from desiccation damage. Four different peptides were compared: 1) PvLEA-22, which consists of two tandem repeats of the 11-mer motif characteristic of LEA proteins from the African sleeping chironomid; 2) a peptide with amino acid composition identical to that of PvLEA-22, but with its sequence scrambled; 3) poly-l-glutamic acid; and 4) poly-l-lysine. Peptides 1) and 2) protected liposomes composed of 1-palmitoyl 2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) against fusion caused by desiccation, as revealed by particle size distribution measurements with dynamic light scattering. Indeed, liposomes maintain their pre-stress size distribution when these peptides are added at a peptide/POPC molar ratio of more than 0.5. Interestingly, peptide 1) achieved the comparable or higher retention of a fluorescent probe inside liposomes than did several native LEA proteins published previously. In contrast, the other peptides exhibited less protective effects. These results demonstrate that the synthetic peptide derived from the G3LEA protein sequence can suppress desiccation-induced liposome fusion. Fourier transform infrared (FT-IR) spectroscopic measurements were performed for the dried mixture of each peptide and liposome. Based on results for the gel-to-liquid crystalline phase transition temperature of the liposome and the secondary structure of the peptide backbone, we discuss possible underlying mechanisms for the protection effect of the synthetic peptide on dried liposomes. PMID:25037007

Furuki, Takao; Sakurai, Minoru

2014-11-01

113

Photodissociation pathways of gas-phase photoactive yellow protein chromophores  

NASA Astrophysics Data System (ADS)

The absorption dynamics of two model chromophores of the photoactive yellow protein were studied in gas-phase experiments. Using different time-resolving techniques with an overall sensitivity ranging from seconds down to a few nanoseconds, complex dynamics were revealed for the p -coumaric acid anion, involving both fragmentation and electron detachment as possible photoresponse channels. For the trans-thiophenyl- p -coumarate model, despite its more complex molecular structure, simpler decay dynamics showing only fragmentation were observed.

Lammich, Lutz; Rajput, Jyoti; Andersen, Lars H.

2008-11-01

114

Information-driven modeling of protein-Peptide complexes.  

PubMed

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

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

2015-01-01

115

Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model  

E-print Network

Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model Marc new potent, non-toxic compounds to treat bacterial infections. Antimicrobial peptides (AMPs active peptides but also to assess its antimicrobial potency. The physicochemical properties considered

Pompeu Fabra, Universitat

116

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

NASA Astrophysics Data System (ADS)

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

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

2004-05-01

117

Conformational transitions in model silk peptides.  

PubMed Central

Protein structural transitions and beta-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 beta-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 beta-sheet form, were characterized using Fourier transform infrared spectroscopy, circular dichroism, and electron diffraction. Polymorphs resembling the silk I, silk II (beta-sheet), and silk III (threefold polyglycine II-like helix) crystal structures were identified for the peptide fibroin C (GAGAGS repetitive sequence). Two peptides based on silk amorphous sequences, fibroin A (GAGAGY) and fibroin V (GDVGGAGATGGS), crystallized as silk I under most conditions. Methanol treatment of fibroin A resulted in a gradual transition from silk I to silk II, with an intermediate state involving a high proportion of beta-turns. Attenuated total reflectance Fourier transform infrared spectroscopy has been used to observe conformational changes as the peptides adsorb from solution onto a hydrophobic surface. Fibroin C has a beta-strand structure in solution but adopts a silk I-like structure upon adsorption, which when dried on the ZnSe crystal contains silk III crystallites. PMID:10777765

Wilson, D; Valluzzi, R; Kaplan, D

2000-01-01

118

Structure and Dynamics of Oligonucleotides in the Gas Phase.  

PubMed

By combining ion-mobility mass spectrometry experiments with sub-millisecond classical and ab initio molecular dynamics we fully characterized, for the first time, the dynamic ensemble of a model nucleic acid in the gas phase under electrospray ionization conditions. The studied oligonucleotide unfolds upon vaporization, loses memory of the solution structure, and explores true gas-phase conformational space. Contrary to our original expectations, the oligonucleotide shows very rich dynamics in three different timescales (multi-picosecond, nanosecond, and sub-millisecond). The shorter timescale dynamics has a quantum mechanical nature and leads to changes in the covalent structure, whereas the other two are of classical origin. Overall, this study suggests that a re-evaluation on our view of the physics of nucleic acids upon vaporization is needed. PMID:25417598

Arcella, Annalisa; Dreyer, Jens; Ippoliti, Emiliano; Ivani, Ivan; Portella, Guillem; Gabelica, Valérie; Carloni, Paolo; Orozco, Modesto

2014-11-21

119

Gas-phase Californium ion chemistry  

Microsoft Academic Search

The gas-phase chemistry of Cf+ was examined, this now being the heaviest element with which such studies have been performed. The emphasis was on the efficiency of dehydrogenation of alkenes by naked Cf+; direct comparison was made between the reactivities of Cf+ and those of Cm+, Pr+, and Tm+. The results with alkenes indicated that Cf+ is inefficient at C?H

John K. Gibson; Richard G. Haire

2000-01-01

120

A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation  

PubMed Central

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

Kang, Myungshim

2010-01-01

121

NMR-derived model for a peptide-antibody complex  

SciTech Connect

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.

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

1990-10-01

122

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)

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.

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

2013-09-01

123

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

PubMed

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

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

2013-09-21

124

Definition of the peptide binding motif within DRB1*1401 restricted epitopes by peptide competition and structural modeling  

PubMed Central

This study identified the peptide-binding motif of HLA-DRB1*1401 (DR1401). First, peptides containing DR1401 restricted epitopes were identified using tetramer guided epitope mapping. Among these, an influenza B peptide was selected for the motif study. After confirming the binding register for this peptide using a set of arginine substitutions, binding affinities were determined for 33 peptides derived from this influenza B sequence with single amino acid substitutions. The DR1401 peptide binding motif was deduced from the relative binding affinities of these peptides and confirmed by structural modeling. Pocket 1 demonstrated a preference for aliphatic anchor residues and methionine. Pocket 4 accommodated methionine and aliphatic residues, but also allowed some polar and charged amino acids. Pocket 6 preferred basic residues but also allowed some polar and aliphatic amino acids. Pocket 9 preferred aliphatic and aromatic amino acids and tolerated some polar residues but excluded all charged residues. Together these preferences define a distinct set of peptides that can be presented by DR1401. The resulting motif was used to verify T cell epitopes within the novel antigenic peptides identified by tetramer guided epitope mapping and within peptides from published reports that contain putative DR1401 epitopes. PMID:18276010

James, Eddie A.; Moustakas, Antonis K.; Berger, DeAnna; Huston, Laurie; Papadopoulos, George K.; Kwok, William W.

2009-01-01

125

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

NASA Astrophysics Data System (ADS)

This paper presents a global sensitivity and uncertainty analyses of the chlorine chemistry included in the Model of Aqueous, Gaseous and Interfacial Chemistry (MAGIC). Uncertainty ranges are established for input parameters (e.g. chemical rate constants, Henry's law constants, etc.) and are used in conjunction with Latin hypercube sampling and multiple linear regression to conduct a sensitivity analysis which determines the correlation between each input parameter and the model output. The contribution of each input parameter to the uncertainty in the model output is calculated by combining the results of the sensitivity analysis with the input parameters' uncertainty ranges. The peak concentration of molecular chlorine, [Cl 2(g)] peak, is used to compare model runs since MAGIC has demonstrated previously the importance of an interfacial reaction between OH (g) and Cl -(aq,surface) in the production of Cl 2(g). Results indicate that the interface reaction rate is most strongly correlated with [Cl 2(g)] peak and is most responsible for the uncertainty in MAGIC's ability to calculate precisely [Cl 2(g)] peak. In addition, the mass accommodation coefficient for OH and the aqueous-phase reaction rate for Cl 2 + OH - ? HOCl + Cl - and 2CO 3- + O 2 + 2H 2O ? 2CO 2·H 2O + 2O 2- also contribute significantly to the uncertainty in [Cl 2(g)] peak.

Nissenson, Paul; Thomas, Jennie L.; Finlayson-Pitts, Barbara J.; Dabdub, Donald

126

Gas-Phase Photoionization Of A Protein  

NASA Astrophysics Data System (ADS)

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

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

2010-07-01

127

Sidechain conformational dependence of hydrogen exchange in model peptides.  

PubMed

Peptide hydrogens that are exposed to solvent in protein X-ray structures exhibit a billion-fold range in hydroxide-catalyzed exchange rates, and these rates have previously been shown to be predictable by continuum dielectric methods to within a factor of 7, based on single protein conformations. When using a protein coil library to model the Boltzmann-weighted conformational distribution for the various N-acetyl-[X-Ala]-N-methylamides and N-acetyl-[Ala-Y]-N-methylamides, the acidity of the central amide in the individual conformers of each peptide spans nearly a million-fold range. Nevertheless, population averaging of these conformer acidities predicts the standard sidechain-dependent hydrogen exchange correction factors for nonpolar model peptides to within a factor of 30% (10(0.11)) with a correlation coefficient r=0.91. Comparison with the analogous continuum dielectric calculations for the other N-acetyl-[X-Y]-N-methylamides indicates that deviations from the isolated residue hypothesis of classical polymer theory predict appreciable errors in the exchange rates for conformationally disordered peptides when the standard sidechain-dependent hydrogen exchange rate correction factors are assumed to be independently additive. Although electronic polarizability generally dominates the dielectric shielding for the approximately 10ps lifetime of peptide ionization, evidence is presented for modest contributions from rapid intrarotamer conformational reorganization of Asn and Gln sidechains. PMID:20627534

Anderson, Janet S; Hernández, Griselda; LeMaster, David M

2010-09-01

128

Atomistic simulations of materials for optical chemical sensors: DFT-D calculations of molecular interactions between gas-phase analyte molecules and simple substrate models.  

PubMed

The structures of complexes of some small molecules (formaldehyde, acetaldehyde, ammonia, methylamine, methanol, ethanol, acetone, benzene, acetonitrile, ethyl acetate, chloroform, and tetrahydrofuran, considered as possible analytes) with ethylbenzene and silanol (C(6)H(5)C(2)H(5) and SiH(3)OH, considered as models of polystyrene and silica gel substrates) and with acridine (C(13)H(9)N, considered as a model of an indicator dye molecule of the acridine series) and the corresponding interaction energies have been calculated using the DFT-D approximation. The PBE exchange-correlation potential was used in the calculations. The structures of complexes between the analyte and the substrate were determined by optimizing their ground-state geometry using the SVP split-valence double-zeta plus polarization basis set. The complex formation energies were refined by single-point calculations at the calculated equilibrium geometries using the sufficiently large triple-zeta TZVPP basis set. The calculated interaction energies are used to assess the possibility of using dyes of the acridine series adsorbed on a polystyrene or silica substrate for detecting the small molecules listed above. PMID:21080019

Safonov, Andrey A; Rykova, Elena A; Bagaturyants, Alexander A; Sazhnikov, Vyacheslav A; Alfimov, Michael V

2011-08-01

129

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

PubMed

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

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

2015-04-15

130

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

131

Concurrent display of both ?- and ?-turns in a model peptide.  

PubMed

This article describes a model peptide that concurrently displays both ?- and ?-turns, as demonstrated by structural investigations using single crystal X-ray crystallography and solution-state NMR studies. The motif reported herein has the potential for the design of novel conformationally ordered synthetic oligomers with structural architectures distinct from those classically observed. PMID:21720634

Srinivas, Deekonda; Vijayadas, Kuruppanthara N; Gonnade, Rajesh; Phalgune, Usha D; Rajamohanan, Pattuparambil R; Sanjayan, Gangadhar J

2011-08-21

132

Concentration dependence of hydration water in a model peptide.  

PubMed

The molecular dynamics of aqueous solutions of a model amphiphilic peptide is studied as a function of concentration by broad-band light scattering experiments. Similarly to protein aqueous solutions, a considerable retardation, of about a factor 6-8, of hydration water dynamics with respect to bulk water is found, showing a slight dependence on solute concentration. Conversely, the average number of water molecules perturbed by the presence of peptide, i.e. the hydration number, appears to be strongly modified by adding solute. Its behaviour, decreasing upon increasing concentration, can be interpreted considering the random close-to-contact condition experienced by solute particles. Overall, the present findings support the view of a "long range" effect of peptides on the surrounding water, extending beyond the first two hydration shells. PMID:24829171

Comez, Lucia; Perticaroli, Stefania; Paolantoni, Marco; Sassi, Paola; Corezzi, Silvia; Morresi, Assunta; Fioretto, Daniele

2014-06-28

133

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

PubMed

Reliable modeling of protein and peptide circular dichroism (CD) spectra in the far UV presents a challenge for current theoretical approaches. In this study, the time-dependent density functional theory (TDDFT), configuration interaction with single excitation (CIS), and transition dipole coupling (TDC) were used to assess the most important factors contributing to the CD spectra of the ?-helical secondary structure. The dependence on the peptide chain length and also the role of the flexibility and solvent environment were investigated with a model oligopeptide Ac-(Ala)(N)-NH-Me, (N = 1, ..., 18). Both the TDDFT and TDC-like methods suggest that the CD curve typical for the ?-helix arises gradually, but its basic characteristic is discernible already for peptides with 4-5 amino acid residues. The calculated dependence was in a qualitative agreement with experimental spectra of short ?-helices stabilized by the histidine-metal binding. The TDDFT computations of the CD were found to be unusually sensitive to the basis set and solvent model. Explicit hydration and temperature fluctuations of the peptide geometry, simulated with the aid of molecular dynamics (MD), significantly influenced the CD and absorption spectral shapes. An extensive averaging over MD configurations is thus required to obtain a converged spectral profile in cluster simulations. On the other hand, both the TDDFT and TDC models indicate only a minor influence of the alanine side chains. The CIS and TDC calculations also point toward a relatively small effect of the helix-helix interaction on the CD spectral profiles. For a model system of two helices, the CIS method predicted larger changes in the spectra than TDC. This suggests other than interactions between peptide chains, such as mutual polarization, can have a minor, but measurable, effect on the CD spectrum. PMID:21322543

Kaminský, Jakub; Kubelka, Jan; Bour, Petr

2011-03-10

134

Enantioselectivity in gas-phase ion-molecule reactions  

NASA Astrophysics Data System (ADS)

Comprehensive understanding of information transfer between chiral molecules in living systems and in supramolecular assemblies requires the quantitative determination of the intrinsic short-range forces controlling enantioselectivity in simplified models, such as diastereomeric ion-molecule complexes in the isolated state. This review article describes the state-of-art in this field. Emphasis is put on the generation of diastereomeric ion-molecule aggregates in the gas phase and the determination of their relative stability and reactivity by mass spectrometric and radiolytic techniques.

Speranza, Maurizio

2004-04-01

135

Gas phase thermochemistry of organogermanium compounds  

SciTech Connect

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.

Engel, J.P.

1993-12-07

136

Learning Peptide-Spectrum Alignment Models for Tandem Mass Spectrometry  

PubMed Central

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

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

2014-01-01

137

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

PubMed

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

Fierabracci, A

2011-01-01

138

UV Damage of Collagen: Insights from Model Collagen Peptides  

PubMed Central

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

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

2012-01-01

139

Combinatorial discovery of peptide dendrimer enzyme models hydrolyzing isobutyryl fluorescein.  

PubMed

Two 6750-membered one-bead-one-compound peptide dendrimer combinatorial libraries L (X(4))(8)(LysX(3))(4)(LysX(2))(2)LysX(1) (X(1-4) = 14 different amino acids or deletion, Lys = branching lysine residue) and AcL (with N-terminal acetylation) were prepared by split-and-mix solid phase peptide synthesis. Screening toward fluorogenic substrates for esterase and aldolase activities using the in silica off-bead assay (N. Maillard et al., J. Comb. Chem. 2009, 11, 667-675) and bead decoding by amino acid analysis revealed histidine containing sequences active against fluorescein diacetate. Isobutyryl fluorescein, a related hydrophobic fluorogenic substrate, was preferentially hydrolyzed by dendrimers from library AcL containing hydrophobic residues such as AcH3 (AcHis)(8)(LysLeu)(4)(LysVal)(2)LysLysOH, compared to simple oligohistidine peptides as reference catalysts. Polycationic dendrimers from library L with multiple free N-termini such as H8 (His)(8)(Lys?Ala)(4)(LysThr)(2)LysaProNH(2) (aPro = (2S,4S)-4-aminoproline) showed stronger reactivity toward 8-acetoxypyrene-1,3,6-trisulfonate with partial acylation of N-termini. These experiments highlight the role of noncatalytic amino acids to determine substrate selectivity in peptide dendrimer esterase models. PMID:21438622

Maillard, Noélie; Biswas, Rasomoy; Darbre, Tamis; Reymond, Jean-Louis

2011-05-01

140

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

E-print Network

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 ...

Rädler, Joachim

141

Gas phase hyper-Rayleigh scattering measurements  

NASA Astrophysics Data System (ADS)

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.

Shelton, David P.

2012-07-01

142

Analysis of Ni nanoparticle gas phase sintering  

NASA Astrophysics Data System (ADS)

The sintering of Ni nanoparticle agglomerates in the gas phase is studied. The partially or completely sintered agglomerates are characterized in flight by in situ electrical mobility measurement and after their deposition by transmission electron microscopy. The mobility diameter, the mean primary particle diameter, and the total surface area of the agglomerates are determined as functions of the sintering temperature. The experimental results are analyzed using an empirical law for the primary particle coarsening as well as by means of a modified Koch-Friedlander theory. It turns out that the activation energy for the dominating diffusion process is Ea=0.6eV/atom , which is characteristic for surface diffusion in Ni. Our analysis provides a consistent picture with respect to both the temperature dependence of the characteristic sintering time and the mean diffusion length.

Tsyganov, Sergej; Kästner, Jochen; Rellinghaus, Bernd; Kauffeldt, Thomas; Westerhoff, Frank; Wolf, Dietrich

2007-01-01

143

Gas-phase thermochemistry of chloropyridines  

NASA Astrophysics Data System (ADS)

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

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

2005-04-01

144

Peptide neuromodulation in invertebrate model systems  

PubMed Central

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

Taghert, Paul H.; Nitabach, Michael N.

2012-01-01

145

Coarse-Grained Modeling of Peptidic/PDMS Triblock Morphology.  

PubMed

The morphology and chain packing structures in block copolymers strongly impact their mechanical response; therefore, to design and develop high performance materials that utilize block copolymers, it is imperative to have an understanding of their self-assembly behavior. In this research, we utilize coarse-grained (CG) molecular dynamics to study the effects of peptidic volume fraction and secondary structure on the morphological development and chain assembly of the triblocks poly(?-benzyl-l-glutamate)-b-poly(dimethylsiloxane)-b-poly(?-benzyl-l-glutamate) (GSG) and poly(dimethylsiloxane)-b-poly(?-benzyl-l-glutamate)-b-poly(dimethylsiloxane) (SGS). This necessitated developing a complete coarse-grained parameter set for poly(dimethylsiloxane) that closely captures the radial pair distribution of a united atom model and the experimental density at 300 K. These parameters are combined with the MARTINI amino acid CG force field and validated against prior reported values of domain spacing and peptide chain packing for GSG. The combined CG parameter set is then used to model SGS, a triblock currently in development for nature-inspired mechanically enhanced hybrid materials. The results reveal that the peptide side chain strongly influences the final morphology. For instance, lamellar or hexagonally packed cylindrical domain formation can result from the variation in side-chain interactions, namely, side-chain sterics preventing curved interface formation by increasing interfacial free volume. Ultimately, this research lays the foundation for future studies involving systems with dispersity, mixtures of secondary structures, and larger multiblock copolymers, such as polyurethanes and polyureas. PMID:25394880

Johnson, J Casey; Korley, LaShanda T J; Tsige, Mesfin

2014-11-26

146

Uncertainties in gas-phase atmospheric iodine chemistry  

NASA Astrophysics Data System (ADS)

We present a comprehensive chemical mechanism for gas-phase iodine, to be used for modelling tropospheric chemistry. The mechanism has been compiled from evaluated data and individual literature studies, where available; a number of key processes have not been studied experimentally or theoretically and in these cases estimations have been made. The uncertainty associated with these assumptions is evaluated. We analyze the mechanism using a box-model under a variety of boundary layer scenarios - representative of environments where iodine species have been observed - to study the response of the chemical system to changes in the kinetic parameters of selected reactions. We focus in particular on key species such as IO, OIO, INO3 and I2Oy and the impact of iodine chemistry on ozone formation and HOx levels. The results indicate that the chemical system is most sensitive to reactions leading to comparatively stable iodine compounds, which should be a focus of future laboratory studies.

Sommariva, R.; Bloss, W. J.; von Glasow, R.

2012-09-01

147

A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism.  

PubMed

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

Oslund, Rob C; Kee, Jung-Min; Couvillon, Anthony D; Bhatia, Vivek N; Perlman, David H; Muir, Tom W

2014-09-17

148

Transferring pharmaceuticals into the gas phase  

NASA Astrophysics Data System (ADS)

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.

Christen, Wolfgang; Krause, Tim; Rademann, Klaus

2008-11-01

149

Modeling of mixed-mode chromatography of peptides.  

PubMed

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

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

2013-03-29

150

Optical properties of anthocyanins in the gas phase  

NASA Astrophysics Data System (ADS)

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

Ge, Xiaochuan; Calzolari, Arrigo; Baroni, Stefano

2015-01-01

151

Uncertainty and sensitivity analysis of gas-phase chemistry in a CHF3 plasma  

NASA Astrophysics Data System (ADS)

A global uncertainty and sensitivity analysis is performed for a detailed gas-phase reaction set in a CHF3 plasma. The goal of this paper is to ascertain the uncertainties in plasma reactor model results (plasma and radical densities) that originate from the uncertainties in the gas-phase chemistry database. We discuss the rates of reactions and their uncertainties. Comparisons with experimental data show that gas-phase rate uncertainties do not explain the disagreements at higher pressures (>30 mTorr). We also find that electron impact dissociation reactions of dominant neutrals are the largest sources of uncertainties. HF kinetics are also found to be critical in determining radical and feedstock gas densities. Relative ion densities are uncertain due to poor understanding of charge transfer mechanisms.

Bose, Deepak; Rao, M. V. V. S.; Govindan, T. R.; Meyyappan, M.

2003-05-01

152

Gas-phase infrared spectroscopy of the protonated dipeptides H+PheAla and H+AlaPhe compared to condensed-phase results  

NASA Astrophysics Data System (ADS)

The influence of the physical environment on the structures of biomolecules is considered here for the dipeptide model H+AlaPhe cation, by making use of infrared multiple-photon dissociation (IRMPD) spectroscopy complemented by DFT calculations. The gas-phase structures of this peptide are also compared to the related peptide cations H+PheAla and H+AlaAla. The gas-phase IRMPD spectra of the Phe-containing cations are compared to previous studies, including the X-ray-crystallographic crystal structure for the H+AlaPheCl-.2H2O salt, a recent IRMPD spectrum of H+AlaAla, and a recent determination of the IR absorption spectrum of the H+AlaPheCl- salt in a liquid-crystal host matrix, as well as recent cryogenic ion trap results for H+TyrAla and H+AlaTyr. Between the gas-phase H+AlaPhe ion and the H+AlaPheCl-.2H2O crystal a conformational switch is observed, induced by hydrogen bonding with a water of crystallization, involving a 180° rotation of the COOH group. The hoped-for comparison of the gas-phase IR spectra with the liquid-crystal matrix IR spectrum was frustrated, because the literature matrix spectrum seems most likely to be that of a protonated homodimer of the dipeptide rather than the protonated monomer. The IRMPD spectra of H+AlaPhe and H+PheAla are very similar, with only minor peak shifts suggesting small differences in local interactions within a similar overall architecture. The H+AlaAla spectrum was also similar, and no significant reorganization of the structure seems to result from the presence or position of the aromatic ring. The spectra give highly satisfactory matches to the predicted IR spectra computed for the most stable conformers of the protonated dipeptides. It is suggested that the NH3+ proton is shared through hydrogen bonding to the amide CO, giving a distinctive broadening of the associated H-bending mode.

Dunbar, Robert C.; Steill, Jeffrey D.; Polfer, Nick C.; Oomens, Jos

2009-06-01

153

Dynamics of the gas phase in a fuel-rod assembly simulator with a spacing grid  

NASA Astrophysics Data System (ADS)

An experimental study of two-phase flow in a model of assembly of 37 fuel rods in a triangular arrangement was performed. Measurements were performed with local gas supply through a unit nozzle. Distributions of the local void fraction were obtained at various values of angular coordinate and distance from a spacing grid. It was shown that most of the gas phase moves in a space produced by the walls of three nearby rods. A significant increase of gas phase concentration takes place in the flow region just after the grid.

Kashinsky, O. N.; Lobanov, P. D.; Kurdyumov, A. S.; Pribaturin, N. A.; Volkov, S. E.

2013-07-01

154

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

E-print Network

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.

Bharat K. Sharma; Subrata Pal

2010-01-14

155

Prediction of antimicrobial activity of synthetic peptides by a decision tree model.  

PubMed

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

Lira, Felipe; Perez, Pedro S; Baranauskas, José A; Nozawa, Sérgio R

2013-05-01

156

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

PubMed Central

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

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

2013-01-01

157

Peptide immunotherapy in models of allergic airways disease   

E-print Network

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

MacKenzie, Karen Joan

2011-11-25

158

Modeling the electrophoresis of highly charged peptides: application to oligolysines.  

PubMed

The "coarse-grained" bead modeling methodology, BMM, is generalized to treat electrostatics at the level of the nonlinear Poisson-Boltzmann equation. This improvement makes it more applicable to the important class of highly charged macroions and highly charged peptides in particular. In the present study, the new nonlinear Poisson-Boltzmann, NLPB-BMM procedure is applied to the free solution electrophoretic mobility of low molecular mass oligolysines (degree of polymerization 1-8) in lithium phosphate buffer at pH 2.5. The ionic strength is varied from 0.01 to 0.10?M) and the temperature is varied from 25 to 50°C. In order to obtain quantitative agreement between modeling and experiment, a small amount of specific phosphate binding must be included in modeling. This binding is predicted to increase with increasing temperature and ionic strength. PMID:22282417

Wu, Hengfu; Allison, Stuart A; Perrin, Catherine; Cottet, Herve

2012-02-01

159

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

SciTech Connect

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.

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

2005-09-01

160

Gas phase reaction of sulfur trioxide with water vapor  

Microsoft Academic Search

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

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

1994-01-01

161

The gas phase oxidation of elemental mercury by ozone  

Microsoft Academic Search

The gas phase reaction between elemental mercury (Hg0) and ozone (03) has been studied in sunlight, in darkness, at different temperatures, and different surface-to-volume (s\\/v) ratios. At 03 concentrations above 20 ppm, a loss of Hg0 and a simultaneous formation of oxidized mercury (Hg(II)) was observed. The results suggest a partly heterogeneous reaction, with a gas phase rate constant of

B. Hall

1995-01-01

162

Detection of peptide-binding sites on protein surfaces: The first step towards the modeling and targeting of peptide-mediated interactions  

PubMed Central

Peptide-mediated interactions, in which a short linear motif binds to a globular domain, play major roles in cellular regulation. An accurate structural model of this type of interaction is an excellent starting point for the characterization of the binding specificity of a given peptide-binding domain. A number of different protocols have recently been proposed for the accurate modeling of peptide-protein complex structures, given the structure of the protein receptor and the binding site on its surface. When no information about the peptide binding site(s) is a priori available, there is a need for new approaches to locate peptide-binding sites on the protein surface. While several approaches have been proposed for the general identification of ligand binding sites, peptides show very specific binding characteristics, and therefore, there is a need for robust and accurate approaches that are optimized for the prediction of peptide-binding sites. Here we present PeptiMap, a protocol for the accurate mapping of peptide binding sites on protein structures. Our method is based on experimental evidence that peptide-binding sites also bind small organic molecules of various shapes and polarity. Using an adaptation of ab initio ligand binding site prediction based on fragment mapping (FTmap), we optimize a protocol that specifically takes into account peptide binding site characteristics. In a high-quality curated set of peptide-protein complex structures PeptiMap identifies for most the accurate site of peptide binding among the top ranked predictions. We anticipate that this protocol will significantly increase the number of accurate structural models of peptide-mediated interactions. PMID:24123488

Lavi, Assaf; Ngan, Chi Ho; Movshovitz-Attias, Dana; Bohnuud, Tanggis; Yueh, Christine; Beglov, Dmitri; Schueler-Furman, Ora; Kozakov, Dima

2013-01-01

163

Charge conductivity in peptides: Dynamic simulations of a bifunctional model supporting experimental data  

E-print Network

Charge conductivity in peptides: Dynamic simulations of a bifunctional model supporting previous finding and the given mechanism of charge and electron transfer in polypeptides are here integrated in a bifunc- tional model involving electronic charge transfer coupled to special internal

Sheu, Sheh-Yi

164

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

PubMed

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

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

2013-11-26

165

Intra-and Intermolecular Effects on 1 H Chemical Shifts in a Silk Model Peptide  

E-print Network

Intra- and Intermolecular Effects on 1 H Chemical Shifts in a Silk Model Peptide Determined by High peptide (Ala-Gly)15 for the crystalline domain of Bombyx mori silk fibroin in silk I and silk II structures, including a treatment of both intra- and intermolecular arrangements. Silk I and silk II

Williamson, Mike P.

166

Vasoactive intestinal peptide mRNA and immunoreactivity are decreased in fetal alcohol syndrome model  

Microsoft Academic Search

Vasoactive intestinal peptide (VIP) regulates growth in the early post-implantation embryo. Previous work has demonstrated that peptide agonists (SALLRSIPA and NAPVSIPQ) from downstream mediators that are regulated by VIP were able to prevent the alcohol-induced fetal death, growth restriction and microcephaly associated with fetal alcohol syndrome. Here we evaluated the role of VIP in this mouse model of fetal alcohol

Catherine Y Spong; Jonathan Auth; Joy Vink; Katie Goodwin; Daniel T Abebe; Joanna M Hill; Douglas E Brenneman

2002-01-01

167

Theoretical and Numerical Studies of Noncontinuum Gas-Phase Heat Conduction in Micro\\/Nano Devices  

Microsoft Academic Search

This article presents a comprehensive study of various modeling techniques for noncontinuum gas-phase heat conduction encountered in micro\\/nano devices over a broad range of Knudsen number. A new slip model is proposed for slip flows and an analytical approach is developed for collisionless steady-state heat conduction inside a fully diffuse enclosure. Excellent agreements with direct simulation Monte Carlo (DSMC) simulations

Taishan Zhu; Wenjing Ye

2010-01-01

168

Surface plasmon sensing of gas phase contaminants using optical fiber.  

SciTech Connect

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.

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

2009-10-01

169

Engine exhaust particulate and gas phase contributions to vascular toxicity.  

PubMed

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

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

2014-05-01

170

Estimation of gas phase mixing in packed beds  

SciTech Connect

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

Frigerio, S. [CMIC Dipartimento di Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan (Italy); Thunman, H.; Leckner, B.; Hermansson, S. [Department of Energy Conversion, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)

2008-04-15

171

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

E-print Network

A Variational Model for Oligomer-Formation Process of GNNQQNY Peptide from Yeast Prion Protein Sup, the peptide GNNQQNY from yeast prion protein Sup35. By examining the free energy surface, we identified

Zhang, Yang

172

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

SciTech Connect

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

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

2009-02-01

173

Partitioning of semivolatile surface-active compounds between bulk, surface and gas phase  

NASA Astrophysics Data System (ADS)

We present a model study demonstrating that surface partitioning of volatile surfactants enhances their uptake by submicron liquid droplets. In submicron-sized droplets, surface partitioning of a surface-active volatile species may significantly decrease its equilibrium partial pressure, thus increasing the total flux of the surfactant from gas phase to aqueous phase. Such uptake of volatile organic species into aqueous aerosols can be followed by aqueous-phase chemistry to form low-volatility secondary organic aerosol material, leading to increased aerosol mass. In the study, we used an air parcel model that includes simplified aqueous- and gas-phase chemistry, condensation/evaporation, and a model of aqueous-phase thermodynamics that takes into account the partitioning of surfactants between the bulk and surface phases. We modeled the uptake and aqueous-phase chemical reactions of methylglyoxal, as it is a moderate surfactant that forms less volatile secondary organic material via aqueous-phase chemical reactions with the hydroxyl radical as well as hydronium and ammonium ions. Our model simulations show an order of magnitude higher uptake of methylglyoxal in aqueous aerosols of cloud condensation nuclei sizes (less than 200 nm in radius) when surface partitioning is taken into account, compared to when surface partitioning is neglected. As a consequence, the production of SOA through the aqueous-phase chemical processing of methylglyoxal is also enhanced, but to a lesser degree, because condensation of the hydroxyl radical from gas phase limits the production.

Romakkaniemi, S.; Kokkola, H.; Smith, J. N.; Prisle, N. L.; Schwier, A. N.; McNeill, V. F.; Laaksonen, A.

2011-02-01

174

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

SciTech Connect

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.

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

2013-09-30

175

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

NASA Technical Reports Server (NTRS)

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

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

1995-01-01

176

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

PubMed

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. PMID:24399766

Bouchoux, Guy

2014-01-01

177

Correlated inflammatory responses and neurodegeneration in peptide-injected animal models of Alzheimer's disease.  

PubMed

Animal models of Alzheimer's disease (AD) which emphasize activation of microglia may have particular utility in correlating proinflammatory activity with neurodegeneration. This paper reviews injection of amyloid- ? (A ? ) into rat brain as an alternative AD animal model to the use of transgenic animals. In particular, intrahippocampal injection of A? 1-42 peptide demonstrates prominent microglial mobilization and activation accompanied by a significant loss of granule cell neurons. Furthermore, pharmacological inhibition of inflammatory reactivity is demonstrated by a broad spectrum of drugs with a common endpoint in conferring neuroprotection in peptide-injected animals. Peptide-injection models provide a focus on glial cell responses to direct peptide injection in rat brain and offer advantages in the study of the mechanisms underlying neuroinflammation in AD brain. PMID:24822221

McLarnon, James G

2014-01-01

178

Correlated Inflammatory Responses and Neurodegeneration in Peptide-Injected Animal Models of Alzheimer's Disease  

PubMed Central

Animal models of Alzheimer's disease (AD) which emphasize activation of microglia may have particular utility in correlating proinflammatory activity with neurodegeneration. This paper reviews injection of amyloid-? (A?) into rat brain as an alternative AD animal model to the use of transgenic animals. In particular, intrahippocampal injection of A?1-42 peptide demonstrates prominent microglial mobilization and activation accompanied by a significant loss of granule cell neurons. Furthermore, pharmacological inhibition of inflammatory reactivity is demonstrated by a broad spectrum of drugs with a common endpoint in conferring neuroprotection in peptide-injected animals. Peptide-injection models provide a focus on glial cell responses to direct peptide injection in rat brain and offer advantages in the study of the mechanisms underlying neuroinflammation in AD brain. PMID:24822221

McLarnon, James G.

2014-01-01

179

Gas-phase silicon micromachining with xenon difluoride  

Microsoft Academic Search

Xenon difluoride is a gas phase, room temperature, isotropic silicon etchant with extremely high selectivity to many materials commonly used in microelectromechancial systems, including photoresists, aluminum, and silicon dioxide. Using a simple vacuum system, the effects of etch aperture and loading were explored for etches between 10 and 200 micrometers . Etch rates as high as 40 micrometers \\/minute were

Floy I. Chang; Richard Yeh; Gisela Lin; Patrick B. Chu; Eric G. Hoffman; Ezekiel J. Kruglick; Kristofer S. Pister; Michael H. Hecht

1995-01-01

180

First measurements of gas phase sulphuric acid in the stratosphere  

Microsoft Academic Search

Measurements of the abundance of gas phase sulfuric acid in the stratosphere are reported. Compositions and abundances of stratospheric negative ions were observed at an altitude of 36.5 km, and the presence of species containing sulfuric acid molecules attached to HSO4(-) core ions was detected. A proposed reaction scheme suggests that the cores of these ions are formed by reactions

F. Arnold; R. Fabian

1980-01-01

181

Optically based diagnostics for gas-phase laser development  

Microsoft Academic Search

In this paper we describe several diagnostics that we have developed to assist the development of high power gas phase lasers including COIL, EOIL, and DPAL. For COIL we discuss systems that provide sensitive measurements of O2(a), small signal gain, iodine dissociation, and temperature. These are key operational parameters within COIL, and these diagnostics have been used world-wide to gain

Wilson T. Rawlins; Seonkyung Lee; Kristin L. Galbally-Kinney; William J. Kessler; Adam J. Hicks; Ian M. Konen; Emily P. Plumb; Steven J. Davis

2010-01-01

182

Thermal transformations of divinyl sulfone in the gas phase  

Microsoft Academic Search

The main products of the gas-phase pyrolysis (580–600°) of divinyl sulfone are SO2, acetylene, and ethylene; butadiene, benzene, toluene, isomeric xylenes, styrene, and benzothiophene are also formed in smaller amounts. In an H2S atmosphere the pyrolysis of divinyl sulfone is apparently accompanied by a partial reduction of the latter to divinyl sulfoxide.

M. G. Voronkov; É. N. Deryagina; É. N. Sukhomazova; V. Yu. Vitkovskii; N. K. Gusarova; B. A. Trofimov

1983-01-01

183

Selected examples of gas-phase ion chemistry studies.  

PubMed

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

Nibbering, Nico M M

2013-01-01

184

Selected Examples of Gas-Phase Ion Chemistry Studies  

PubMed Central

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

Nibbering, Nico M. M.

2013-01-01

185

Gas-Phase Combustion Synthesis of Nonoxide Nanoparticles in Microgravity  

NASA Technical Reports Server (NTRS)

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.

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

2001-01-01

186

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

NASA Astrophysics Data System (ADS)

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

Bapat, Parimal V.

187

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

PubMed

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

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

2013-07-12

188

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

PubMed Central

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

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

2011-01-01

189

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

190

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

PubMed

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

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

2014-10-21

191

Gas Phase Theoretical Kinetics for Astrochemistry  

NASA Astrophysics Data System (ADS)

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

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

2012-05-01

192

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

NASA Astrophysics Data System (ADS)

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

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

2012-07-01

193

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

SciTech Connect

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

Cole, Callie A.; Wehres, Nadine; Yang Zhibo; Thomsen, Ditte L.; Bierbaum, Veronica M. [Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, CO 80309-0215 (United States); Snow, Theodore P., E-mail: Callie.Cole@colorado.edu, E-mail: Nadine.Wehres@colorado.edu, E-mail: Zhibo.Yang@colorado.edu, E-mail: Veronica.Bierbaum@colorado.edu, E-mail: Theodore.Snow@colorado.edu, E-mail: dlt@chem.ku.dk [Center for Astrophysics and Space Astronomy, 389 UCB, University of Colorado, Boulder, CO 80309-0389 (United States)

2012-07-20

194

Carbonic anhydrase-inhibitor binding: From solution to the gas phase  

SciTech Connect

In this report, we compare the kinetic stabilities of noncovalent complexes between bovine carbonic anhydrase II(BCAII, EC 4.2.1.1) and para-substituted benzenesulfonamide inhibitors in the gas phase and in solution. These BCAII-inhibitor systems are attractive model systems due to the stability of carbonic anhydrase (CA) and its well characterized structure and ligand complexes, providing a basis for inferences regarding the protein structure in the gas phase and its ligand interactions. CA is a roughly spherical Zn(II) metalloenzyme having a conical binding pocket which catalyzes the hydration of CO{sub 2} to bicarbonate. A large body of data correlate structures of sulfonamide ligands with their binding constants to CA. A set of eight inhibitors was selected for this study, covering a wide range of binding affinities and varying in the length of their tails and aromatic content. The results demonstrate that relative stabilities of BCAII-inhibitor complexes differ substantially between the gas and liquid phases and also show the dominant role of polar surface interactions in the gas phase. 12 refs., 1 fig., 1 tab.

Wu, Q.; Bruce, J.E.; Smith, R.D. [Pacific Northwest National Lab., Richland, WA (United States)] [Pacific Northwest National Lab., Richland, WA (United States); Gao, J.; Joseph-McCarthy, D.; Sigal, G.B.; Whitesides, G.M. [Harvard Univ., Cambridge, MA (United States)] [Harvard Univ., Cambridge, MA (United States)

1997-02-05

195

Melittin peptides exhibit different activity on different cells and model membranes.  

PubMed

Melittin (MLT) is a lytic peptide with a broad spectrum of activity against both eukaryotic and prokaryotic cells. To understand the role of proline and the thiol group of cysteine in the cytolytic activity of MLT, native MLT and cysteine-containing analogs were prepared using solid phase peptide synthesis. The antimicrobial and cytolytic activities of the monomeric and dimeric MLT peptides against different cells and model membranes were investigated. The results indicated that the proline residue was necessary for antimicrobial activity and cytotoxicity and its absence significantly reduced lysis of model membranes and hemolysis. Although lytic activity against model membranes decreased for the MLT dimer, hemolytic activity was increased. The native peptide and the MLT-P14C monomer were mainly unstructured in buffer while the dimer adopted a helical conformation. In the presence of neutral and negatively charged vesicles, the helical content of the three peptides was significantly increased. The lytic activity, therefore, is not correlated to the secondary structure of the peptides and, more particularly, on the propensity to adopt helical conformation. PMID:25200682

Jamasbi, Elaheh; Batinovic, Steven; Sharples, Robyn A; Sani, Marc-Antoine; Robins-Browne, Roy Michael; Wade, John D; Separovic, Frances; Hossain, Mohammed Akhter

2014-12-01

196

Formation and Dissociation of Phosphorylated Peptide Radical Cations  

NASA Astrophysics Data System (ADS)

In this study, we generated phosphoserine- and phosphothreonine-containing peptide radical cations through low-energy collision-induced dissociation (CID) of the ternary metal-ligand phosphorylated peptide complexes [CuII(terpy) p M]·2+ and [CoIII(salen) p M]·+ [ p M: phosphorylated angiotensin III derivative; terpy: 2,2':6',2''-terpyridine; salen: N, N '-ethylenebis(salicylideneiminato)]. Subsequent CID of the phosphorylated peptide radical cations ( p M·+) revealed fascinating gas-phase radical chemistry, yielding (1) charge-directed b- and y-type product ions, (2) radical-driven product ions through cleavages of peptide backbones and side chains, and (3) different degrees of formation of [M - H3PO4]·+ species through phosphate ester bond cleavage. The CID spectra of the p M·+ species and their non-phosphorylated analogues featured fragment ions of similar sequence, suggesting that the phosphoryl group did not play a significant role in the fragmentation of the peptide backbone or side chain. The extent of neutral H3PO4 loss was influenced by the peptide sequence and the initial sites of the charge and radical. A preliminary density functional theory study, at the B3LYP 6-311++G(d,p) level of theory, of the neutral loss of H3PO4 from a prototypical model— N-acetylphosphorylserine methylamide—revealed several factors governing the elimination of neutral phosphoryl groups through charge- and radical-induced mechanisms.

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

2012-12-01

197

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

PubMed

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

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

2007-06-01

198

A model for the controlled assembly of semiconductor peptides  

NASA Astrophysics Data System (ADS)

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.

Kim, Se Hye; Parquette, Jon R.

2012-10-01

199

Hydration of Gas-Phase Ions Formed by Electrospray Ionization  

PubMed Central

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

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

2005-01-01

200

Measurement and speciation of gas phase peroxides in the atmosphere  

NASA Astrophysics Data System (ADS)

The utility of an improved gas phase sampler and a recently developed nonenzymatic measurement method for H2O2 and HOCH2OOH(HMHP) is demonstrated. The gas phase sampler is equipped with a surfaceless intake to alleviate heterogeneous loss of H2O2 in the sampling line. The nonenzymatic method employs the aqueous phase Fenton reaction for H2O2 measurement and is capable of speciation between H2O2 and HMHP, using a dual channel technique. By adding a third channel employing the well-established method of p-hydroxyphenylacetic acid and horseradish peroxidase for total peroxide measurement, it is possible to differentiate H2O2, HMHP, and other organic peroxides, if present. Preliminary data analysis indicates that the measured total peroxides range from 0.4 to about 6 ppbv, depending on meteorological conditions, and that organic peroxides, mostly HMHP, constitute between 20 and 80 percent of the total peroxides.

Lee, J. H.; Leahy, D. F.; Tang, I. N.; Newman, L.

1993-02-01

201

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

PubMed

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

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

2014-01-01

202

Gas phase fractionation method using porous ceramic membrane  

DOEpatents

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.

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

1996-01-01

203

Scale up of gas-phase chlorination reactors using CFD  

Microsoft Academic Search

Gas-phase chlorination of methyl chloride is an important industrial process producing widely applied chlorinated derivatives. Control over reactor stability and product distribution necessitates a thorough study of the strongly coupled turbulent flow and reaction processes in chlorination reactors. In this work, a hybrid finite-volume (FV)\\/transported probability density function (PDF) method is employed to analyze the performance of a coaxial jet-stirred

Ying Liu; V. Raman; R. O. Fox; A. D. Harvey

2004-01-01

204

Experimental study of gas phase titanium and aluminum oxide clusters  

Microsoft Academic Search

We present an experimental study of the vibrational properties of gas phase titanium oxide and aluminum oxide clusters. The titanium and aluminum oxide clusters have a stoichiometry of (Ti2O3) x-(TiO2)y (with (x, y) from (2, 4) to (11, 29)) and AlO-(Al2O3)n (5 <= n <= 70). The vibrational properties of the clusters are obtained using infrared resonance enhanced multi-photon ionization

K. Demyk; D. van Heijnsbergen; G. von Helden; G. Meijer

2004-01-01

205

Decay Pathways of Pyrimidine Bases: From Gas Phase to Solution  

Microsoft Academic Search

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

Wei Kong; Yonggang He; Chengyin Wu

206

Structure of triplex DNA in the gas phase.  

PubMed

Extensive (more than 90 microseconds) molecular dynamics simulations complemented with ion-mobility mass spectrometry experiments have been used to characterize the conformational ensemble of DNA triplexes in the gas phase. Our results suggest that the ensemble of DNA triplex structures in the gas phase is well-defined over the experimental time scale, with the three strands tightly bound, and for the most abundant charge states it samples conformations only slightly more compact than the solution structure. The degree of structural alteration is however very significant, mimicking that found in duplex and much larger than that suggested for G-quadruplexes. Our data strongly supports that the gas phase triplex maintains an excellent memory of the solution structure, well-preserved helicity, and a significant number of native contacts. Once again, a linear, flexible, and charged polymer as DNA surprises us for its ability to retain three-dimensional structure in the absence of solvent. Results argue against the generally assumed roles of the different physical interactions (solvent screening of phosphate repulsion, hydrophobic effect, and solvation of accessible polar groups) in modulating the stability of DNA structures. PMID:22420643

Arcella, Annalisa; Portella, Guillem; Ruiz, Maria Luz; Eritja, Ramon; Vilaseca, Marta; Gabelica, Valérie; Orozco, Modesto

2012-04-18

207

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

EPA Science Inventory

Gas Phase Selective Oxidation of Alcohols Using Light-Activated Titanium Dioxide and Molecular Oxygen Gas phase selective oxidations of various primary and secondary alcohols are studied in an indigenously built stainless steel up-flow photochemical reactor using ultravi...

208

Abeta peptide vaccination prevents memory loss in an animal model of Alzheimer's disease  

Microsoft Academic Search

Vaccinations with amyloid-beta peptide (AB) can dramatically reduce amyloid deposition in a transgenic mouse model of Alzheimer's disease. To determine if the vaccinations had deleterious or beneficial functional consequences, we tested eight months of Abeta vaccination in a different transgenic model for Alzheimer's disease in which mice develop learning deficits as amyloid accumulates . Here we show that vaccination with

Dave Morgan; David M. Diamond; Paul E. Gottschall; Kenneth E. Ugen; Chad Dickey; John Hardy; Karen Duff; Paul Jantzen; Giovanni DiCarlo; Donna Wilcock; Karen Connor; Jaime Hatcher; Caroline Hope; Marcia Gordon; Gary W. Arendash

2000-01-01

209

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)

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.

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

1992-01-01

210

Influence of Basic Residue Content on Fragment Ion Peak Intensities in Low-Energy Collision-Induced Dissociation Spectra of Peptides  

PubMed Central

The primary utility of trypsin digestion in proteomics is that it cleaves proteins at predictable locations, but it is also notable for yielding peptides that terminate in basic arginine and lysine residues. Tryptic peptides fragment in ion trap tandem mass spectrometry to produce prominent C-terminal y series ions. Alternative proteolytic digests may produce peptides that do not follow these rules. In this study, we examine 2568 peptides generated through proteinase K digestion, a technique that produces a greater diversity of basic residue content in peptides. We show that the position of basic residues within peptides influences the peak intensities of b and y series ions; a basic residue near the N-terminus of a peptide can lead to prominent b series peaks rather than the intense y series peaks associated with tryptic peptides. The effects of presence and position for arginine, lysine, and histidine are explored separately and in combination. Arg shows the most dominant effects followed by His and then by Lys. Fragment ions containing basic residues produce more intense peaks than those without basic residues. Doubly charged precursor ions have generally been modeled as producing only singly charged fragment ions, but fragment ions that contain two basic residues may accept both protons during fragmentation. By characterizing the influence of basic residues on gas-phase fragmentation of peptides, this research makes possible more accurate fragmentation models for peptide identification algorithms. PMID:14987077

Tabb, David L.; Huang, Yingying; Wysocki, Vicki H.; Yates, John R.

2010-01-01

211

Mass spectrometry of peptides and proteins Vicki H. Wysockia,*, Katheryn A. Resingb,*, Qingfen Zhanga  

E-print Network

. The current approaches being used for protein identification include top-down and bottom-up sequencing. Top-down introduced. Bottom-up sequencing, a traditional approach that fragments peptides in the gas phase after proteins and protein complexes [1], frag- ment ions produced by gas-phase activation of protein ions (top-down

Wysocki, Vicki H.

212

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

PubMed

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

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

2010-11-15

213

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

PubMed

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

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

2005-06-01

214

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

PubMed Central

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

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

2012-01-01

215

Dissecting the proline effect: dissociations of proline radicals formed by electron transfer to protonated Pro-Gly and Gly-Pro dipeptides in the gas phase.  

PubMed

We report a combined experimental and computational study of the proline effect in model dipeptides Pro-Gly and Gly-Pro. Gas-phase protonated peptide ions were discharged by glancing collisions with potassium or cesium atoms at 3 keV collision energies, and the peptide radical intermediates and their dissociation products were analyzed following collisional ionization to anions. The charge reversal (+CR-) mass spectra of (Pro-Gly + H)+(1a+) and (Gly-Pro + H)+ (2a+) showed dramatic differences and thus provided a sensitive probe of ion structure. Whereas 1a+ completely dissociated upon charge inversion, 2a+ gave a nondissociated anion as the most abundant product. Ab initio and density functional theory calculations provided structures and vertical recombination energies (REvert) for 1a+ and 2a+. The recombination energies, REvert = 3.07 and 3.36 eV for 1a+ and 2a+, respectively, were lower than the alkali metal ionization energies and indicated that the collisional electron transfer to the peptide ions was endoergic. Radical 1a* was found to exist in a very shallow local energy minimum, with transition state energies for loss and migration of H indicating very facile dissociation. In contrast, radical 2a* was calculated to spontaneously isomerize upon electron capture to a stable dihydroxycarbinyl isomer (2e*) that can undergo consecutive and competitive isomerizations by proline ring opening and intramolecular hydrogen atom transfers to yield stable radical isomers. Radical 2e* and its stable isomers were calculated to have substantial electron affinities and thus can form the stable anions that were observed in the +CR- mass spectra. The calculated TS energies and RRKM kinetic analysis indicated that peptide N-C alpha bond dissociations compete with pyrrolidine ring openings triggered by radical sites at both the N-terminal and C-terminal sides of the proline residue. Open-ring intermediates were found in which loss of an H atom was energetically preferred over backbone dissociations. This provided an explanation for the proline effect causing low incidence of electron capture dissociations of N-C alpha bonds adjacent to proline residues in tryptic peptides and also for some peculiar behavior of proline-containing protein cation-radicals. PMID:17550253

Hayakawa, Shigeo; Hashimoto, Mami; Matsubara, Hiroshi; Turecek, Frantisek

2007-06-27

216

Revision of the thermodynamics of the proton in gas phase.  

PubMed

Proton transfer is ubiquitous in various physical/chemical processes, and the accurate determination of the thermodynamic parameters of the proton in the gas phase is useful for understanding and describing such reactions. However, the thermodynamic parameters of such a proton are usually determined by assuming the proton as a classical particle whatever the temperature. The reason for such an assumption is that the entropy of the quantum proton is not always soluble analytically at all temperatures. Thereby, we addressed this matter using a robust and reliable self-consistent iterative procedure based on the Fermi-Dirac formalism. As a result, the free proton gas can be assumed to be classical for temperatures higher than 200 K. However, it is worth mentioning that quantum effects on the gas phase proton motion are really significant at low temperatures (T ? 120 K). Although the proton behaves as a classical particle at high temperatures, we strongly recommend the use of quantum results at all temperatures, for the integrated heat capacity and the Gibbs free energy change. Therefore, on the basis of the thermochemical convention that ignores the proton spin, we recommend the following revised values for the integrated heat capacity and the Gibbs free energy change of the proton in gas phase and, at the standard pressure (1 bar): ?H0?T = 6.1398 kJ mol(-1) and ?G0?T = -26.3424 kJ mol(-1). Finally, it is important noting that the little change of the pressure from 1 bar to 1 atm affects notably the entropy and the Gibbs free energy change of the proton. PMID:25338234

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

2014-11-20

217

A multiwatt all gas-phase iodine laser (AGIL)  

NASA Astrophysics Data System (ADS)

The demonstration and characterization of a multiwatt All Gas-phase Iodine Laser (AGIL) are described. A 20-cm subsonic reactor was used to produce NCl(a1?) for a series parametric studies of the I*(2P1/2) - I(2P3/2) small signal gain and extracted power dependence on reactant flow rates and reaction time. A reduction in the flow channel height led to improved performance. The highest measured gain was 4.2 x 10-4 cm-1 and the highest power observed was 31 W.

Manke, Gerald C., II; Cooper, Chris B.; Dass, Shiv C.; Madden, Timothy J.; Hager, Gordon D.

2004-05-01

218

A multiwatt all gas-phase iodine laser (AGIL)  

NASA Astrophysics Data System (ADS)

The demonstration and characterization of a multiwatt All Gas-phase Iodine Laser (AGIL) are described. A 20-cm subsonic reactor was used to produce NCl(a1?) for a series parametric studies of the I*(2P1/2) - I(2P3/2) small signal gain and extracted power dependence on reactant flow rates and reaction time. A reduction in the flow channel height led to improved performance. The highest measured gain was 4.2 x 10-4 cm-1 and the highest power observed was 31 W.

Manke, Gerald C., II; Cooper, Chris B.; Dass, Shiv C.; Madden, Timothy J.; Hager, Gordon D.

2004-09-01

219

Mulitwatt all gas-phase iodine laser (AGIL)  

NASA Astrophysics Data System (ADS)

The demonstration and characterization of a multi-watt All Gas-phase Iodine Laser (AGIL) are described. A 20-cm subsonic reactor was used to produce NCl(a1?) for a series of parametric studies of the I*(2P1/2)-I(2P3/2) small signal gain and extracted power dependence on reactant flow rates and reaction time. The highest measured gain was 2.5x10-4 cm-1 and the highest power observed was 18 W.

Manke, Gerald C., II; Cooper, Chris B.; Dass, Shiv C.; Madden, Timothy J.; Hager, Gordon D.

2003-06-01

220

What Determines the Activity of Antimicrobial and Cytolytic Peptides in Model Membranes†  

PubMed Central

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

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

2011-01-01

221

Comparative study of generalized born models: Born radii and peptide folding.  

PubMed

In this study, we have implemented four analytical generalized Born (GB) models and investigated their performance in conjunction with the GROMOS96 force field. The four models include that of Still and co-workers, the HCT model of Cramer, Truhlar, and co-workers, a modified form of the AGB model of Levy and co-workers, and the GBMV2 model of Brooks and co-workers. The models were coded independently and implemented in the GROMOS software package and in TINKER. They were compared in terms of their ability to reproduce the results of Poisson-Boltzmann (PB) calculations and in their performance in the ab initio peptide folding of two peptides, one that forms a beta-hairpin in solution and one that forms an alpha-helix. In agreement with previous work, the GBMV2 model is most successful in reproducing PB results while the other models tend to underestimate the effective Born radii of buried atoms. In contrast, stochastic dynamics simulations on the folding of the two peptides, the C-terminus beta-hairpin of the B1 domain of protein G and the alanine-based alpha-helical peptide 3K(I), suggest that the simpler GB models are more effective in sampling conformational space. Indeed, the Still model used in conjunction with the GROMOS96 force field is able to fold the hairpin peptide to a native-like structure without the benefit of enhanced sampling techniques. This is due in part to the properties of the united-atom GROMOS96 force field which appears to be more flexible, and hence to sample more efficiently, than force fields such as OPLSAA. Our results suggest a general strategy which involves using different combinations of force fields and solvent models in different applications, for example, using GROMOS96 and a simple GB model in sampling and OPLSAA and a more accurate GB model in refinement. The fact that various methods have been implemented in a unified way should facilitate the testing and subsequent use of different methods to evaluate conformational free energies in different applications. Our results also bear on some general issues involved in peptide folding and structure prediction which are addressed in the Discussion. PMID:16851315

Zhu, Jiang; Alexov, Emil; Honig, Barry

2005-02-24

222

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

E-print Network

Peptide self-assembly as a model of proteins in the pre-genomic world Indraneel Ghosh1 and Jean-based biopolymers have been designed to self assemble. Addresses 1 Department of Chemistry, University of Arizona a range of catalytic activities [3,4]. However, there has also been great interest in exploring other self-assembling

Ghosh, Indraneel

223

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

E-print Network

Energetics and Partition of Two Cecropin-Melittin Hybrid Peptides to Model Membranes of Different Superior Te´cnico, UTL, P-1049-001 Lisbon, Portugal ABSTRACT The energetics and partition of two hybrid particularly successful approach is based on hybrid sequences or chimera, derived from naturally occurring a

Pompeu Fabra, Universitat

224

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

NASA Astrophysics Data System (ADS)

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 form: (Glu)5(Gly-Ala-Pro-Gly-Pro-Pro)6(Glu)5, or (Glu)5(Gly-Pro-Ala-Gly-Pro-Pro)6(Glu)5. The glutamic acid capping the ends of the hexapeptide sequences imparts solubility in water. Depending upon concentration and temperature, the peptides form lyotropic liquid crystalline structures, and maintain their order when dried to powders or films suitable for X-ray and optical studies. Through the use of the high intensity source of X-radiation at the Brookhaven National Synchrotron Light Source, phase transformation kinetics and structure development are studied in-situ, providing time-resolved characterization of these peptides. Two-dimensional optical ellipsometry provides direct measure of the optical anisotropy and retardance of the structures. The goal of our research is to evaluate the ability of these model peptides for self-assembly into liquid crystalline and true three-dimensional crystalline phases and to assess the temperature stability of resultant higher order structures.

Georgiev, Georgie; Cebe, Peggy; Valluzzi, Regina; Kaplan, David

2003-03-01

225

Molecular geometries and energetics of metal-containing systems using an improved ASED-MO model: a systematic test to group 1 and 2 metal containing systems in the gas phase  

NASA Astrophysics Data System (ADS)

Accurate potential energy curves for highly polar metal-containing systems of the group 1 and 2 metals have been calculated by an improved ASED-MO model. The major components of the improvements consist of the addition of an intramolecular Madelung-type potential to the Born-Oppenheimer energy, accounting for the electrostatic attractive interactions between the charged atoms in the molecule and the usage of Slater-type orbital exponents dependent on the atomic net charges. The new computational scheme has successfully been applied in predicting the structural and energetic parameters of the whole series of the neutral and ionic (cationic and anionic) group 1 and 2 metal oxide diatomics in both their ground and selected low-lying electronic states, as well as the corresponding series of the metal monohydroxides. The importance of the inclusion of the intramolecular Madelung-type potential for the satisfactory description of a highly ionic bonding has been demonstrated by applying the new theoretical model on the series of the 'unknown' molecule/dipole CH4...MO and CH4...MO(+) (M = Be, Mg, Ca, Sr and Ba) complexes involving both a highly ionic M-O and a very weak Van der Waals type CH4...MO interactions.

Stiakaki, Maria-Aglaia D.; Tsipis, Athanasios C.; Tsipis, Constantinos A.; Xanthopoulos, Constantinos E.

1994-12-01

226

Molecular geometries and energetics of metal-containing systems using an improved ASED-MO model: a systematic test to group 1 and 2 metal containing systems in the gas phase  

NASA Astrophysics Data System (ADS)

Accurate potential energy curves for highly polar metal-containing systems of the group 1 and 2 metals have been calculated by an improved ASED-MO model. The major components of the improvements consist of the addition of an intramolecular Madelung-type potential to the Born-Oppenheimer energy, accounting for the electrostatic attractive interactions between the charged atoms in the molecule and the usage of Slater-type orbital exponents dependent on the atomic net charges. The new computational scheme has successfully been applied in predicting the structural and energetic parameters of the whole series of the neutral and ionic (cationic and anionic) group 1 and 2 metal oxide diatomics in both their ground and selected low-lying electronic states, as well as the corresponding series of the metal monohydroxides. The importance of the inclusion of the intramolecular Madelung-type potential for the satisfactory description of a highly ionic bonding has been demonstrated by applying the new theoretical model on the series of the "unknown" molecule/dipole CH 4·MO and CH 4·MO + ( M = Be, Mg, Ca, Sr and Ba) complexes involving both a highly ionic M-O and a very weak Van der Waals type CH 4⋯MO interactions.

Stiakaki, Maria-Aglaia D.; Tsipis, Athanasios C.; Tsipis, Constantinos A.; Xanthopoulos, Constantinos E.

1994-12-01

227

A comparative study of interatomic potentials for copper and aluminum gas phase sputter atom transport simulations  

NASA Astrophysics Data System (ADS)

A comparative study of interatomic potential models for use in gas phase sputter atom transport simulations is presented. Quantum chemical interatomic potentials for argon-copper and argon-aluminum are calculated using Kohn-Sham density functional theory utilizing the PW91 functional. These potentials (PW91) are compared to the commonly used Born-Mayer potentials calculated by Abrahamson [Phys. Rev. 178 (1969) 76] using the Thomas-Fermi-Dirac model (TFD) and the screened Coulomb potentials derived from the "universal" form calculated by Ziegler, Biersack and Littmark (ZBL). Monte Carlo simulations of gas phase sputter atom transport were performed to determine the average energy of atoms arriving at the substrate versus pressure for the three potential models. Overall, the ZBL potential gave results in much better agreement with the PW91 potential than the TFD potential. A characteristic thermalization pressure-distance product of ˜0.11 mTorr cm was found for both copper and aluminum using the PW91 potential.

Kuwata, Keith T.; Erickson, Rachel I.; Doyle, James R.

2003-04-01

228

Mass transfer between a multicomponent trapped gas phase and a mobile water phase: Experiment and theory  

NASA Astrophysics Data System (ADS)

Gas tracer experiments were carried out in dynamically compressed sediments to investigate the mass transfer between a trapped multicomponent gas phase and a mobile water phase. The saturation state of the column was characterized by three independent methods: (1) by gravimetric measurements, (2) by bromide tracer tests, and (3) by hydraulic conductivity measurements. For inverse modeling a new kinetic model was developed allowing volume change of the entrapped gas. The new kinetic model consistently explains oxygen elution curves, the time evolution of the integral gas saturation, and integral hydraulic conductivity. The sensitivity of three different velocity-dependent mass transfer correlations to the dissolution process was investigated: (1) a classical square-root, single-sphere correlation, Sh ˜ Pe0.5, (2) a multisphere correlation, Sh ˜ Pen (n = 0.5-1.0), and (3) an empirical correlation, Sh ˜ Pe0.8. It was found that all correlations yield nearly the same elution curves for 10 gas tracer experiments with three different two-component gas phases: O2/He, O2/N2, and O2/Ar and for different flow velocities ranging from 5 to 20 m d-1. For all gas tracer experiments a distinct minimum of the longitudinal dispersivity was found during gas dissolution, i.e., in the unsaturated state. For the saturated state we found that the experimental values could be described by Saffman's theory: ?p ? Pe ln (Pe) with a normalized mean square root error of 6%.

Geistlinger, Helmut; Beckmann, Annika; Lazik, Detlef

2005-11-01

229

Preconceptual design of the gas-phase decontamination demonstration cart  

SciTech Connect

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.

Munday, E.B.

1993-12-01

230

Gas-phase Dissociation of homo-DNA Oligonucleotides  

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

231

Naphthol coupling monitored by infrared spectroscopy in the gas phase.  

PubMed

The reaction mechanism of copper(II)-mediated naphthol coupling in the presence of TMEDA (N,N,N',N'-tetramethylethylenediamine) is studied using infrared multiphoton dissociation (IRMPD) spectroscopy and DFT calculations. It is shown that the coupling reaction proceeds in ad hoc formed binuclear clusters [(1-H)(2)Cu(2)Cl(TMEDA)(2)](+), where (1-H) is a deprotonated naphthol molecule (methyl ester of 3-hydroxy-2-naphthoic acid). The IRMPD spectra of the isolated cluster in the gas phase reveal that it contains two uncoupled naphtholate subunits and only the irradiation promotes the coupling reaction, which is thus observed as a genuine gas-phase reaction. The driving force for the C-C coupling is a keto-enol tautomerization of the initial coupling product, and the formation of the corresponding binol in the cluster is exothermic by 0.61 eV. In contrast, analogous C-O and O-O couplings are endothermic reactions. PMID:19954233

Roithová, Jana; Milko, Petr

2010-01-13

232

Proteochemometric modelling of antibody-antigen interactions using SPOT synthesised peptide arrays.  

PubMed

Proteochemometrics is a technology for the study of molecular recognition based on chemometric techniques. Here we applied it to analyse the amino acids and amino acid physico-chemical properties that are involved in antibodies' recognition of peptide antigens. To this end, we used a study system comprised by a diverse single chain antibody library derived from the murine mAb anti-p24 (HIV-1) antibody CB4-1, evaluated on peptide arrays manufactured by SPOT synthesis. The binding pattern obtained was correlated to physico-chemical descriptors (z-scales) of antibodies and peptides amino acids using partial least-squares projections to latent structures. Cross terms derived from antibody and antigen descriptors were included, which substantially improved the proteochemometric model. The final model was statistically highly satisfactory with a correlation coefficient R(2) = 0.73 and predictive ability Q(2) = 0.68. The physico-chemical properties of each interacting amino acid residue of both the peptides and the antibodies being essential for the antigen-antibody recognition could be retrieved from the model. The study shows for the first time the feasibility of using proteochemometrics to analyse the molecular recognition of antigens by antibodies. PMID:17588963

Mandrika, Ilona; Prusis, Peteris; Yahorava, Sviatlana; Shikhagaie, Medya; Wikberg, Jarl E S

2007-06-01

233

Peptide neuroregulators: the opioid system as a model.  

PubMed Central

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

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

1985-01-01

234

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

SciTech Connect

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.

Sylwester, Eric Robert

1998-10-01

235

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

SciTech Connect

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.

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

2009-03-31

236

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

Microsoft Academic Search

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

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

2002-01-01

237

Antitumor efficacy, pharmacokinetic and biodistribution studies of the anticancer peptide CIGB-552 in mouse models.  

PubMed

Accumulation of the COMMD1 protein as a druggable pharmacology event to target cancer cells has not been evaluated so far in cancer animal models. We have previously demonstrated that a second-generation peptide, with cell-penetrating capacity, termed CIGB-552, was able to induce apoptosis mediated by stabilization of COMMD1. Here, we explore the antitumor effect by subcutaneous administration of CIGB-552 in a therapeutic schedule. Outstandingly, a significant delay of tumor growth was observed at 0.2 and 0.7?mg/kg (p?models. Furthermore, we evidenced that (131)I-CIGB-552 peptide was actually accumulated in the tumors after administration by subcutaneous route. A typical serine-proteases degradation pattern for CIGB-552 in BALB/c mice serum was identified. Further, biological characterization of the main metabolites of the peptide CIGB-552 suggests that the cell-penetrating capacity plays an important role in the cytotoxic activity. This report is the first in describing the antitumor effect induced by systemic administration of a peptide that targets COMMD1 for stabilization. Moreover, our data reinforce the perspectives of CIGB-552 for cancer targeted therapy. PMID:25044757

Vallespí, Maribel G; Pimentel, Gilmara; Cabrales-Rico, Ania; Garza, Julio; Oliva, Brizaida; Mendoza, Osmani; Gomez, Yolanda; Basaco, Tais; Sánchez, Iraida; Calderón, Carlos; Rodriguez, Juan C; Markelova, Maria Rivera; Fichtner, Iduna; Astrada, Soledad; Bollati-Fogolín, Mariela; Garay, Hilda E; Reyes, Osvaldo

2014-11-01

238

Assessment of the effect of macromolecular crowding on aggregation behaviour of a model amyloidogenic Peptide.  

PubMed

Accumulation of ordered protein aggregates (or amyloids) represents a hallmark of many diseases (e.g., Alzheimer's disease, type II diabetes, Parkinson's diseases etc.), results from intermolecular association of partially unfolded proteins/ peptides. Such associations usually take place in highly crowded conditions. The aggregates, which are formed under in vitro and in vivo conditions exhibit substantial variations in their structure and function. Such heterogeneities in amyloids might arise due to macromolecular crowding that is usually omitted under in vitro conditions. The current study is an attempt to assess the effects of macromolecular crowding on amyloid formation using a model amyloidogenic peptide. The sequence of the peptide was derived from C-terminal region (RATQIPSYKKLIMY) of PAP(248-286), which naturally occurs in human semen as amyloid aggregates and is known for boosting HIV infectivity. This model peptide forms sedimentable and fibrillar aggregates in aqueous buffer and shows the characteristic features of amyloids. In the presence of macromolecular crowders the morphological features of the amyloids are significantly altered and resulted in the formation of shorter amyloid aggregates. The current study assumes the hypothesis that macromolecular crowding in the biological system favours formation of heterogeneous classes of aggregates and each of them might differ in their biophysical and biological properties. PMID:25267253

Gaharwar, Bharti; Gour, Shalini; Kaushik, Vibha; Gupta, Nimisha; Kumar, Vijay; Hause, Gerd; Yadav, Jay Kant

2015-01-01

239

Reactions of An Aromatic ?,?-Biradical with Amino Acids and Dipeptides in the Gas Phase  

PubMed Central

Gas-phase reactivity of a positively charged aromatic ?,?-biradical (N-methyl-6,8-didehydroquinolinium) was examined toward six aliphatic amino acids and fifteen dipeptides by using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) and laser-induced acoustic desorption (LIAD). While previous studies have revealed that H-atom and NH2 abstractions dominate the reactions of related monoradicals with aliphatic amino acids and small peptides, several additional, unprecedented reaction pathways were observed for the reactions of the biradical. For amino acids, these are 2H-atom abstraction, H2O abstraction, addition – CO2, addition – HCOOH and formation of a stable adduct. The biradical reacts with aliphatic dipeptides similarly as with aliphatic amino acids, but undergoes also one additional reaction pathway, addition/C-terminal amino acid elimination (addition – CO – NHCHRC). These reactions are initiated by H-atom abstraction by the biradical from the amino acid or peptide, or nucleophilic addition of an NH2 or a HO group of the amino acid or peptide at the radical site at C-6 in the biradical. Reactions of the unquenched C-8 radical site then yield the products not observed for related monoradicals. The biradical reacts with aromatic dipeptides with an aromatic ring in N-terminus (i.e., Tyr-Leu, Phe-Val and Phe-Pro) similarly as with aliphatic dipeptides. However, for those aromatic dipeptides that contain an aromatic ring in the C-terminus (i.e., Leu-Tyr and Ala-Phe), one additional pathway, addition/N-terminal amino acid elimination (addition – CO – NHCHRN), was observed. This reaction is likely initiated by radical addition of the biradical at the aromatic ring in the C-terminus. Related monoradicals add to aromatic amino acids and small peptides, which is followed by C?-C? bond cleavage, resulting in side-chain abstraction by the radical. For biradicals, with one unquenched radical site after the initial addition, the reaction ultimately results in the loss of the N-terminal amino acid. Similar to monoradicals, the C-S bond in amino acids and dipeptides was found to be especially susceptible to biradical attack. PMID:20705478

Fu, Mingkun; Li, Sen; Archibold, Enada; Yurkovich, Michael J.; Nash, John J.; Kenttämaa, Hilkka I.

2010-01-01

240

Synthesis and Gas Phase Thermochemistry of Germanium-Containing Compounds  

SciTech Connect

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.

Nathan Robert Classen

2002-12-31

241

Raman study of vibrational dynamics of aminopropylsilanetriol in gas phase.  

PubMed

Raman spectrum of aminopropylsilanetriol (APST) in gas phase has been recorded at room temperature in macro chamber utilizing two-mirror technique over the sample tube. Unlike predominantly trans molecular conformation in condensed phase, the spectra of vapor show that the molecules are solely in gauche conformation with intramolecular hydrogen bond N···HO which reduces the molecular energy in respect to trans conformation by 0.152 eV. The assignment of the molecular spectra based on the DFT calculation is presented. The strong vibrational bands at 354 cm(-1), 588 cm(-1) and 3022 cm(-1) are proposed for verifying the existence of the ring like, hydrogen bonded structure. Special attention was devoted to the high frequency region, where hydrogen bond vibrations are coupled to stretchings of amino and silanol groups. PMID:24021947

Volovšek, V; Danani?, V; Bistri?i?, L; Movre Šapi?, I; Furi?, K

2014-01-01

242

Gas-phase synthesis of magnetic metal/polymer nanocomposites.  

PubMed

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

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

2014-12-19

243

Conformational Study of Taurine in the Gas Phase  

NASA Astrophysics Data System (ADS)

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

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

2009-08-01

244

Optically based diagnostics for gas-phase laser development  

NASA Astrophysics Data System (ADS)

In this paper we describe several diagnostics that we have developed to assist the development of high power gas phase lasers including COIL, EOIL, and DPAL. For COIL we discuss systems that provide sensitive measurements of O2(a), small signal gain, iodine dissociation, and temperature. These are key operational parameters within COIL, and these diagnostics have been used world-wide to gain a better understanding of this laser system. Recently, we have developed and integrated a similar suite of diagnostics for scaling the EOIL system and will provide examples of current studies. We are also developing diagnostics for the emerging DPAL laser. These include monitors for small signal gain that will provide both a more fundamental understanding of the kinetics of DPAL and valuable data for advanced resonator design. We will stress the application of these diagnostics to realistic laser systems.

Rawlins, Wilson T.; Lee, Seonkyung; Galbally-Kinney, Kristin L.; Kessler, William J.; Hicks, Adam J.; Konen, Ian M.; Plumb, Emily P.; Davis, Steven J.

2010-11-01

245

Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase  

NASA Astrophysics Data System (ADS)

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.

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

2007-03-01

246

Silicon Nanowire-Based Devices for Gas-Phase Sensing  

PubMed Central

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

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

2014-01-01

247

Tautomerism of cytosine probed by gas phase IR spectroscopy  

NASA Astrophysics Data System (ADS)

The tautomerism of the gaseous protonated cytosine is studied using infrared multiple photon dissociation (IRMPD) spectroscopy of singly hydrated complexes of protonated cytosine in the 2700-3750 cm-1 wavenumber range. The hydrated complexes are formed through argon-mediated collisions between bare electrosprayed cytosine and low-pressure water vapor. In the spectra, where X-H (XC, O, and N) stretching vibrations are probed, evidence is found for the coexistence in the gas phase of hydrated complexes of two different cytosine tautomers. As the addition of a water molecule to either tautomer of protonated cytosine is energetically highly unlikely to induce interconversion, it is deduced that both C(2)O and N(3) protonated tautomers of cytosine are formed under electrospray conditions.

Bakker, Joost M.; Salpin, Jean-Yves; Maître, Philippe

2009-06-01

248

Structures of platinum oxide clusters in the gas phase.  

PubMed

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

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

2013-02-14

249

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

PubMed Central

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

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

250

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

PubMed

Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow. PMID:25375223

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

2014-12-01

251

The gas-phase iron abundance in Herbig-Haro objects  

NASA Technical Reports Server (NTRS)

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.

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

1994-01-01

252

Aqueous and Gas Phase Sorption Properties of Mercury in Burned Soils  

NASA Astrophysics Data System (ADS)

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

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

2008-12-01

253

Surfactants from the gas phase may promote cloud droplet formation  

PubMed Central

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

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

2013-01-01

254

On the maximum charge state and proton transfer reactivity of peptide and protein ions formed by electrospray ionization.  

PubMed

A relatively simple model for calculation of the energetics of gas-phase proton transfer reactions and the maximum charge state of multiply protonated ions formed by electrospray ionization is presented. This model is based on estimates of the intrinsic proton transfer reactivity of sites of protonation and point charge Coulomb interactions. From this model, apparent gas-phase basicities (GB(app)) of multiply protonated ions are calculated. Comparison of this value to the gas-phase basicity of the solvent from which an ion is formed enables a maximum charge state to be calculated. For 13 commonly electrosprayed proteins, our calculated maximum charge states are within an average of 6% of the experimental values reported in the literature. This indicates that the maximum charge state for proteins is determined by their gas-phase reactivity. Similar results are observed for peptides with many basic residues. For peptides with few basic residues, we find that the maximum charge state is better correlated to the charge state in solution. For low charge state ions, we find that the most basic sites Arg, Lys, and His are preferentially protonated. A significant fraction of the less basic residues Pro, Trp, and Gln are protonated in high charge state ions. The calculated GB(app) of individual protonation sites varies dramatically in the high charge state ions. From these values, we calculate a reduced cross section for proton transfer reactivity that is significantly lower than the Langevin collision frequency when the GB(app) of the ion is approximately equal to the GB of the neutral base. PMID:24214055

Schnier, P D; Gross, D S; Williams, E R

1995-11-01

255

Protonating polymer oligomers in the gas phase to change fragmentation pathways.  

PubMed

Ionization of polymers in mass spectrometry is usually achieved by forming metal ion adducts. The metal ion has been shown by Wesdemiotis to often play a spectator role in the collision-induced dissociation (CID) chemistry of these species, wherein they fragment according to a free-radical mechanism similar to that found in their pyrolysis. The result is a predominance of low-mass ions in the CID mass spectrum. We have changed this behavior by generating protonated oligomers in the gas phase by first forming proton-bound complexes of the oligomers with amino acids or peptides by electrospray ionization. These complexes dissociate first by loss of the amino acid/peptide to form protonated oligomers, which then undergo a unique fragmentation chemistry. In this article we discuss the results for poly(methyl methacrylate) (PMMA) and poly(butyl acrylate) (PBA). Initially, protonated PMMA and PBA lose methanol and butanol, respectively, from the side chains of the respective monomers. The resulting PMMA-derived ion then undergoes a series of neutral losses corresponding to 32 and 28 Da, methanol and carbon monoxide. This continues as collision energy increases until a final, carbon-rich backbone ion is formed, which then undergoes a classic hydrocarbon fragmentation pattern. The PBA-derived ions are proposed to fragment by the loss of butylether molecules to form anhydride rings along the oligomer chain. The number of ether molecules lost corresponded to half the number of available side chains in the oligomer. The resulting poly-anhydride ion dissociates by small molecule loss. Mechanisms have been suggested for the fragmentation chemistry of these two classes of oligomers. PMID:18845449

Alhazmi, Abdulrahman M; Mayer, Paul M

2009-01-01

256

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

NASA Astrophysics Data System (ADS)

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.

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

2011-09-01

257

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

PubMed Central

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

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

2011-01-01

258

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

PubMed

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 100nm. During incubation, the fibrils aggregate irreversibly into longer fibrils and fibrillar aggregates. At peptide concentrations in the range 3-6.5g/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

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

2015-01-01

259

Effect of gas-phase transport in molten carbonate fuel cell  

Microsoft Academic Search

Electrode reaction characteristics involving gas-phase transport effect have been investigated with several 100 cm2 class molten carbonate fuel cells (MCFCs). Although the MCFCs operate on gas-phase reactants at relatively high temperature, most of studies on the electrode reaction kinetics have been confined within kinetic-control and liquid-phase mass-transfer regions. To evaluate the gas-phase transport effect in the MCFC, an inert gas

Choong-Gon Lee; Byoung-Sam Kang; Hai-Kyung Seo; Hee-Chun Lim

2003-01-01

260

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

PubMed

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

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

2015-01-21

261

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

E-print Network

cleavages are shown in red, whereas side chain loss ions are in other colors.???????.?????? 15 2 Tandem mass spectra for (a) [RVGVAPG+H] + , (b) [RVGVAPG+Na] + and (c) [RVGVAPG+Cu] + ???.?????. 29 3 Tandem mass spectra for (a) [HVGVAPG...+H] + , (b) [HVGVAPG+Na] + and (c) [HVGVAPG+Cu] + ????????. 33 4 Tandem mass spectra for (a) [KVGVAPG+H] + , (b) [KVGVAPG+Na] + and (c) [KVGVAPG+Cu] + ????????. 37 5 Tandem mass spectra for (a) [DVGVAPG+H] + , (b) [DVGVAPG+Na] + and (c...

Slaton, James Garrett

2009-05-15

262

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

NASA Astrophysics Data System (ADS)

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

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

1997-11-01

263

Characterization of antimicrobial peptide activity by electrochemical impedance spectroscopy  

E-print Network

Characterization of antimicrobial peptide activity by electrochemical impedance spectroscopy Accepted 21 June 2008 Available online 1 July 2008 Keywords: Antimicrobial peptides Cationic peptides exposure to antimicrobial peptides (AMPs). We show that two model cationic peptides, very similar

Wimley, William C.

264

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

NASA Technical Reports Server (NTRS)

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

Radhakrishnan, Krishnan; Bittker, David A.

1993-01-01

265

CS-AMPPred: an updated SVM model for antimicrobial activity prediction in cysteine-stabilized peptides.  

PubMed

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

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

2012-01-01

266

Enhancement of gas-phase diffusion in the presence of liquid  

NASA Astrophysics Data System (ADS)

Gas diffusion in porous media occurs in both the gas and liquid phases. In many instances, gas diffusion in the liquid phase is ignored. However, under many conditions, gas diffusion in the liquid phase may be more important than gas diffusion in the gas phase. Two different cases will be examined in this work. The first case is a continuous liquid path between the gas concentrations of interest modeled after Jury et al. (1984). The second case is the situation at low liquid saturation where liquid islands exist. For the first case, Jury's model can be rewritten as a ratio of the total gas diffusion in the gas and liquid phases to that just in the gas phase. The liquid diffusion coefficient is approximately 10-4 times the gas diffusion coefficient consistent with Jury et al. (1984). The ratio of total diffusion to gas-phase diffusion is then only a function of Henry's constant and the liquid saturation. For higher values of Henry's constant, such as for CO2 and O2, the effect of diffusion in the liquid phase is small except at high liquid saturations. For small values of Henry's constant, such as for some VOCs and explosive compounds, diffusion in the liquid phase dominates for low and moderate liquid saturation values. The second case is the enhancement of diffusion caused by liquid islands at low liquid saturation. Enhanced vapor diffusion across liquid islands has been observed and modeled by Webb and Ho (1999), where condensation and evaporation occur on opposite ends of the liquid island. Vapor diffusion enhancement of up to a factor of 10 has been observed. Similarly, gas can diffuse through the liquid island. For high values of Henry's constant, gas diffusion through liquid islands is negligible and can be ignored. For small values of Henry's constant, diffusion through liquid islands may be much greater than diffusion through gas, so the rate is enhanced. The work was sponsored by the Geneva International Center for Humanitarian Demining (GICHD) under the direction of Havard Bach. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL85000.

Webb, S.; Angert, A.

2003-04-01

267

Energetics of Selected Gas Phase Ion-Molecule Reactions  

NASA Astrophysics Data System (ADS)

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.

Paul, Gary John Charles

1990-01-01

268

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

NASA Astrophysics Data System (ADS)

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

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

2011-09-01

269

A model genetic system for testing the in vivo function of peptide toxins.  

PubMed

We have developed a model genetic system for analyzing the function of peptide toxins from animal venoms. We engineered and propagated strains of Drosophila melanogaster expressing heat-inducible transgenes encoding either kappa-ACTX-Hv1c or omega-ACTX-Hv1a, two insect-specific neurotoxic peptides found in the venom of the Australian funnel-web spider Hadronyche versuta. Heat induction of transgene expression for 20 min was sufficient to kill all transgenic flies, indicating that the ion channels targeted by these toxins are viable insecticide targets. The unusual phenotype of flies induced to express omega-ACTX-Hv1a recapitulates that of a hypomorphic allele of the high-voltage-activated calcium channel Dmca1D, suggesting that this is likely to be the target of omega-ACTX-Hv1a. PMID:17141372

Tedford, Hugo W; Maggio, Francesco; Reenan, Robert A; King, Glenn

2007-01-01

270

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

SciTech Connect

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

Garrison, W.M.

1982-08-01

271

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

SciTech Connect

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

Yongqing Huang; Freiser, B.S. (Purdue Univ., West Lafayette, IN (USA))

1989-03-29

272

Project ARGO: Gas phase formation in simulated microgravity  

NASA Technical Reports Server (NTRS)

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.

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

1993-01-01

273

Gas phase structures of peroxides: experiments and computational problems.  

PubMed

Gas-phase structures of several organic and inorganic peroxides X-O-O-X and X-O-O-X', which have been determined experimentally by gas electron diffraction and/or microwave spectroscopy, are discussed. The O?O bond length in these peroxides varies from 1.481(8) Å in Me3 SiOOSiMe3 to 1.214(2) Å in FOOF and the dihedral angle ?(XO-OX) between 0° in HC(O)O-OH and near 180° in Bu(t) O-OBu(t) . Some of the peroxides cause problems for quantum chemistry, since several computational methods fail to reproduce the experimental structures. Extreme examples are MeO-OMe and FO-OF. In the case of MeO-OMe only about half of the more than 100 computational methods reported in the literature reproduce the experimentally determined double-minimum shape of the torsional potential around the O?O bond correctly. For FO-OF only a small number of close to 200 computational methods reproduce the O?O and O?F bond lengths better than ±0.02 Å. PMID:25475056

Oberhammer, Heinz

2015-02-01

274

Seven-coordinate homoleptic metal carbonyls in the gas phase.  

PubMed

Gas-phase metal carbonyl cations of the vanadium-group metals (V(+), Nb(+), Ta(+)) were produced in a molecular beam by laser vaporization and then mass-analyzed and size-selected in a time-of-flight spectrometer and studied with IR laser photodissociation spectroscopy in the carbonyl-stretching region. The abundances in the mass spectra, the fragmentation patterns, and the IR spectra provided a combined approach that revealed the coordination numbers in these systems. Although seven-coordinate structures would have 18 electrons in each case, V(CO)(6)(+) was found to be formed rather than V(CO)(7)(+). Nb(+) formed both six- and seven-coordinate species, while Ta(+) formed only the Ta(CO)(7)(+) complex. Density functional theory computations were used to predict the IR spectra for these systems, which are dramatically different for the six- and seven-coordinate structures and in excellent agreement with the measurements. V(CO)(6)(+) and Nb(CO)(6)(+) have structures slightly distorted from octahedral, while Nb(CO)(7)(+) and Ta(CO)(7)(+) have C(3v) capped octahedral structures. PMID:19522497

Ricks, Allen M; Reed, Zach D; Duncan, Michael A

2009-07-01

275

Full field gas phase velocity measurements in microgravity  

NASA Technical Reports Server (NTRS)

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.

Griffin, Devon W.; Yanis, William

1995-01-01

276

Directed gas-phase formation of the ethynylsulfidoboron molecule.  

PubMed

As a member of the organo sulfidoboron (RBS) family, the hitherto elusive ethynylsulfidoboron molecule (HCCBS) has been formed via the bimolecular reaction of the boron monosulfide radical (BS) with acetylene (C2H2) under single collision conditions in the gas phase, exploiting the crossed molecular beams technique. The reaction mechanism follows indirect dynamics via a barrierless addition of the boron monosulfide radical with its boron atom to the carbon atom of the acetylene molecule, leading to the trans-HCCHBS intermediate. As predicted by ab initio electronic structure calculations, the initial collision complex either isomerizes to its cis-form or undergoes a hydrogen atom migration to form H2CCBS. The cis-HCCHBS intermediate either isomerizes via hydrogen atom shift from the carbon to the boron atom, leading to the HCCBHS isomer, or decomposes to ethynylsulfidoboron (HCCBS). Both H2CCBS and HCCBHS intermediates were predicted to fragment to ethynylsulfidoboron via atomic hydrogen losses. Statistical (RRKM) calculations report yields to form the ethynylsulfidoboron molecule from cis-HCCHBS, H2CCBS, and HCCBHS to be 21%, 7%, and 72%, respectively, under current experimental conditions. Our findings open up an unconventional path to access the previously obscure class of organo sulfidoboron molecules, which are difficult to access through "classical" formation. PMID:24842647

Yang, Tao; Parker, Dorian S N; Dangi, Beni B; Kaiser, Ralf I; Stranges, Domenico; Su, Yuan-Hsiang; Chen, Si-Ying; Chang, Agnes H H; Mebel, Alexander M

2014-06-11

277

Gas phase photolysis of pinonaldehyde in the presence of sunlight  

NASA Astrophysics Data System (ADS)

The photolysis of pinonaldehyde in the presence of sunlight and in the presence/absence of an OH radical scavenger (cyclohexane) was studied in a large outdoor smog chamber. More than nine reaction products were identified or tentatively identified and quantified in this study using gas chromatography-mass spectrometry. Carbon yields for pinonaldehyde photolysis in the absence of an OH scavenger are: norpinonaldehyde (21.7%); pinonic acid (11.2%); 3-acetyl-2,2-dimethyl-cyclobutyl-methanol (5.3%); 2,2,3-trimethyl-cyclobutylethanone (2.9%); and 10-oxonorpinonaldehyde (1.9%). Carbon yields for pinonaldehyde photolysis in the presence of cyclohexane are: norpinonaldehyde (20.1%); pinonic acid (0.4%); 3-acetyl-2,2-dimethyl-cyclobutyl-methanol (2.7%); 2,2,3-trimethyl-cyclobutyl-ethanone (1.3%); and 10-oxonorpinonaldehyde (1.0%). The uncertainty in the yield data is estimated to be ˜26%. The results show that pinonaldehyde photolysis is an important part of its overall atmospheric chemistry. A detailed mechanism for pinonaldehyde photolysis in the presence/absence of cyclohexane is proposed, and a kinetic mechanism was used to simulate the gas phase reactions of pinonaldehyde. Observed temporal profiles of pinonaldehyde and its photooxidation products were used to estimate photolysis quantum yields for pinonaldehyde. The atmospheric implications of the data are discussed.

Jaoui, M.; Kamens, R. M.

278

CHAOS II: Gas-Phase Abundances in NGC 5194  

E-print Network

We have observed NGC5194 (M51a) as part of the CHemical Abundances of Spirals (CHAOS) project. Using the Multi Object Double Spectrographs (MODS) on the Large Binocular Telescope (LBT) we are able to measure one or more of the temperature-sensitive auroral lines ([O III] 4363, [N II] 5755, [S III] 6312) and thus measure "direct" gas-phase abundances in 29 individual HII regions. [O III] 4363 is only detected in two HII regions both of which show indications of excitation by shocks. We compare our data to previous direct abundances measured in NGC5194 and find excellent agreement for all but one region (Delta[log(O/H)] ~ 0.04). We find no evidence of trends in Ar/O, Ne/O, or S/O within NGC5194 or compared to other galaxies. We find modest negative gradients in both O/H and N/O with very little scatter (sigma = -0.62) suggests secondary nitrogen production is responsible for a significantly larger fraction of nitrogen (e.g., factor of 8-10) relative to primary production mechanisms than predicted by theoretica...

Croxall, Kevin V; Berg, Danielle; Skillman, Evan D; Moustakas, John

2015-01-01

279

Star Formation and Gas Phase History of the Cosmic Web  

E-print Network

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

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

2014-01-01

280

H Solid-State NMR Study of Lipid Clustering by Cationic Antimicrobial and Cell-Penetrating Peptides in Model Bacterial Membranes  

E-print Network

/POPG (3:1) membranes, and membranes containing one of four cationic peptides: two antimicrobial peptidesA 2 H Solid-State NMR Study of Lipid Clustering by Cationic Antimicrobial and Cell-Penetrating Peptides in Model Bacterial Membranes Byungsu Kwon, Alan J. Waring,§ and Mei Hong * Department

Hong, Mei

281

DETERMINATION OF GAS-PHASE DIMETHYL SULFATE AND MONOMETHYL HYDROGEN SULFATE  

EPA Science Inventory

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

282

Theoretical Analysis of Oscillatory Burning of Homogeneous Solid Propellant Including Non-Steady Gas Phase Effects  

Microsoft Academic Search

This paper presents a theoretical analysis of the linear burning response of an homogeneous solid propellant to pressure fluctuations. The major contribution of this work is to take into account the non-steady effects of the gas phase in a systematic way and thus, eliminate the strong limitation of previous analysis in which the gas-phase is assumed to respond in a

PAUL CLAVIN; DAVID LAZIMI

1992-01-01

283

Why the Langevin-Debye theory of molecular polarisation fails in gas phase  

Microsoft Academic Search

The classical polarization formula of Langevin, which holds in the solid\\/liquid state, does not satisfy many experimental facts in gas phase, especially in diluted gas mixtures. The new formulation of the molecular polarization in gas phase is obtained on phenomenological grounds analysing the motion that polar molecules undergo under an electric field. It is shown that the polarization amplitude in

M. Michelini

284

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

E-print Network

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

Howk, Jay Christopher

285

Phage Display Screening for Tumor Necrosis Factor-?-Binding Peptides: Detection of Inflammation in a Mouse Model of Hepatitis  

PubMed Central

TNF-? is one of the most abundant cytokines produced in many inflammatory and autoimmune conditions such as multiple sclerosis, chronic hepatitis C, or neurodegenerative diseases. These pathologies remain difficult to diagnose and consequently difficult to treat. The aim of this work is to offer a new diagnostic tool by seeking new molecular probes for medical imaging. The target-specific part of the probe consists here of heptameric peptides selected by the phage display technology for their affinity for TNF-?. Several affinity tests allowed isolating 2 peptides that showed the best binding capacity to TNF-?. Finally, the best peptide was synthesized in both linear and cyclic forms and tested on the histological sections of concanavalin-A-(ConA-)treated mice liver. In this well-known hepatitis mouse model, the best results were obtained with the cyclic form of peptide 2, which allowed for the staining of inflamed areas in the liver. The cyclic form of peptide 2 (2C) was, thus, covalently linked to iron oxide nanoparticles (magnetic resonance imaging (MRI) contrast agent) and tested in the ConA-induced hepatitis mouse model. The vectorized nanoparticles allowed for the detection of inflammation as well as of the free peptide. These ex vivo results suggest that phage display-selected peptides can direct imaging contrast agents to inflammatory areas. PMID:23533448

Sclavons, Coralie; Burtea, Carmen; Boutry, Sébastien; Laurent, Sophie; Vander Elst, Luce; Muller, Robert N.

2013-01-01

286

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

SciTech Connect

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.

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

287

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

NASA Technical Reports Server (NTRS)

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

Raju, Manthena S.

1998-01-01

288

Theoretical study on isomerization and peptide bond cleavage at aspartic residue.  

PubMed

Isomerization and peptide bond cleavage at aspartic residue (Asp) in peptide models have been reported. In this study, the mechanisms and energies concerning the isomerization and peptide bond cleavage at Asp residue were investigated by the density functional theory (DFT) at B3LYP/6-311++G(d,p). The integral equation formalism-polarizable continuum model (IEF-PCM) was utilized to calculate solvation effect by single-point calculation of the gas-phase B3LYP/6-311++G(d,p)-optimized structure. Mechanisms and energies of the dehydration in isomerization reaction of Asp residue were comparatively analyzed with the deamidation reaction of Asn residue. The results show that the succinimide intermediate was formed preferentially through the step-wise reaction via the tetrahedral intermediate. The cleavage at C-terminus is more preferential than those at N-terminus. In comparison to isomerization, peptide bond cleavage is ? 20 kcal mol(-1) and lower in activation barrier than the isomerization. So, in this case, the isomerization of Asp is inhibited by the peptide bond cleavage. PMID:23754169

Sang-aroon, Wichien; Ruangpornvisuti, Vithaya

2013-09-01

289

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

PubMed Central

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

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

2000-01-01

290

Models of Self-Peptide Sampling by Developing T Cells Identify Candidate Mechanisms of Thymic Selection  

PubMed Central

Conventional and regulatory T cells develop in the thymus where they are exposed to samples of self-peptide MHC (pMHC) ligands. This probabilistic process selects for cells within a range of responsiveness that allows the detection of foreign antigen without excessive responses to self. Regulatory T cells are thought to lie at the higher end of the spectrum of acceptable self-reactivity and play a crucial role in the control of autoimmunity and tolerance to innocuous antigens. While many studies have elucidated key elements influencing lineage commitment, we still lack a full understanding of how thymocytes integrate signals obtained by sampling self-peptides to make fate decisions. To address this problem, we apply stochastic models of signal integration by T cells to data from a study quantifying the development of the two lineages using controllable levels of agonist peptide in the thymus. We find two models are able to explain the observations; one in which T cells continually re-assess fate decisions on the basis of multiple summed proximal signals from TCR-pMHC interactions; and another in which TCR sensitivity is modulated over time, such that contact with the same pMHC ligand may lead to divergent outcomes at different stages of development. Neither model requires that T and T are differentially susceptible to deletion or that the two lineages need qualitatively different signals for development, as have been proposed. We find additional support for the variable-sensitivity model, which is able to explain apparently paradoxical observations regarding the effect of partial and strong agonists on T and T development. PMID:23935465

Bains, Iren; van Santen, Hisse M.; Seddon, Benedict; Yates, Andrew J.

2013-01-01

291

Gas-phase interactions of organotin compounds with glycine.  

PubMed

Gas-phase interactions of organotins with glycine have been studied by combining mass spectrometry experiments and quantum calculations. Positive-ion electrospray spectra show that the interaction of di- and tri-organotins with glycine results in the formation of [(R)2Sn(Gly)-H](+) and [(R)3Sn(Gly)](+) ions, respectively. Di-organotin complexes appear much more reactive than those involving tri-organotins. (MS/MS) spectra of the [(R)3Sn(Gly)](+) ions are indeed simple and only show elimination of intact glycine, generating the [(R)3Sn](+) carbocation. On the other hand, MS/MS spectra of [(R)2Sn(Gly)-H](+) complexes are characterized by numerous fragmentation processes. Six of them, associated with elimination of H2O, CO, H2O?+?CO and formation of [(R)2SnOH](+) (-57?u),[(R)2SnNH2](+) (-58?u) and [(R)2SnH](+) (-73?u), are systematically observed. Use of labeled glycines notably concludes that the hydrogen atoms eliminated in water and H2O?+?CO are labile hydrogens. A similar conclusion can be made for hydrogens of [(R2)SnOH](+) and [(R2)SnNH2](+) ions. Interestingly, formation [(R)2SnH](+) ions is characterized by a migration of one the ? hydrogen of glycine onto the metallic center. Finally, several dissociation routes are observed and are characteristic of a given organic substituent. Calculations indicated that the interaction between organotins and glycine is mostly electrostatic. For [(R)2Sn(Gly)-H](+) complexes, a preferable bidentate interaction of the type ?(2)-O,NH2 is observed, similar to that encountered for other metal ions. [(R)3Sn](+) ions strongly stabilize the zwitterionic form of glycine, which is practically degenerate with respect to neutral glycine. In addition, the interconversion between both forms is almost barrierless. Suitable mechanisms are proposed in order to account for the most relevant fragmentation processes. PMID:23832935

Latrous, Latifa; Tortajada, Jeanine; Haldys, Violette; Léon, Emmanuelle; Correia, Catarina; Salpin, Jean-Yves

2013-07-01

292

Gas-Phase Combustion Synthesis of Aluminum Nitride Powder  

NASA Technical Reports Server (NTRS)

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.

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

1996-01-01

293

Measurement of Gas-phase Acids in Diesel Exhaust  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

294

IV-VI semiconductor lasers for gas phase biomarker detection  

NASA Astrophysics Data System (ADS)

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.

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

2007-09-01

295

Infrared spectra of dimethylphenanthrenes in the gas phase.  

PubMed

Infrared spectra of atmospherically and astronomically important dimethylphenanthrenes (DMPs), namely 1,9-DMP, 2,4-DMP, and 3,9-DMP, were recorded in the gas phase from 400 to 4000 cm(-1) with a resolution of 0.5 cm(-1) at 110 °C using a 7.2 m gas cell. DFT calculations at the B3LYP/6-311G** level were carried out to get the harmonic and anharmonic frequencies and their corresponding intensities for the assignment of the observed bands. However, spectral assignments could not be made unambiguously using anharmonic or selectively scaled harmonic frequencies. Therefore, the scaled quantum mechanical (SQM) force field analysis method was adopted to achieve more accurate assignments. In this method force fields instead of frequencies were scaled. The cartesian force field matrix obtained from the gaussian calculations was converted to a nonredundant local coordinate force field matrix and then the force fields were scaled to match experimental frequencies in a consistent manner using a modified version of the UMAT program of the QCPE package. Potential energy distributions (PEDs) of the normal modes in terms of nonredundant local coordinates obtained from these calculations helped us derive the nature of the vibration at each frequency. The intensity of observed bands in the experimental spectra was calculated using estimated vapor pressures of the DMPs. An error analysis of the mean deviation between experimental and calculated intensities reveal that the observed methyl C-H stretching intensity deviates more compared to the aromatic C-H and non C-H stretching bands. PMID:21797244

Das, Prasanta; Arunan, E; Das, Puspendu K

2012-06-21

296

Infrared spectroscopy of ionized corannulene in the gas phase  

NASA Astrophysics Data System (ADS)

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

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

2011-02-01

297

Towards the chemometric dissection of peptide--HLA-A*0201 binding affinity: comparison of local and global QSAR models.  

PubMed

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

Doytchinova, Irini A; Walshe, Valerie; Borrow, Persephone; Flower, Darren R

2005-03-01

298

Absolute Standard Hydrogen Electrode Potential Measured by Reduction of Aqueous Nanodrops in the Gas Phase  

PubMed Central

In solution, half-cell potentials are measured relative to those of other half cells, thereby establishing a ladder of thermochemical values that are referenced to the standard hydrogen electrode (SHE), which is arbitrarily assigned a value of exactly 0 V. Although there has been considerable interest in, and efforts toward, establishing an absolute electrochemical half-cell potential in solution, there is no general consensus regarding the best approach to obtain this value. Here, ion-electron recombination energies resulting from electron capture by gas-phase nanodrops containing individual [M(NH3)6]3+, M = Ru, Co, Os, Cr, and Ir, and Cu2+ ions are obtained from the number of water molecules that are lost from the reduced precursors. These experimental data combined with nanodrop solvation energies estimated from Born theory and solution-phase entropies estimated from limited experimental data provide absolute reduction energies for these redox couples in bulk aqueous solution. A key advantage of this approach is that solvent effects well past two solvent shells, that are difficult to model accurately, are included in these experimental measurements. By evaluating these data relative to known solution-phase reduction potentials, an absolute value for the SHE of 4.2 ± 0.4 V versus a free electron is obtained. Although not achieved here, the uncertainty of this method could potentially be reduced to below 0.1 V, making this an attractive method for establishing an absolute electrochemical scale that bridges solution and gas-phase redox chemistry. PMID:18288835

Donald, William A.; Leib, Ryan D.; O'Brien, Jeremy T.; Bush, Matthew F.; Williams, Evan R.

2008-01-01

299

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

SciTech Connect

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

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

2013-04-27

300

The Application of Gaussian Mixture Models for Signal Quantification in MALDI-ToF Mass Spectrometry of Peptides  

PubMed Central

Matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) coupled with stable isotope standards (SIS) has been used to quantify native peptides. This peptide quantification by MALDI-TOF approach has difficulties quantifying samples containing peptides with ion currents in overlapping spectra. In these overlapping spectra the currents sum together, which modify the peak heights and make normal SIS estimation problematic. An approach using Gaussian mixtures based on known physical constants to model the isotopic cluster of a known compound is proposed here. The characteristics of this approach are examined for single and overlapping compounds. The approach is compared to two commonly used SIS quantification methods for single compound, namely Peak Intensity method and Riemann sum area under the curve (AUC) method. For studying the characteristics of the Gaussian mixture method, Angiotensin II, Angiotensin-2-10, and Angiotenisn-1-9 and their associated SIS peptides were used. The findings suggest, Gaussian mixture method has similar characteristics as the two methods compared for estimating the quantity of isolated isotopic clusters for single compounds. All three methods were tested using MALDI-TOF mass spectra collected for peptides of the renin-angiotensin system. The Gaussian mixture method accurately estimated the native to labeled ratio of several isolated angiotensin peptides (5.2% error in ratio estimation) with similar estimation errors to those calculated using peak intensity and Riemann sum AUC methods (5.9% and 7.7%, respectively). For overlapping angiotensin peptides, (where the other two methods are not applicable) the estimation error of the Gaussian mixture was 6.8%, which is within the acceptable range. In summary, for single compounds the Gaussian mixture method is equivalent or marginally superior compared to the existing methods of peptide quantification and is capable of quantifying overlapping (convolved) peptides within the acceptable margin of error. PMID:25372836

Spainhour, John Christian G.; Janech, Michael G.; Schwacke, John H.; Velez, Juan Carlos Q.; Ramakrishnan, Viswanathan

2014-01-01

301

Gas-phase-dependent properties of SnO2 (110), (100), and (101) single-crystal surfaces: Structure, composition, and electronic properties  

E-print Network

Gas-phase-dependent properties of SnO2 (110), (100), and (101) single-crystal surfaces: Structure surface, leaving a SnO surface layer with a 1 1 periodicity. For the 110 surface the lowest energy surface under reducing conditions was predicted for a model with a SnO surface layer with all bridging oxygen

Diebold, Ulrike

302

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

PubMed Central

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

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

2013-01-01

303

Gas-phase reaction of N2O5 with water vapor: Importance of heterogeneous hydrolysis of N2O5 and surface desorption of HNO3 in a large Teflon chamber  

Microsoft Academic Search

Laboratory measurements of the gas-phase hydrolysis of N2O5 are always preturbed by wall reactions. Their contribution could be quantified in a large double-walled teflon bag chamber by introducing HNO3 into the chamber and analysing its temporal evolution in the gas-phase at low and high relative humidities, and by varying the surface-to-volume ratio of the chamber. By fitting a model to

Andreas Wahner; Thomas F. Mentel; Martin Sohn

1998-01-01

304

Modeling the thermal unfolding 2DIR spectra of a ?-hairpin peptide based on the implicit solvent MD simulation.  

PubMed

We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a ?-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition. PMID:23496267

Wu, Tianmin; Yang, Lijiang; Zhang, Ruiting; Shao, Qiang; Zhuang, Wei

2013-07-25

305

High resolution trapped ion mobility spectrometery of peptides.  

PubMed

In the present work, we employ trapped ion mobility spectrometry (TIMS) for conformational analysis of several model peptides. The TIMS distributions are extensively compared to recent ion mobility spectrometry (IMS) studies reported in the literature. At a resolving power (R) exceeding 250, many new features, otherwise hidden by lower resolution IMS analyzers, are revealed. Though still principally limited by the plurality of conformational states, at present, TIMS offers R up to ?3 to 8 times greater than modern drift tube or traveling wave IMS techniques, respectively. Unlike differential IMS, TIMS not only is able to resolve congested conformational features but also can be used to determine information about their relative size, via the ion-neutral collision cross section, offering a powerful new platform to probe the structure and dynamics of biochemical systems in the gas phase. PMID:24862843

Silveira, Joshua A; Ridgeway, Mark E; Park, Melvin A

2014-06-17

306

Modeling the Interaction between Integrin-Binding Peptide (RGD) and Rutile Surface: The Effect of Na+ on Peptide Adsorption  

SciTech Connect

The dynamics of a single tripeptide Arg-Gly-Asp (RGD) adsorbing onto negatively charged hydroxylated rutile (110) surface in aqueous solution was studied using molecular dynamics (MD) simulations. The results indicate that the adsorbed Na{sup +} ions play an important role in determining the binding geometry of RGD. With an initial 'horseshoe' configuration, the charged side groups (COO{sup -} and NH{sub 2}) of the peptide are able to interact with the surface through direct hydrogen bonds (H bonds) in the very early stage of adsorption. The Na{sup +} ions approach the positively charged Arg side chain, competing with the Arg side chain for adsorption to the negatively charged hydroxyl oxygen. In coordination with the structural adjustment of the peptide, the Arg residue is driven to detach from the rutile surface. In contrast, the Na+ ions in close proximity to the negatively charged Asp side chain contribute to the binding of the COO{sup -} group on the surface, helping the carboxyl oxygen not involved in COO{sup -}-surface H bonds to orientate toward the hydroxyl hydrogens. Once both carboxyl oxygens form enough H bonds with the hydroxyl hydrogens, the redundant ions move toward a more favorable adsorption site.

Wu, Chunya [Harbin Institute of Technology; Skelton, Adam [Vanderbilt University; Chen, Mingjun [Harbin Institute of Technology; Vlcek, Lukas [ORNL; Cummings, Peter T [ORNL

2011-01-01

307

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

PubMed

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

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

2015-01-01

308

Detection methods for atoms and radicals in the gas phase  

NASA Astrophysics Data System (ADS)

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

Hack, W.

309

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

NASA Technical Reports Server (NTRS)

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

Rhatigan, Jennifer L.

2001-01-01

310

Antitumor effects of EGFR antisense guanidine-based peptide nucleic acids in cancer models.  

PubMed

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

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

2013-02-15

311

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

EPA Science Inventory

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

312

Microsolvation of 2-azetidinone: a model for the peptide group-water interactions.  

PubMed

2-Azetidinone-water clusters can be considered as appropriate models for investigating the interaction of the peptide functional group with water. The rotational spectra of 2-azetidinone-(H2O)n (n = 1, 2) complexes have been studied in the 6-18 GHz frequency range using a molecular beam Fourier transform microwave spectrometer. Two different isomers have been observed for the 1?:?1 adduct. The most stable (1?:?1a) is stabilized by two hydrogen bonds O-HO[double bond, length as m-dash]C and N-HO with water closing a ring with the peptide group. For the other conformer (1?:?1b), water is placed on the other side of the carbonyl group stabilized by O-HO[double bond, length as m-dash]C and C-HO hydrogen bonds. In 2-azetidinone-(H2O)2 the water molecules close a ring with the peptide group forming three different hydrogen bonds: O-HO[double bond, length as m-dash]C, O-HO and N-HO. The spectra of the parent and several isotopologues of each cluster have been investigated in order to determine their structures. The hydrogen bond geometries show that the dominant interaction is the O-HO[double bond, length as m-dash]C hydrogen bond, in good agreement with the observed preference of water to interact with this group in proteins. A comparison between the geometries of the different observed adducts shows clearly how cooperative hydrogen bonding plays an important role in the stabilization of these complexes. No detectable structural changes have been observed for 2-azetidinone upon hydration with one water molecule. PMID:25478744

López, Juan C; Sánchez, Raquel; Blanco, Susana; Alonso, José L

2015-01-21

313

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

NASA Astrophysics Data System (ADS)

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.

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

2008-11-01

314

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

SciTech Connect

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

Stanley, A.E.; Ludwick, L.M.; White, D.; Andrews, D.E.; Godbey, S.E. (AMSMI-RD-WS-CM, Redstone Arsenal, AL (United States))

1992-12-01

315

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

NASA Technical Reports Server (NTRS)

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.

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

1988-01-01

316

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

SciTech Connect

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

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

2009-04-03

317

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

SciTech Connect

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.

Hall G. E.; Goncharov, V.

2012-05-29

318

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

NASA Astrophysics Data System (ADS)

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 (?,?) maps of the local-mode frequencies and couplings. Performing conformational averages of the (?,?) maps with respect to the most important peptide conformational states in solution (?,?,PII, 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.

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

2005-06-01

319

In vivo characterization of the peptide deformylase inhibitor LBM415 in murine infection models.  

PubMed

LBM415 is an antibacterial agent belonging to the peptide deformylase inhibitor class of compounds. It has previously been shown to demonstrate good activity in vitro against a range of pathogens. In this study, the in vivo efficacy of LBM415 was evaluated in various mouse infection models. We investigated activity against a systemic infection model caused by intraperitoneal inoculation of Staphylococcus aureus (methicillin [meticillin] susceptible [MSSA] and methicillin resistant [MRSA]) and Streptococcus pneumoniae (penicillin susceptible [PSSP] and multidrug resistant [MDRSP]), a thigh infection model caused by intramuscular injection of MRSA, and a lung infection produced by intranasal inoculation of PSSP. In the systemic MSSA and MRSA infections, LBM415 was equivalent to linezolid and vancomycin. In the systemic PSSP infection, LBM415 was equivalent to linezolid, whereas against systemic MDRSP infection, the LBM415 50% effective dose (ED50) was 4.8 mg/kg (dosed subcutaneously) and 36.6 mg/kg (dosed orally), compared to 13.2 mg/kg for telithromycin and >60 mg/kg for penicillin V and clarithromycin. In the MRSA thigh infection, LBM415 significantly reduced thigh bacterial levels compared to those of untreated mice, with levels similar to those after treatment with linezolid at the same dose levels. In the pneumonia model, the ED50 to reduce the bacterial lung burden by >4 log10 in 50% of treated animals was 23.3 mg/kg for LBM415, whereas moxifloxacin showed an ED50 of 14.3 mg/kg. In summary, LBM415 showed in vivo efficacy in sepsis and specific organ infection models irrespective of resistance to other antibiotics. Results suggest the potential of peptide deformylase inhibitors as a novel class of therapeutic agents against antibiotic-resistant pathogens. PMID:19596876

Osborne, Colin S; Neckermann, Georg; Fischer, Evelin; Pecanka, Robert; Yu, Donghui; Manni, Kari; Goldovitz, Julie; Amaral, Kerri; Dzink-Fox, JoAnn; Ryder, Neil S

2009-09-01

320

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

PubMed

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

Fields, Gregg B

2010-03-21

321

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

PubMed Central

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

2013-01-01

322

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

PubMed

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

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

2014-01-01

323

Apoptosis imaging studies in various animal models using radio-iodinated peptide.  

PubMed

Apoptosis has a role in many medical disorders and treatments; hence, its non-invasive evaluation is one of the most riveting research topics. Currently annexin V is used as gold standard for imaging apoptosis. However, several drawbacks, including high background, slow body clearance, make it a suboptimum marker for apoptosis imaging. In this study, we radiolabeled the recently identified histone H1 targeting peptide (ApoPep-1) and evaluated its potential as a new apoptosis imaging agent in various animal models. ApoPep-1 (CQRPPR) was synthesized, and an extra tyrosine residue was added to its N-terminal end for radiolabeling. This peptide was radiolabeled with (124)I and (131)I and was tested for its serum stability. Surgery- and drug-induced apoptotic rat models were prepared for apoptosis evaluation, and PET imaging was performed. Doxorubicin was used for xenograft tumor treatment in mice, and the induced apoptosis was studied. Tumor metabolism and proliferation were assessed by [(18)F]FDG and [(18)F]FLT PET imaging and compared with ApoPep-1 after doxorubicin treatment. The peptide was radiolabeled at high purity, and it showed reasonably good stability in serum. Cell death was easily imaged by radiolabeled ApoPep-1 in an ischemia surgery model. And, liver apoptosis was more clearly identified by ApoPep-1 rather than [(124)I]annexin V in cycloheximide-treated models. Three doxorubicin doses inhibited tumor growth, which was evaluated by 30-40 % decreases of [(18)F]FDG and [(18)F]FLT PET uptake in the tumor area. However, ApoPep-1 demonstrated more than 200 % increase in tumor uptake after chemotherapy, while annexin V did not show any meaningful uptake in the tumor compared with the background. Biodistribution data were also in good agreement with the microPET imaging results. All of the experimental data clearly demonstrated high potential of the radiolabeled ApoPep-1 for in vivo apoptosis imaging. PMID:25430587

Kwak, Wonjung; Ha, Yeong Su; Soni, Nisarg; Lee, Woonghee; Park, Se-Il; Ahn, Heesu; An, Gwang Il; Kim, In-San; Lee, Byung-Heon; Yoo, Jeongsoo

2015-01-01

324

Gramicidin S: a peptide model for protein glycation and reversal of glycation using nucleophilic amines.  

PubMed

Nonenzymatic glycation of proteins has been implicated in various diabetic complications and age-related disorders. Proteins undergo glycation at the N-terminus or at the epsilon-amino group of lysine residues. Glycation of proteins proceeds through the stages of Schiff base formation, conversion to ketoamine product and advanced glycation end products. Gramicidin S, which has two ornithine residues, was used as a model system to study the various stages of glycation of proteins using electrospray ionization mass spectrometry. The proximity of two ornithine residues in the peptide favors the glycation reaction. Formation of advanced glycation end products and diglycation on ornithine residues in gramicidin S were observed. The formation of Schiff base adduct is reversible, whereas the Amadori rearrangement to the ketoamine product is irreversible. Nucleophilic amines and hydrazines can deglycate the Schiff base adduct of glucose with peptides and proteins. Hydroxylamine, isonicotinic acid hydrazide and aminoguanidine effectively removed glucose from the Schiff base adduct of gramicidin S. Hydroxylamine is more effective in deglycating the adduct compared with isonicotinic acid hydrazide and aminoguanidine. The observation that the hydrazines are effective in deglycating the Schiff base adduct even in the presence of high concentrations of glucose, may have a possible therapeutic application in preventing complications of diabetes mellitus. Hydrazines may be used to distinguish between the Schiff base and the ketoamine products formed at the initial stages of glycation. PMID:12102724

Shakkottai, V G; Sudha, R; Balaram, P

2002-08-01

325

Therapeutic effect of a TM4SF5-specific peptide vaccine against colon cancer in a mouse model  

PubMed Central

Molecular-targeted therapy has gained attention because of its high efficacy and weak side effects. Previously, we confirmed that transmembrane 4 superfamily member 5 protein (TM4SF5) can serve as a molecular target to prevent or treat hepatocellular carcinoma (HCC). We recently extended the application of the peptide vaccine, composed of CpG-DNA, liposome complex, and TM4SF5 peptide, to prevent colon cancer in a mouse model. Here, we first implanted mice with mouse colon cancer cells and then checked therapeutic effects of the vaccine against tumor growth. Immunization with the peptide vaccine resulted in robust production of TM4SF5-specific antibodies, alleviated tumor growth, and reduced survival rate of the tumor-bearing mice. We also found that serum levels of VEGF were markedly reduced in the mice immunized with the peptide vaccine. Therefore, we suggest that the TM4SF5-specific peptide vaccine has a therapeutic effect against colon cancer in a mouse model. [BMB Reports 2014; 47(4): 215-220] PMID:24286311

Kwon, Sanghoon; Kim, Young-Eun; Park, Jeong-A; Kim, Doo-Sik; Kwon, Hyung-Joo; Lee, Younghee

2014-01-01

326

Amyloid peptides ABri and ADan show differential neurotoxicity in transgenic Drosophila models of familial British and Danish dementia  

PubMed Central

Background Familial British and Familial Danish dementias (FBD and FDD, respectively) are associated with mutations in the BRI2 gene. Processing of the mutated BRI2 protein leads to the accumulation in the brain of the 34-mer amyloid Bri (ABri) and amyloid Dan (ADan) peptides, accompanied by neurofibrillary tangles. Recently, transgenic mice successfully reproduced different aspects of FDD, while modeling of FBD in vivo has been more difficult. In this work we have modeled FBD and FDD in Drosophila and tested the hypothesis that ABri and ADan are differentially neurotoxic. Results By using site-directed insertion, we generated transgenic lines carrying ABri, ADan, Bri2-23 (the normal product of wild-type BRI2 processing) and amyloid-? (A?) 1–42 as a well-characterized neurotoxic peptide, alone or with a His-tag. Therefore, we avoided random insertion effects and were able to compare levels of accumulation accurately. Peptides were expressed with the GAL4-Upstream Activating Sequence (UAS) system using specific drivers. Despite low levels of expression, toxicity in the eye was characterized by mild disorganization of ommatidia and amyloid peptides accumulation. The highest toxicity was seen for ADan, followed by A?42 and ABri. Pan-neuronal expression in the CNS revealed an age-dependent toxicity of amyloid peptides as determined by the ability of flies to climb in a geotaxis paradigm when compared to Bri2-23. This effect was stronger for ADan, detected at 7 days post-eclosion, and followed by ABri and A?42, whose toxicity became evident after 15 and 21 days, respectively. Histological analysis showed mild vacuolization and thioflavine-S-negative deposits of amyloid peptides. In contrast, the over-expression of amyloid peptides in the specific subset of lateral neurons that control circadian locomotor activity showed no toxicity. Conclusions Our results support the differential neurotoxicity of ADan and ABri in the Drosophila eye and CNS at low expression levels. Such differences may be partially attributed to rates of aggregation and accumulation. In the CNS, both peptides appear to be more neurotoxic than wild-type A?42. These Drosophila models will allow a systematic and unambiguous comparison of differences and similarities in the mechanisms of toxicity of diverse amyloid peptides associated with dementia. PMID:24405716

2014-01-01

327

Machine learning based prediction for peptide drift times in ion mobility spectrometry  

PubMed Central

Motivation: Ion mobility spectrometry (IMS) has gained significant traction over the past few years for rapid, high-resolution separations of analytes based upon gas-phase ion structure, with significant potential impacts in the field of proteomic analysis. IMS coupled with mass spectrometry (MS) affords multiple improvements over traditional proteomics techniques, such as in the elucidation of secondary structure information, identification of post-translational modifications, as well as higher identification rates with reduced experiment times. The high throughput nature of this technique benefits from accurate calculation of cross sections, mobilities and associated drift times of peptides, thereby enhancing downstream data analysis. Here, we present a model that uses physicochemical properties of peptides to accurately predict a peptide's drift time directly from its amino acid sequence. This model is used in conjunction with two mathematical techniques, a partial least squares regression and a support vector regression setting. Results: When tested on an experimentally created high confidence database of 8675 peptide sequences with measured drift times, both techniques statistically significantly outperform the intrinsic size parameters-based calculations, the currently held practice in the field, on all charge states (+2, +3 and +4). Availability: The software executable, imPredict, is available for download from http:/omics.pnl.gov/software/imPredict.php Contact: rds@pnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20495001

Shah, Anuj R.; Agarwal, Khushbu; Baker, Erin S.; Singhal, Mudita; Mayampurath, Anoop M.; Ibrahim, Yehia M.; Kangas, Lars J.; Monroe, Matthew E.; Zhao, Rui; Belov, Mikhail E.; Anderson, Gordon A.; Smith, Richard D.

2010-01-01

328

A three-dimensional model of the delta-opioid pharmacophore: comparative molecular modeling of peptide and nonpeptide ligands.  

PubMed

A comparative molecular modeling study of delta-opioid ligands was performed under the assumption that potent peptide and nonpeptide agonists may have common three-dimensional (3D) arrangement of pharmacophore groups upon binding to the delta-receptor. Low-energy conformations of the agonists 7-spiroindanyloxymorphone (SIOM) and 2-methyl-4a-alpha-(3-hydroxyphenyl)-1,2,3,4,4a,5,12, 12a-alpha-octahydro-quinolino[2,3,3-g]isoquinoline (TAN-67), and a partial agonist oxomorphindole (OMI) were determined by high-temperature molecular dynamics (MD). A good spatial overlap was found for the pharmacophore groups of SIOM, TAN-67, and OMI, including the basic nitrogen, phenol hydroxyl, and two aromatic ring. Based on this overlap we proposed a 3D pharmacophore model for nonpeptide delta-opioid agonists with a distance of 7.0 +/- 1.3 A between the two aromatic rings and of 8.2 +/- 1.0 A between the nitrogen and phenyl ring. The potent and highly delta-opioid receptor selective agonist [(2S,3R)-TMT(1)]DPDPE, which shares global backbone constraints of the 14-membered disulfide cycle and a strong preference for the trans rotamer of the TMT(1) side chain, was chosen as a peptide template of the delta-opioid pharmacophore. Extensive MD simulations at 300 K with the AMBER force field were performed for [(2S,3R)-TMT(1)]DPDPE and the less potent [(2S, 3S)-TMT(1)]DPDPE analogue. Multiple MD trajectories were collected for each peptide starting from the x-ray structures of DPDPE and [L-Ala(3)]DPDPE and from models proposed in the literature. Low-energy MD conformations were filtered by the nonpeptide pharmacophore query and then directly superimposed with SIOM, OMI, and TAN-67. Two conformers of [(2S,3R)-TMT(1)]DPDPE that showed the best overlap with the nonpeptide pharmacophore (rms deviation peptides. The proposed 3D models were used for rational design of new nonpeptide delta-receptor ligands. PMID:10766952

Shenderovich, M D; Liao, S; Qian, X; Hruby, V J

2000-06-01

329

Elementary Reactions and Their Role in Gas-Phase Prebiotic Chemistry  

PubMed Central

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

Balucani, Nadia

2009-01-01

330

The role of stabilised Criegee intermediate in gas phase H2SO4 formation  

NASA Astrophysics Data System (ADS)

Sulfuric acid in the gas phase plays a central role in new particle formation and in particle growth. Fine particles directly affect human health via inhalation and have an important impact on climate. In the gas phase, sulfuric acid is known to be formed from the oxidation of SO2 by the OH radical in the presence of oxygen and water. In the last decade, new measurements of OH and H2SO4 have shown relatively high concentrations of H2SO4 during nighttime when the corresponding concentration of OH radicals was too low to explain such high concentrations of sulfuric acid. New laboratory experiments, in addition to theoretical studies, have shown that a possible candidate for the oxidation of SO2 is Stabilized Criegee Intermediates (SCIs) arising from the ozonolysis of alkenes. The rate coefficient for the reaction of CH2OO + SO2 has been measured at 3.9 x 10-11 cm3 molecule-1 s-1 indicating a probable competing role for the SCI in the production of sulfuric acid. Measurements of a fraction of atmospheric SCIs with laser-induced fluorescence (LIF) have been made using a chemical subtraction method both in the laboratory and in the field. The SCIs undergo unimolecular decomposition at low pressure inside the instrument forming OH that is then detected. Model results and laboratory tests confirm our findings. This new instrumental setup has been used in several environments including Finland (HUMPPA-COPEC), Spain (DOMINO HOx) and Germany (HOPE 2012) revealing a unique SCI signal strongly influenced by different kinds of vegetation and meteorological conditions. Results from the HUMPPA campaign show a missing H2SO4 production after taking into account the contribution of the OH radical. The SCIs signal measured with our instrument shows a good correlation with this missing production confirming the important role of the SCI in the oxidation of SO2 and in the formation of sulfuric acid. Using the missing H2SO4 production rate together with the rate coefficient for the reaction CH2COO + SO2, it has been possible to calculate a lower limit for the concentration of SCIs in the atmosphere, while the estimated VOCs concentration from the total OH reactivity provides an upper limit.

Novelli, A.; Hens, K.; Kubistin, D.; Tatum Ernest, C.; Trawny, K.; Rudolf, M.; Auld, J.; Axinte, R.; Hosaynali Beygi, Z.; Nölscher, A.; Paasonen, P.; Sipilä, M.; Keronen, P.; Petdjd, T. T.; Adame, J.; Elste, T.; Werner, A.; Englert, J.; Plass-Duelmer, C.; Fischer, H.; Williams, J.; Vereecken, L.; Martinez, M.; Lelieveld, J.; Harder, H. D.

2012-12-01

331

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)

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.

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

2012-11-01

332

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

SciTech Connect

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)

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

333

Effect of antisense peptide binding on the dimerization of human cystatin C--gel electrophoresis and molecular modeling studies.  

PubMed

Human cystatin C (HCC) shows a tendency to dimerize. This process is particularly easy in the case of the L68Q HCC mutant and might lead to formation of amyloid deposits in brain arteries of young adults. Our purpose was to find ligands of monomeric HCC that can prevent its dimerization. Eleven antisense peptide ligands of monomeric HCC were designed and synthesized. The influence of these ligands on HCC dimerization was studied using gel electrophoresis and molecular modeling methods. The results suggest that all the designed peptides interact with monomeric HCC facilitating its dimerization rather than preventing it. PMID:15094836

Stachowiak, Krystyna; Rodziewicz-Motowid?o, Sylwia; Sosnowska, Renata; Kasprzykowski, Franciszek; ?ankiewicz, Leszek; Grubb, Anders; Grzonka, Zbigniew

2004-01-01

334

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

PubMed Central

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

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

2010-01-01

335

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

PubMed

Substance P (RPKPQQFFGLM-NH2) [M + 3H](3+) ions have been shown to exist as two conformers: one that is kinetically trapped and one that is thermodynamically more stable and therefore energetically preferred. Molecular dynamics (MD) simulations suggested that the kinetically trapped population is stabilized by interactions between the charge sites and the polar side chains of glutamine (Q) located at positions 5 and 6 and phenylalanine (F) located at positions 7 and 8. Here, the individual contributions of these specific intramolecular interactions are systematically probed through site-directed alanine mutations of the native amino acid sequence. Ion mobility spectrometry data for the mutant peptide ions confirm that interactions between the charge sites and glutamine/phenylalanine (Q/F) side chains afford stabilization of the kinetically trapped ion population. In addition, experimental data for proline-to-alanine mutations at positions 2 and 4 clearly show that interactions involving the charge sites and the Q/F side chains are altered by the cis/trans orientations of the proline residues and that mutation of glycine to proline at position 9 supports results from MD simulations suggesting that the C-terminus also provides stabilization of the kinetically trapped conformation. PMID:25402008

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

2014-12-11

336

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

PubMed

The daily and seasonal atmospheric concentrations, deposition fluxes and emission sources of a few C3-C9 gaseous alkyl nitrates (ANs) at the Belgian coast (De Haan) on the Southern North Sea were determined. An adapted sampler design for low- and high-volume air-sampling, optimized sample extraction and clean-up, as well as identification and quantification of ANs in air samples by means of gas chromatography mass spectrometry, are reported. The total concentrations of ANs ranged from 0.03 to 85 pptv and consisted primarily of the nitro-butane and nitro-pentane isomers. Air mass backward trajectories were calculated by the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model to determine the influence of main air masses on AN levels in the air. The shorter chain ANs have been the most abundant in the Atlantic/Channel/UK air masses, while longer chain ANs prevailed in continental air. The overall mean N fluxes of the ANs were slightly higher for summer than those for winter-spring, although their contributions to the total nitrogen flux were low. High correlations between AN and HNO? levels were observed during winter/spring. During summer, the shorter chain ANs correlated well with precipitation. Source apportionment by means of principal component analysis indicated that most of the gas phase ANs could be attributed to traffic/combustion, secondary photochemical formation and biomass burning, although marine sources may also have been present and a contributing factor. PMID:24952420

Dirtu, Alin C; Buczy?ska, Anna J; Godoi, Ana F L; Favoreto, Rodrigo; Bencs, László; Potgieter-Vermaak, Sanja S; Godoi, Ricardo H M; Van Grieken, René; Van Vaeck, Luc

2014-10-01

337

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

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

338

A Kinetic Study of the Gas-Phase Reaction of OH with Br2  

PubMed Central

An experimental, temperature-dependent kinetic study of the gas-phase reaction of the hydroxyl radical with molecular bromine (reaction 1) has been performed using a pulsed laser photolysis/pulsed-laser-induced fluorescence technique over a wide temperature range of 297 – 766 K, and at pressures between 6.68 and 40.29 kPa of helium. The experimental rate coefficients for reaction 1 demonstrate no correlation with pressure and exhibit a negative temperature dependence with a slight negative curvature in the Arrhenius plot. A non-linear least-squares fit with two floating parameters of the temperature dependent k1(T) data set using an equation of the form k1(T) = ATn yields the recommended expression k1(T) = 1.85×10?9T ? 0.66 cm3 molecule?1 s?1 for the temperature dependence of the reaction 1 rate coefficient. The potential energy surface (PES) of reaction 1 was investigated using quantum chemistry methods. The reaction proceeds through formation of a weakly bound OH···Br2 complex and a PES saddle point with an energy below that of the reactants. Temperature dependence of the reaction rate coefficient was modeled using the RRKM method on the basis of the calculated PES. PMID:16854030

Bryukov, Mikhail G.; Dellinger, Barry; Knyazev, Vadim D.

2011-01-01

339

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

NASA Technical Reports Server (NTRS)

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

Powell, Michael R.

1991-01-01

340

Side-Chain Interactions Determine Amyloid Formation by Model Polyglutamine Peptides in Molecular Dynamics Simulations  

PubMed Central

The pathological manifestation of nine hereditary neurodegenerative diseases is the presence within the brain of aggregates of disease-specific proteins that contain polyglutamine tracts longer than a critical length. To improve our understanding of the processes by which polyglutamine-containing proteins misfold and aggregate, we have conducted molecular dynamics simulations of the aggregation of model polyglutamine peptides. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms, depending on the residue being modeled. The effects of hydrophobicity on the system are studied by varying the strength of the hydrophobic interaction from 12.5% to 5% of the hydrogen-bonding interaction strength. In our simulations, we observe the spontaneous formation of aggregates and annular structures that are made up of ?-sheets starting from random configurations of random coils. This result was interesting because tubular protofibrils were recently found in experiments on polyglutamine aggregation and because of Perutz's prediction that polyglutamine would form water-filled nanotubes. PMID:16565057

Marchut, Alexander J.; Hall, Carol K.

2006-01-01

341

Probing the Radical and Base Dual Properties of Peptide Sulfinyl Radicals via Mass Spectrometry.  

PubMed

Heteroatom-centered radicals are known to play critical roles in atmospheric chemistry, organic synthesis, and biology. While most studies have focused on the radical reactivity such as hydrogen abstraction, the base properties of heteroatom-centered radicals have long been overlooked, despite the profound consequences, such as their ability to participate in hydrogen-bonding networks. In this study, we use the sulfinyl radical (-SO(•)) as a model to show that the dual properties of heteroatom-centered radicals, that is, their ability to function as a radical and a base, can coexist in peptides and be differentiated by examining the loss of hydrosulfinyl radical (SOH) upon unimolecular dissociation of the peptide sulfinyl radical ions in the gas phase. The loss of SOH can result from two channels; one involves hydrogen atom abstraction, which reflects the radical property; the other is initiated by proton transfer to the sulfinyl radical, manifesting its base property. Tuning of the two properties of peptide sulfinyl radicals can be achieved by varying the chemical properties of the neighboring functional groups, which demonstrates the influence of the local chemical environment on the behavior of the radical species. The experimental approach established in this study to probe the dual chemical property of the peptide sulfinyl radical can be potentially applied to studying other types of heteroatom-centered radical species of biological significance. PMID:25428214

Tan, Lei; Ture?ek, František; Francisco, Joseph S; Xia, Yu

2014-12-18

342

Determination of peptide topology through time-resolved double-resonance under electron capture dissociation conditions.  

PubMed

Characterizing the conformation of biomolecules by mass spectrometry still represents a challenge. With their knotted structure involving a N-terminal macrolactam ring where the C-terminal tail of the peptide is threaded and sterically trapped, lasso peptides constitute an attractive model for developing methods for characterizing gas-phase conformation, through comparison with their unknotted topoisomers. Here, the kinetics of electron capture dissociation (ECD) of a lasso peptide, capistruin, was investigated by electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry and compared to that of its branched-cyclic topoisomer, lactam-capistruin. Both peptides produced rather similar ECD spectra but showed different extent of H(•) transfer from c(i)' to z(j)(•) ions. Time-resolved double-resonance experiments under ECD conditions were performed to measure the formation rate constants of typical product ions. Such experiments showed that certain product ions, in particular those related to H(•) transfer, proceeded through long-lived complexes for capistruin, while fast dissociation processes predominated for lactam-capistruin. The formation rate constants of specific ECD product ions enabled a clear differentiation of the lasso and branched-cyclic topoisomers. These results indicate that the formation kinetics of ECD product ions constitute a new way to explore the conformation of biomolecules and distinguish between topoisomers and, more generally, conformers. PMID:22571326

Pérot-Taillandier, Marie; Zirah, Séverine; Rebuffat, Sylvie; Linne, Uwe; Marahiel, Mohamed A; Cole, Richard B; Tabet, Jean-Claude; Afonso, Carlos

2012-06-01

343

[Synthetic peptide vaccines].  

PubMed

This review considers the stages of the development of synthetic peptide vaccines against infectious agents, novel approaches and technologies employed in this process, including bioinformatics, genomics, proteomics, large-scale peptide synthesis, high-throughput screening methods, the use of transgenic animals for modelling human infections. An important role for the development and selection of efficient adjuvants for peptide immunogens is noted. Examples of synthetic peptide vaccine developments against three infectious diseases (malaria, hepatitis C, and foot-and-mouth disease) are given. PMID:21516776

Mo?sa, A A; Kolesanova, E F

2011-01-01

344

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

E-print Network

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.

Ma, Xiaoguang

2012-01-01

345

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

E-print Network

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.

Xiaoguang Ma; Feng Wang

2012-11-01

346

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

SciTech Connect

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

Han, J.; Figiel, J.J.; Crawford, M.H.; Banas, M.A.; Bartram, M.E.; Biefeld, R.M. [Sandia National Labs., Albuquerque, NM (United States); Song, Y.K.; Nurmikko, A.V. [Brown Univ., Providence, RI (United States). Div. of Engineering

1998-06-01

347

Do all the protic ionic liquids exist as molecular aggregates in the gas phase?  

PubMed

According to an EI-MS study of 1,1,3,3-tetramethylguanidium-based protic ionic liquids (PILs), it has been concluded that not all PILs exist as molecular aggregates in the gas phase. The detection of both ions of m/z 115.0 and m/z 116.0 for the 1,1,3,3-tetramethylguanidinium trifluoromethylsulfonate (TMGS) protic ionic liquid indicates that both the molecular and ionic aggregates co-exist in the gas phase, which is to say that the TMGS may also evaporate via the ionic aggregates just like aprotic ionic liquids. Furthermore, investigation on triethylamine-based and 1-methylimidazole-based PILs confirmed that the gas phase structure of PILs depends on both the acidity and basicity of the corresponding acid and base. PMID:21897972

Zhu, Xiao; Wang, Yong; Li, Haoran

2011-10-21

348

Gas-phase ambident reactivity of imidate anions (-NR1(CO)R2)  

NASA Astrophysics Data System (ADS)

It is shown by use of the method of Fourier transform ion cyclotron resonance mass spectrometry that imidate anions, generated by deprotonation of formamide, acetamide, N-methylformamide and trifluoroacetamide, exhibit an ambident chemical behavior in their gas-phase reactions with unsaturated perfluorocarbon compounds. This ambident behavior implies a competition between addition via the nitrogen and oxygen nucleophilic centers and appears to parallel the previously-studied ambident behavior of enolate anions in the gas phase. Rationalization of the selectivity of the studied imidate anion reactions has been discussed in terms of electrostatic and specific orbital interactions in the reaction complex. Likewise, thio-imidate anions generated by deprotonation of thioacetamide show an ambident chemical behavior which allows a fair competition between addition via the nitrogen and sulfur nucleophilic centers in the gas-phase reactions with unsaturated perfluorocarbon compounds.

Freriks, Ivo L.; de Koning, Leo J.; Nibbering, Nico M. M.

1992-09-01

349

Influence of gas phase equilibria on the chemical vapor deposition of graphene.  

PubMed

We have investigated the influence of gas phase chemistry on the chemical vapor deposition of graphene in a hot wall reactor. A new extended parameter space for graphene growth was defined through literature review and experimentation at low pressures (?0.001 mbar). The deposited films were characterized by scanning electron microscopy, Raman spectroscopy, and dark field optical microscopy, with the latter showing promise as a rapid and nondestructive characterization technique for graphene films. The equilibrium gas compositions have been calculated across this parameter space. Correlations between the graphene films grown and prevalent species in the equilibrium gas phase revealed that deposition conditions associated with a high acetylene equilibrium concentration lead to good quality graphene deposition, and conditions that stabilize large hydrocarbon molecules in the gas phase result in films with multiple defects. The transition between lobed and hexagonal graphene islands was found to be linked to the concentration of the monatomic hydrogen radical, with low concentrations associated with hexagonal islands. PMID:23484546

Lewis, Amanda M; Derby, Brian; Kinloch, Ian A

2013-04-23

350

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

DOEpatents

The present invention relates to a device for separation and characterization of gas-phase ions. The device incorporates an ion source, a field asymmetric waveform ion mobility spectrometry (FAIMS) analyzer, an ion mobility spectrometry (IMS) drift tube, and an ion detector. In one aspect of the invention, FAIMS operating voltages are electrically floated on top of the IMS drift voltage. In the other aspect, the FAIMS/IMS interface is implemented employing an electrodynamic ion funnel, including in particular an hourglass ion funnel. The present invention improves the efficiency (peak capacity) and sensitivity of gas-phase separations; the online FAIMS/IMS coupling creates a fundamentally novel two-dimensional gas-phase separation technology with high peak capacity, specificity, and exceptional throughput.

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

2006-12-12

351

pH-responsive endosomolytic pseudo-peptides for drug delivery to multicellular spheroids tumour models.  

PubMed

Endosomolytic polymers can aid in the endosomal release of therapeutics to improve intracellular drug delivery. pH-responsive biomimetic pseudo-peptides were synthesised by grafting l-phenylalanine onto the pendant carboxylic acids of a polyamide, poly(l-lysine isophthalamide). PP-75 (stoichiometric l-phenylalanine grafting of 75 mol%) was determined to have the best endosomolytic property. The mean hydrodynamic size of PP-75 decreased with lower pH as the polymers adopted a more compact conformation due to protonation of acidic groups and increase in hydrophobicity. PP-75 was demonstrated to deliver model drugs effectively in three dimensional (3D) magnetic HeLa multicellular spheroids used as in vitro tumour models. These spheroids can be isolated easily and quickly by magnetic separation. Due to its relatively small size, PP-75 was able to penetrate from the exterior to the interior of these spheroids and was internalised by the cells in the spheroids. It could retain its pH-mediated membrane-lytic capability in 3D drug delivery by releasing internalised calcein from intracellular endosomes in the tumour models. Furthermore, cell viability results suggest that PP-75 showed no significant cytotoxicity towards cells in the spheroids. The pH-responsive PP-75 can potentially enhance the extracellular and intracellular delivery of therapeutics in tumours. PMID:21272931

Ho, Vincent H B; Slater, Nigel K H; Chen, Rongjun

2011-04-01

352

A beta peptide vaccination prevents memory loss in an animal model of Alzheimer's disease.  

PubMed

Vaccinations with amyloid-beta peptide (A beta) can dramatically reduce amyloid deposition in a transgenic mouse model of Alzheimer's disease. To determine if the vaccinations had deleterious or beneficial functional consequences, we tested eight months of A beta vaccination in a different transgenic model for Alzheimer's disease in which mice develop learning deficits as amyloid accumulates. Here we show that vaccination with A beta protects transgenic mice from the learning and age-related memory deficits that normally occur in this mouse model for Alzheimer's disease. During testing for potential deleterious effects of the vaccine, all mice performed superbly on the radial-arm water-maze test of working memory. Later, at an age when untreated transgenic mice show memory deficits, the A beta-vaccinated transgenic mice showed cognitive performance superior to that of the control transgenic mice and, ultimately, performed as well as nontransgenic mice. The A beta-vaccinated mice also had a partial reduction in amyloid burden at the end of the study. This therapeutic approach may thus prevent and, possibly, treat Alzheimer's dementia. PMID:11140686

Morgan, D; Diamond, D M; Gottschall, P E; Ugen, K E; Dickey, C; Hardy, J; Duff, K; Jantzen, P; DiCarlo, G; Wilcock, D; Connor, K; Hatcher, J; Hope, C; Gordon, M; Arendash, G W

353

Gas-phase thermal dissociation of uranium hexafluoride: Investigation by the technique of laser-powered homogeneous pyrolysis  

SciTech Connect

In the gas-phase, uranium hexafluoride decomposes thermally in a quasi-unimolecular reaction to yield uranium pentafluoride and atomic fluorine. We have investigated this reaction using the relatively new technique of laser-powered homogeneous pyrolysis, in which a megawatt infrared laser is used to generate short pulses of high gas temperatures under strictly homogeneous conditions. In our investigation, SiF/sub 4/ is used as the sensitizer to absorb energy from a pulsed CO/sub 2/ laser and to transfer this energy by collisions with the reactant gas. Ethyl chloride is used as an external standard ''thermometer'' gas to permit estimation of the unimolecular reaction rate constants by a relative rate approach. When UF/sub 6/ is the reactant, CF/sub 3/Cl is used as reagent to trap atomic fluorine reaction product, forming CF/sub 4/ as a stable indicator which is easily detected by infrared spectroscopy. Using these techniques, we estimate the UF/sub 6/ unimolecular reaction rate constant near the high-pressure limit. In the Appendix, we describe a computer program, written for the IBM PC, which predicts unimolecular rate constants based on the Rice-Ramsperger-Kassel theory. Parameterization of the theoretical model is discussed, and recommendations are made for ''appropriate'' input parameters for use in predicting the gas-phase unimolecular reaction rate for UF/sub 6/ as a function of temperature and gas composition and total pressure. 85 refs., 17 figs., 14 tabs.

Bostick, W.D.; McCulla, W.H.; Trowbridge, L.D.

1987-04-01

354

Modeling of Peptides Connecting the Ligand Binding and Transmembrane Domains in the GluR2 Glutamate Receptor  

PubMed Central

Ligand-gated Glutamate receptors (GluR) mediate synaptic signals in the nervous system. Ionotropic GluRs of AMPA type, the subject of the present study, are tetrameric assemblies of monomer subunits, each of which is constructed in a modular fashion from functional subdomains. The extracellular ligand binding domain (LBD) changes its conformation upon binding of an agonist ligand followed by opening of a transmembrane (TM) ion channel. Peptides connecting the LBD and TM domains facilitate gating of the channel, and their structure and composition are important for the receptor functioning. In this study we used Replica Exchange Molecular Dynamics (REMD) simulations to model S1M1 and S2M3 connecting peptides of the GluR2 receptor in two implicit solvents, water and interfacial water/lipid medium characterized by lower polarity. Propensity of these peptides to form helical structures was analyzed using helicity measure derived from the free energy of the simulated ensembles of structures. The S1M1 and S2M3 connecting peptides were not helical in our simulations in both dielectric environments in the absence of the rest of the protein. The structures of the LBD fragment with known high resolution ?-helical structure and of the TM3 helix were successfully predicted in the simulations, which in part validate our results. The S2M3 peptide which is important in gating formed a well-defined coil structure and salt-bridges with the S2 domain. The S1M1 peptide formed a loop structure via formation of internal salt-bridges. Potential implications of these structures on function of the receptor are discussed. PMID:19205024

Speranskiy, K.; Kurnikova, M. G.

2010-01-01

355

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

PubMed Central

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

Atkinson, R; Arey, J

1994-01-01

356

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

NASA Technical Reports Server (NTRS)

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

Butler, Bruce D.

1996-01-01

357

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

PubMed Central

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

Ryvkin, Faina; Greenaway, Frederick T.

2010-01-01

358

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

PubMed

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

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

2014-10-01

359

Capture of gas-phase arsenic oxide by lime: kinetic and mechanistic studies.  

PubMed

Trace metal emission from coal combustion is a major concern for coal-burning utilities. Toxic compounds such as arsenic species are difficult to control because of their high volatility. Mineral sorbents such as lime and hydrated lime have been shown to be effective in capturing arsenic from the gas phase over a wide temperature range. In this study, the mechanism of interaction between arsenic oxide (As2O3) and lime (CaO) is studied over the range of 300-1000 degrees C. The interaction between these two components is found to depend on the temperature; tricalcium orthoarsenate (Ca3As2O8) is found to be the product of the reaction below 600 degrees C, whereas dicalcium pyroarsenate (Ca2As2O7) is found to be the reaction product in the range of 700-900 degrees C. Maximum capture of arsenic oxide is found to occur in the range of 500-600 degrees C. At 500 degrees C, a high reactivity calcium carbonate is found to capture arsenic oxide by a combination of physical and chemical adsorption. Intrinsic kinetics of the reaction between calcium oxide and arsenic oxide in the medium-temperature range of 300-500 degrees C is studied in a differential bed flow-through reactor. Using the shrinking core model, the order of reaction with respect to arsenic oxide concentration is found to be about 1, and the activation energy is calculated to be 5.1 kcal/mol. The effect of initial surface area of CaO sorbent is studied over a range of 2.7-45 m2/g using the grain model. The effect of other major acidic flue gas species (SO2 and HCl) on arsenic capture is found to be minimal under the conditions of the experiment. PMID:11349294

Jadhav, R A; Fan, L S

2001-02-15

360

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study  

NASA Astrophysics Data System (ADS)

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.

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

2014-10-01

361

Gas phase water in the surface layer of protoplanetary disks  

E-print Network

Recent observations of the ground state transition of HDO at 464 GHz towards the protoplanetary disk of DM Tau have detected the presence of water vapor in the regions just above the outer disk midplane (Ceccarelli et al 2005). In the absence of non-thermal desorption processes, water should be almost entirely frozen onto the grain mantles and HDO undetectable. In this Letter we present a chemical model that explores the possibility that the icy mantles are photo-desorbed by FUV (6eV water vapor above the disk midplane over the entire disk. Assuming a photo-desorption yield of 10^{-3}, the water abundance in this layer is predicted to be ~ 3 x 10^{-7} and the average H2O column density is ~ 1.6x 10^{15} cm^{-2}. The predictions are very weakly dependent on the details of the model, like the incident FUV radiation field, and the gas density in the disk. Based on this model, we predict a gaseous HDO/H2O ratio in DM Tau of ~1%. In addition, we predict the ground state transition of water at 557 GHz to be undetectable with ODIN and/or HSO-HIFI.

C. Dominik; C. Ceccarelli; D. Hollenbach; M. Kaufman

2005-10-21

362

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

SciTech Connect

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

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

363

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

PubMed

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 1009.50Da 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

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

2015-05-01

364

Antitumor and modeling studies of a penetratin-peptide that targets E2F-1 in small cell lung cancer  

PubMed Central

E2F-1, a key transcription factor necessary for cell growth, DNA repair, and differentiation, is an attractive target for development of anticancer drugs in tumors that are E2F “oncogene addicted”. We identified a peptide isolated from phage clones that bound tightly to the E2F-1 promoter consensus sequence. The peptide was coupled to penetratin to enhance cellular uptake. Modeling of the penetratin-peptide (PEP) binding to the DNA E2F-1 promoter demonstrated favorable interactions that also involved the participation of most of the penetratin sequence. The penetratin-peptide (PEP) demonstrated potent in vitro cytotoxic effects against a range of cancer cell lines, particularly against Burkitt lymphoma cells and small cell lung cancer (SCLC) cells. Further studies in the H-69 SCLC cell line showed that the PEP inhibited transcription of E2F-1 and also several important E2F-regulated enzymes involved in DNA synthesis, namely, thymidylate synthase, thymidine kinase, and ribonucleotide reductase. As the PEP was found to be relatively unstable in serum, it was encapsulated in PEGylated liposomes for in vivo studies. Treatment of mice bearing the human small cell lung carcinoma H-69 with the PEP encapsulated in PEGylated liposomes (PL-PEP) caused tumor regression without significant toxicity. The liposome encapsulated PEP has promise as an antitumor agent, alone or in combination with inhibitors of DNA synthesis. PMID:23792570

Xie, Xiaoqi; Kerrigan, John E; Minko, Tamara; Garbuzenko, Olga; Lee, Kuo-Chieh; Scarborough, Alex; Abali, Emine Ercikan; Budak-Alpdogan, Tulin; Johnson-Farley, Nadine; Banerjee, Debabrata; Scotto, Kathleen W; Bertino, Joseph R

2013-01-01

365

Spinal actions of ?-conotoxins, CVID, MVIIA and related peptides in a rat neuropathic pain model  

PubMed Central

BACKGROUND AND PURPOSE Antagonists of the N-type voltage gated calcium channel (VGCC), Cav2.2, have a potentially important role in the treatment of chronic neuropathic pain. ?-conotoxins, such MVIIA and CVID are effective in neuropathic pain models. CVID is reported to have a greater therapeutic index than MVIIA in neuropathic pain models, and it has been suggested that this is due to faster reversibility of binding, but it is not known whether this can be improved further. EXPERIMENTAL APPROACH We examined the potency of CVID, MVIIA and two intermediate hybrids ([K10R]CVID and [R10K]MVIIA) to reverse signs of neuropathic pain in a rat nerve ligation model in parallel with production of side effects. We also examined the potency and reversibility to inhibit primary afferent synaptic neurotransmission in rat spinal cord slices. KEY RESULTS All ?-conotoxins produced dose-dependent reduction in mechanical allodynia. They also produced side effects on the rotarod test and in a visual side-effect score. CVID displayed a marginally better therapeutic index than MVIIA. The hybrids had a lesser effect in the rotarod test than either of their parent peptides. Finally, the conotoxins all presynaptically inhibited excitatory synaptic neurotransmission into the dorsal horn and displayed recovery that was largely dependent upon the magnitude of inhibition and not the conotoxin type. CONCLUSIONS AND IMPLICATIONS These findings indicate that CVID provides only a marginal improvement over MVIIA in a preclinical model of neuropathic pain, which appears to be unrelated to reversibility from binding. Hybrids of these conotoxins might provide viable alternative treatments. PMID:23713957

Jayamanne, A; Jeong, H J; Schroeder, C I; Lewis, R J; Christie, M J; Vaughan, C W

2013-01-01

366

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 Central

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

Yang, Zehong; Zhao, Xiaojun

2011-01-01

367

Endogenous peptides of a soluble major histocompatibility complex class I molecule, H-2Lds: sequence motif, quantitative binding, and molecular modeling of the complex  

PubMed Central

To gain insight into the rules that govern the binding of endogenous and viral peptides to a given major histocompatibility complex (MHC) class I molecule, we characterized the amino acid sequences of a set of self peptides bound by a soluble analogue of murine H-2Ld, H-2Lds. We tested corresponding synthetic peptides quantitatively for binding in several different assays, and built three-dimensional computer models of eight peptide/H-2Lds complexes, based on the crystallographic structure of the human HLA-B27/peptide complex. Comparison of primary and tertiary structures of bound self and antigenic peptides revealed that residues 2 and 9 were not only restricted in sequence and tolerant of conservative substitutions, but were spatially constrained in the three-dimensional models. The degree of sequence variability of specific residues in MHC-restricted peptides reflected the lack of structural constraint on those amino acids. Thus, amino acid residues that define a peptide motif represent side chains required or preferred for a close fit with the MHC class I heavy chain. PMID:1281216

1992-01-01

368

Insights on the Interactions of Synthetic Amphipathic Peptides with Model Membranes as Revealed by 31P and 2H Solid-State NMR and Infrared Spectroscopies  

PubMed Central

We studied the interaction between synthetic amphipathic peptides and model membranes by solid-state NMR and infrared spectroscopies. Peptides with 14 and 21 amino acids composed of leucines and phenylalanines modified by the addition of crown ethers were synthesized. The 14-mer and 21-mer peptides both possess a helical amphipathic structure. To shed light on their membrane interaction, 31P and 2H solid-state NMR experiments were performed on both peptides in interaction with dimyristoylphosphatidylcholine vesicles in the absence and presence of cholesterol, dimyristoylphosphatidylglycerol vesicles, and oriented bicelles. 31P NMR experiments on multilamellar vesicles reveal that the dynamics and/or orientation of the polar headgroups are weakly yet markedly affected by the presence of the peptides, whereas 31P NMR experiments on bicelles indicate no significant changes in the morphology and orientation of the bicelles. On the other hand, 2H NMR experiments on vesicles reveal that the acyl chain order is affected differently depending on the membrane lipidic composition and on the peptide hydrophobic length. Finally, infrared spectroscopy was used to study the interfacial region of the bilayer. Based on these studies, mechanisms of membrane perturbation are proposed for the 14-mer and 21-mer peptides in interaction with model membranes depending on the bilayer composition and peptide length. PMID:16533836

Ouellet, Marise; Bernard, Geneviève; Voyer, Normand; Auger, Michèle

2006-01-01

369

Antimicrobial peptides  

PubMed Central

With increasing antibiotics resistance, there is an urgent need for novel infection therapeutics. Since antimicrobial peptides provide opportunities for this, identification and optimization of such peptides have attracted much interest during recent years. Here, a brief overview of antimicrobial peptides is provided, with focus placed on how selected hydrophobic modifications of antimicrobial peptides can be employed to combat also more demanding pathogens, including multi-resistant strains, without conferring unacceptable toxicity. PMID:24758244

2014-01-01

370

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)

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.

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

2004-03-01

371

Gas phase dispersion in a small rotary kiln  

SciTech Connect

A study was made of nonideal flow of gas in a rotary kiln reactor. A rotating tube 0.165 m in diameter by 2.17 m long, with internal lifting flights, was operated at room temperature. Rotational speeds from 2.0 to 7.0 rpm, air flow rates from 0.351 to 4.178 m/sup 3//h, and solid contents of 0.0, 5.1, and 15.3% of tube volume were studied. Residence time distribution of the gas was measured by means of the pulse injection technique using a helium tracer. A model was developed based on dispersive flow that exchanges with a deadwater region. Two parameters, a dispersion number describing bulk gas flow and an interchange factor describing exchange between the flow region and the gas trapped in the solids bed, were sufficient to correlate the data, but these parameters are sensitive to experimental error. The model is applicable to analysis of other flow systems, such as packed beds.

Spencer, B.B.

1981-07-01

372

The interstellar gas-phase chemistry of HCN and HNC  

NASA Astrophysics Data System (ADS)

We review the reactions involving hydrogen cyanide (HCN) and hydrogen isocyanide (HNC) in dark molecular clouds to elucidate new chemical sources and sinks of these isomers. We find that the most important reactions for the HCN-HNC system are dissociative recombination (DR) reactions of HCNH+ (HCNH+ + e-), the ionic CN + H3+, HCN + C+, HCN and HNC reactions with H+/He+/H3+/H3O+/HCO+, the N + CH2 reaction and two new reactions: H + CCN and C + HNC. We test the effect of the new rate constants and branching ratios on the predictions of gas-grain chemical models for dark cloud conditions. The rapid C + HNC reaction keeps the HCN/HNC ratio significantly above 1 as long as the carbon atom abundance remains high. However, the reaction of HCN with H3+ followed by DR of HCNH+ acts to isomerize HCN into HNC when carbon atoms and CO are depleted leading to an HCN/HNC ratio close to or slightly greater than 1. This agrees well with observations in TMC-1 and L134N taking into consideration the overestimation of HNC abundances through the use of the same rotational excitation rate constants for HNC as for HCN in many radiative transfer models.

Loison, Jean-Christophe; Wakelam, Valentine; Hickson, Kevin M.

2014-09-01

373

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

E-print Network

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

Davis, Ben G.

374

ANALYSIS OF A GAS-PHASE PARTITIONING TRACER TEST CONDUCTED THROUGH FRACTURED MEDIA  

EPA Science Inventory

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

375

Evaluated Gas Phase Basicities and Proton Affinities of Molecules; Heats of Formation of Protonated Molecules  

Microsoft Academic Search

The available data on gas phase basicities and proton affinities of molecules are compiled and evaluated. Tables giving the molecules ordered (1) according to proton affinity and (2) according to empirical formula, sorted alphabetically are provided. The heats of formation of the molecules and the corresponding protonated species are also listed.

Sharon G. Lias; Joel F. Liebman; Rhoda D. Levin

1984-01-01

376

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...

377

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 ...

378

In situ gas-phase hydrosilylation of plasma-synthesized silicon nanocrystals.  

PubMed

Surface passivation of semiconductor nanocrystals (NCs) is critical in enabling their utilization in novel optoelectronic devices, solar cells, and biological and chemical sensors. Compared to the extensively used liquid-phase NC synthesis and passivation techniques, gas-phase routes provide the unique opportunity for in situ passivation of semiconductor NCs. Herein, we present a method for in situ gas-phase organic functionalization of plasma-synthesized, H-terminated silicon (Si) NCs. Using real-time in situ attenuated total reflection Fourier transform IR spectroscopy, we have studied the surface reactions during hydrosilylation of Si NCs at 160 °C. First, we show that, during gas-phase hydrosilylation of Si NCs using styrene (1-alkene) and acetylene (alkyne), the reaction pathways of the alkenes and alkynes chemisorbing onto surface SiH(x) (x = 1-3) species are different. Second, utilizing this difference in reactivity, we demonstrate a novel pathway to enhance the surface ligand passivation of Si NCs via in situ gas-phase hydrosilylation using the combination of a short-chain alkyne (acetylene) and a long-chain 1-alkene (styrene). The quality of surface passivation is further validated through IR and photoluminescence measurements of Si NCs exposed to air. PMID:21774486

Jariwala, Bhavin N; Dewey, Oliver S; Stradins, Paul; Ciobanu, Cristian V; Agarwal, Sumit

2011-08-01

379

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

E-print Network

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

Schlegel, H. Bernhard

380

Electronic Structure and Spectra of Catechol and Alizarin in the Gas Phase and Attached to Titanium  

E-print Network

Electronic Structure and Spectra of Catechol and Alizarin in the Gas Phase and Attached to Titanium and alizarin molecules upon binding to titanium. Catechol and alizarin are similar chromophores with analogous electronic spectra in the free state. Binding alizarin to titanium red-shifts the spectrum. The binding

381

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

E-print Network

Infrared Spectroscopy of Cationized Arginine in the Gas Phase: Direct Evidence for the Transition methyl ester (ArgOMe) are investigated with infrared spectroscopy and ab initio calculations. Infrared to the nonzwitterionic form is directly related to proton affinity.14,15 This relationship can be far less direct for non

Cohen, Ronald C.

382

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...

383

Self-Assembly of Well-Defined Nanostructures by Hydrogen Bonding in the Gas Phase  

Microsoft Academic Search

Micrometer-long nanobelt and nanowires from deposition of perylenediimide (PTCDI) and naphthalenediimide (NPDI) in glass substrates from the gas phase were demonstrated. The electron diffraction pattern of PTCDI shows that the PTCDI molecules are oriented with their long axis perpendicular to the belt and the - stacking direction parallel to the belt. No crystal structure of the NPDI nanowires was observed.

Hai-Feng Ji; Ravish Majithia; Xin Yang; Xiaohe Xu; Karren Leslie More

2008-01-01

384

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

ERIC Educational Resources Information Center

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…

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

2010-01-01

385

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/...

386

Carbonic Anhydrase-Inhibitor Binding: From Solution to the Gas Phase  

E-print Network

Carbonic Anhydrase-Inhibitor Binding: From Solution to the Gas Phase Qinyuan Wu,,§ Jinming Gao stabilities of nonco- valent complexes between bovine carbonic anhydrase II (BCAII, EC 4.2.1.1) and para systems due to the stability of carbonic anhydrase (CA) and its well characterized structure and ligand

Gao, Jinming

387

Probing the Energetics of Dissociation of Carbonic Anhydrase-Ligand Complexes in the Gas Phase  

E-print Network

Probing the Energetics of Dissociation of Carbonic Anhydrase-Ligand Complexes in the Gas Phase comparing the stability of carbonic anhydrase-benzenesulfonamide complexes in the presence and absence mass spectrometry (ESI-FTICR-MS) to study the relative stabilities of noncovalent complexes of carbonic

Prentiss, Mara

388

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

E-print Network

region.1,2 Doping with indium, gallium, or aluminum improves these properties.3-5 These characteristicsMolecular Orbital Studies of Zinc Oxide Chemical Vapor Deposition: Gas-Phase Hydrolysis of Diethyl deposition of zinc oxide thin films can be carried out with diethyl zinc and water vapor. The present study

Schlegel, H. Bernhard

389

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

EPA Science Inventory

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

390

A Fortran computer code package for the evaluation of gas-phase, multicomponent transport properties  

Microsoft Academic Search

This report documents a Fortran computer code package that is used for the evaluation of gas-phase multicomponent viscosities, thermal conductivities, diffusion coefficients, and thermal diffusion coefficients. The package is in two parts. The first is a preprocessor that computes polynomial fits to the temperature dependent parts of the pure species viscosities and binary diffusion coefficients. The coefficients of these fits

Robert J. Kee; Graham Dixon-Lewis; Jürgen Warnatz; Michael E. Coltrin; J. A. Miller

1986-01-01

391

Sequential flow injection analysis of ammonium and nitrate using gas phase molecular absorption spectrometry  

Microsoft Academic Search

A flow injection method on the basis of gas phase molecular absorption is described for the sequential determination of ammonium and nitrate. Two hundred microliters of sample solution is injected into the flow line. For ammonium determination, the sample zone is directed to a line in which reacts with NaOH (13M) and produces ammonia. But for nitrate determination, the sample

B. Haghighi; S. Farrokhi Kurd

2004-01-01

392

Accelerated decomposition of gas phase metal organic molecules determined by radical reactions  

NASA Astrophysics Data System (ADS)

The reactivity of gas phase radicals generated during the MOCVD of GaAs, GaN, ZnS, ZnSe, and CdTe was studied using density functional theory. Calculations were performed with B3LYP functionals and different basis sets. It was found that the production of CH 3 through surface reactions is an intrinsic part of the growth process when using Ga(CH 3) 3, Zn(CH 3) 2, or Cd(CH 3) 2 as gas phase precursors. After being generated, CH 3 can react with the organometallic molecules or with H 2, if it is used as carrier gas, to give CH 4 and H. Atomic hydrogen is much more reactive than CH 3 and can easily decompose Ga(CH 3) 3 and Cd(CH 3) 2 to GaCH 3 and CdCH 3, which leads to an increase of the film growth rate. When reacting with H 2Se, H can start a radical chain mechanism that can eventually determine the formation of large ZnSe gas phase adducts. Finally, it was found that H can react with NH 3 to give NH 2, which can then react with Ga(CH 3) 3 to give Ga(CH 3) 2NH 2 and successively form GaN gas phase adducts.

Cavallotti, Carlo; Moscatelli, Davide; Masi, Maurizio; Carrà, Sergio

2004-05-01

393

Molecular structures of gas-phase polyatomic molecules determined by spectroscopic methods  

Microsoft Academic Search

Spectroscopic data related to the structures of polyatomic molecules in the gas phase have been reviewed, critically evaluated, and compiled. All reported bond distances and angles have been classified as equilibrium (re), average (rz), substitution (rs), or effective (ro) parameters, and have been given a quality rating which is a measure of the parameter uncertainty. The surveyed literature includes work

Marlin D. Harmony; Victor W. Laurie; Robert L. Kuczkowski; R. H. Schwendeman; D. A. Ramsay; Frank J. Lovas; Walter J. Lafferty; Arthur G. Maki

1979-01-01

394

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

EPA Science Inventory

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

395

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

EPA Science Inventory

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

396

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

E-print Network

Magnetizabilities and Nuclear Shielding Constants of the Fluoromethanes in the Gas Phase The effects of a dielectric medium on the magnetizabilities and nuclear shielding constants an important role, as is clearly demonstrated for the magnetizability of the CH3F molecule where

Helgaker, Trygve

397

Solid and gas phase inventory of the low mass protostar Elias 29 (ae Oph)  

E-print Network

CHAPTER 7 Solid and gas phase inventory of the low mass protostar Elias 29 (ae Oph) To be submitted ) Class I protostellar object Elias 29 in the ae Ophiuchi molecular cloud. It provides a unique amount outflow. In many aspects, Elias 29 resembles the Herbig Ae star AB Aur, although Elias 29 is less evolved

Boogert, Adwin

398

Gas-Phase Tropospheric Chemistry of Volatile Organic Compounds: 1. Alkanes and Alkenes  

Microsoft Academic Search

Literature data (through mid-1996) concerning the gas-phase reactions of alkanes and alkenes (including isoprene and monoterpenes) leading to their first generation products are reviewed and evaluated for tropospheric conditions. The recommendations of the most recent IUPAC evaluation [J. Phys. Chem. Ref. Data, 26, No. 3 (1997)] are used for the ?C3 organic compounds, unless more recent data necessitates reevaluation. The

Roger Atkinson

1997-01-01

399

Adapting gas-phase electron scattering R -matrix calculations to a condensed-matter environment  

Microsoft Academic Search

We investigate how gas phase R -matrix calculations for electron collisions with the water molecule can be efficiently used in a condensed environment. The electron band structure of cubic ice being fairly well studied, we try to reproduce it using a generalization of the Korringa-Kohn-Rostoker band calculation method. We find two cutoffs have to be applied to the R -matrix

Laurent Caron; D. Bouchiha; J. D. Gorfinkiel; L. Sanche

2007-01-01

400

Gas-Phase Ignition of Premixed Fuel by Catalytic Bodies in Stagnation Flow  

Microsoft Academic Search

Abstract-In this paper the gas-phase ignition of a premixed fuel by catalytic surfaces of finite sizes is studied, using asymptotic methods. The flow selected for this analysis was the planar stagnation flow. The ignition is generated by a finite thickness plate, the lower surface of which is at a uniform high temperature. This study considers two principal cases: the slightly

C. TREVIÑO

1983-01-01

401

Evidence for Unfolding and Refolding of Gas-Phase Cytochrome Ions in a Paul Trap  

Microsoft Academic Search

The folding pathways of gas-phase cytochrome c ions produced by electrospray ionization have been studied by an ion trapping\\/ion mobility technique that allows conformations to be examined over extended timescales (10 ms to 10 s). The results show that the 9 charge state emerges from solution as a compact structure and then rapidly unfolds into several substantially more open structures,

Ethan R. Badman; Sunnie Myung; David E. Clemmer

2005-01-01

402

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

E-print Network

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 ...

Lindquist, Susan

403

Peptide-Mediated Liposomal Doxorubicin Enhances Drug Delivery Efficiency and Therapeutic Efficacy in Animal Models  

PubMed Central

Lung cancer ranks among the most common malignancies, and is the leading cause of cancer-related mortality worldwide. Chemotherapy for lung cancer can be made more specific to tumor cells, and less toxic to normal tissues, through the use of ligand-mediated drug delivery systems. In this study, we investigated the targeting mechanism of the ligand-mediated drug delivery system using a peptide, SP5-2, which specifically binds to non-small cell lung cancer (NSCLC) cells. Conjugation of SP5-2 to liposomes enhanced the amount of drug delivered directly into NSCLC cells, through receptor-mediated endocytosis. Functional SP5-2 improved the therapeutic index of Lipo-Dox by enhancing therapeutic efficacy, reducing side effects, and increasing the survival rate of tumor-bearing mice in syngenic, metastatic and orthotopic animal models. Accumulation of SP5-2-conjugated liposomal doxorubicin (SP5-2-LD) in tumor tissues was 11.2-fold higher than that of free doxorubicin, and the area under the concentration-time curve (AUC0–72 hours) was increased 159.2-fold. Furthermore, the experiment of bioavailability was assessed to confirm that SP5-2 elevates the uptake of the liposomal drugs by the tumor cells in vivo. In conclusion, the use of SP5-2-conjugated liposomes enhances pharmacokinetic properties, improves efficacy and safety profiles, and allows for controlled biodistribution and drug release. PMID:24386166

Chang, De-Kuan; Li, Pi-Chun; Lu, Ruei-Min; Jane, Wann-Neng; Wu, Han-Chung

2013-01-01

404

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

PubMed Central

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

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

2014-01-01

405

Activity of Potent and Selective Host Defense Peptide Mimetics in Mouse Models of Oral Candidiasis  

PubMed Central

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

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

2014-01-01

406

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

PubMed

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

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

2014-07-01

407

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

PubMed Central

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

Gallaher, William R.; Garry, Robert F.

2015-01-01

408

Modeling of the ebola virus delta Peptide reveals a potential lytic sequence motif.  

PubMed

Filoviruses, such as Ebola and Marburg viruses, cause severe outbreaks of human infection, including the extensive epidemic of Ebola virus disease (EVD) in West Africa in 2014. In the course of examining mutations in the glycoprotein gene associated with 2014 Ebola virus (EBOV) sequences, a differential level of conservation was noted between the soluble form of glycoprotein (sGP) and the full length glycoprotein (GP), which are both encoded by the GP gene via RNA editing.