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1

Gas phase hydrogen deuterium exchange reactions of a model peptide: FT-ICR and computational analyses of metal induced conformational mutations  

Microsoft Academic Search

We utilized gas phase hydrogen\\/deuterium (H\\/D) exchange reactions and ab initio calculations to investigate the complexation\\u000a between a model peptide (Arg-Gly-Asp?RGD) with various alkali metal ions. The peptide conformation is drastically altered\\u000a upon alkali metal ion complexation. The associated conformational changes depend on both the number and type of complexing\\u000a alkali metal ions. Sodium has a smaller ionic diameter and

T. Solouki; R. C. Fort; A. Alomary; A. Fattahi

2001-01-01

2

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

3

Gas phase hydrogen deuterium exchange reactions of a model peptide: FT-ICR and computational analyses of metal induced conformational mutations.  

PubMed

We utilized gas phase hydrogen/deuterium (H/D) exchange reactions and ab initio calculations to investigate the complexation between a model peptide (Arg-Gly-Asp[triple bond]RGD) with various alkali metal ions. The peptide conformation is drastically altered upon alkali metal ion complexation. The associated conformational changes depend on both the number and type of complexing alkali metal ions. Sodium has a smaller ionic diameter and prefers a multidentate interaction that involves all three amino acids of the peptide. Conversely, potassium and cesium form different types of complexes with the RGD. The [RGD + 2Cs - H]+ species exhibit the slowest H/D exchange reactivity (reaction rate constant of approximately 6 x 10(-13) cm3molecule(-1)s(-1) for the fastest exchanging labile hydrogen with ND3). The reaction rate constant of the protonated RGD is two orders of magnitude faster than that of the [RGD + 2Cs - H]+. Addition of the first cesium to the RGD reduces the H/D exchange reaction rate constant (i.e., D0) by a factor of seven whereas sodium reduces this value by a factor of thirty. Conversely, addition of the second alkali metal ions has the opposite effect; the rate of D0 disappearance for all [RGD + 2Met - H]+ species (Met[triple bond]Na, K, and Cs) decreases with the alkali metal ion size. PMID:11766754

Solouki, T; Fort, R C; Alomary, A; Fattahi, A

2001-12-01

4

Solution Versus Gas-Phase Modification of Peptide Cations with NHS-Ester Reagents  

NASA Astrophysics Data System (ADS)

A comparison between solution and gas phase modification of primary amine sites in model peptide cations with N-hydroxysuccinimide (NHS) ester reagents is presented. In all peptides, the site of modification in solution was directed to the N-terminus by conducting reactions at pH = 5, whereas for the same peptides, a lysine residue was preferentially modified in the gas phase. The difference in pKa values of the N-terminus and ?-amino group of the lysine allows for a degree of control over sites of protonation of the peptides in aqueous solution. With removal of the dielectric and multiple charging of the peptide ions in the gas phase, the accommodation of excess charge can affect the preferred sites of reaction. Interaction of the lone pair of the primary nitrogen with a proton reduces its nucleophilicity and, as a result, its reactivity towards NHS-esters. While no evidence for reaction of the N-terminus with sulfo-NHS-acetate was noted in the model peptide cations, a charge inversion experiment using bis[sulfosuccinimidyl] suberate, a cross-linking reagent with two sulfo-NHS-ester functionalities, showed modification of the N-terminus. Hence, an unprotonated N-terminus can serve as a nucleophile to displace NHS, which suggests that its lack of reactivity with the peptide cations is likely due to the participation of the N-terminus in solvating excess charge.

Mentinova, Marija; Barefoot, Nathan Z.; McLuckey, Scott A.

2012-02-01

5

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

E-print Network

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

Clemmer, David E.

6

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 show that average volumes of individual Xxx residues in the gas phase are 5 to 15% smaller than when display preferential alignments.3 A key parameter in understanding packing is the volume that individual

Clemmer, David E.

7

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

8

Can metal ions be used as gas-phase disulfide bond cleavage reagents? A survey of coinage metal complexes of model peptides containing an intermolecular disulfide bond.  

PubMed

The role that a metal ion can have in promoting disulfide bond cleavage has been assessed by surveying the tandem mass spectra of the following metal complexes of model peptides containing an intermolecular disulfide bond: [M--H+Cu(II)](+); [M--H+Cu(II)(bipy)](+); [M+Ag(I)](+); and [M+Au(I)(PMe(3))](+). In comparison to previously studied protonated peptides, these binary and ternary metal complexes generally yield more abundant S--S and/or C--S bond cleavage. In general, [M--H+Cu(II)](+) ions cleave the adjacent C--S bond more readily, while the [M+Au(I)(PMe(3))](+) ion cleaves the S--S bond more readily. The ternary metal complex [M--H+Cu(II)(bipy)](+), on the other hand, fragments by exclusive loss of the bipyridyl ligand for the larger model peptides studied. Of all coinage metal systems studied, Me(3)PAu(+) is superior in promoting disulfide bond cleavage. PMID:17654640

Lioe, Hadi; Duan, Mubing; O'Hair, Richard A J

2007-01-01

9

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

PubMed

Peptide sequence scrambling during mass spectrometry-based gas-phase fragmentation analysis causes misidentification of peptides and proteins. Thus, there is a need to develop an efficient approach to probing the gas-phase fragment ion isomers related to sequence scrambling and the underlying fragmentation mechanism, which will facilitate the development of bioinformatics algorithm for proteomics research. Herein, we report on the first use of electron transfer dissociation (ETD)-produced diagnostic fragment ions to probe the components of gas-phase peptide fragment ion isomers. In combination with ion mobility spectrometry (IMS) and formaldehyde labeling, this novel strategy enables qualitative and quantitative analysis of b-type fragment ion isomers. ETD fragmentation produced diagnostic fragment ions indicative of the precursor ion isomer components, and subsequent IMS analysis of b ion isomers provided their quantitative and structural information. The isomer components of three representative b ions (b9, b10, and b33 from three different peptides) were accurately profiled by this method. IMS analysis of the b9 ion isomers exhibited dynamic conversion among these structures. Furthermore, molecular dynamics simulation predicted theoretical drift time values, which were in good agreement with experimentally measured values. Our results strongly support the mechanism of peptide sequence scrambling via b ion cyclization, and provide the first experimental evidence to support that the conversion from molecular precursor ion to cyclic b ion (M ? (c)b) pathway is less energetically (or kinetically) favored. PMID:24313304

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

2014-03-18

10

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

NASA Astrophysics Data System (ADS)

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

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

2008-12-01

11

Near-edge X-ray absorption mass spectrometry of a gas-phase peptide.  

PubMed

We have studied the dissociation of the gas-phase protonated peptide leucine enkephalin [YGGFL+H](+) upon X-ray absorption in the region of the C K-edge. The yield of photodissociation products was recorded as a function of photon energy. The total photoabsorption yield is qualitatively similar to near-edge X-ray absorption fine structure (NEXAFS) spectra recorded from condensed phase peptides and proteins. Fragment specificity reveals distinct quantitative differences between spectra obtained for different masses. Fragmentation channels can be assigned to specific electronic transitions some of which are site specific. For instance, C 1s ? ?(?) excitations in the leucine enkephalin aromatic side chains lead to relatively little fragmentation, whereas such excitations along the peptide backbone induce strong fragmentation. PMID:23061512

González-Magaña, O; Reitsma, G; Tiemens, M; Boschman, L; Hoekstra, R; Schlathölter, T

2012-11-01

12

Gas-phase diffusion in porous media: Comparison of models  

SciTech Connect

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

Webb, S.W.

1998-09-01

13

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

14

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.; Grohn, A.J.

2013-01-01

15

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

16

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

17

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

E-print Network

SAWYER Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2004 Major Subject: Chemistry INVESTIGATION... OF THE EFFECT OF INTRA-MOLECULAR INTERACTIONS ON THE GAS-PHASE CONFORMATION OF PEPTIDES AS PROBED BY ION MOBILITY-MASS SPECTROMETRY, GAS-PHASE HYDROGEN/DEUTERIUM EXCHANGE, AND MOLECULAR MECHANICS A Dissertation by HOLLY ANN SAWYER Submitted to Texas A...

Sawyer, Holly Ann

2006-04-12

18

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

NASA Astrophysics Data System (ADS)

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

Mentinova, Marija; McLuckey, Scott A.

2011-05-01

19

Modeling nongray gas-phase and soot radiation in luminous turbulent nonpremixed jet flames  

Microsoft Academic Search

Much progress has been made in radiative heat transfer modeling with respect to treatment of nongray radiation from both gas-phase species and soot particles, while radiation modeling in turbulent flame simulations is still in its infancy. Aiming at reducing this gap, this paper introduces state-of-the-art models of gas-phase and soot radiation to turbulent flame simulations. The full-spectrum k-distribution method (Modest,

L. Wang; M. F. Modest; D. C. Haworth; S. R. Turns

2005-01-01

20

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

E-print Network

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

Slaton, James Garrett

2009-05-15

21

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

PubMed

We present evidence that following near-UV excitation, protonated tyrosine- or phenylalanine-containing peptides undergo intersystem crossing to produce a triplet species. This pathway competes with direct dissociation from the excited electronic state and with dissociation from the electronic ground state subsequent to internal conversion. We employ UV-IR double-resonance photofragment spectroscopy to record conformer-specific vibrational spectra of cold peptides pre-excited to their S1 electronic state. The absorption of tunable IR light by these electronically excited peptides leads to a drastic increase in fragmentation, selectively enhancing the loss of neutral phenylalanine or tyrosine side-chain, which are not the lowest dissociation channels in the ground electronic state. The recorded IR spectra evolve upon increasing the time delay between the UV and IR pulses, reflecting the dynamics of the intersystem crossing on a timescale of ?80 ns and <10 ns for phenylalanine- and tyrosine-containing peptides, respectively. Once in the triplet state, phenylalanine-containing peptides may live for more than 100 ms, unless they absorb IR photons and undergo dissociation by the loss of an aromatic side-chain. We discuss the mechanism of this fragmentation channel and its possible implications for photofragment spectroscopy and peptide photostability. PMID:25338898

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

2014-10-21

22

Liquid Hot NAGMA Cooled to 0.4 K: Benchmark Thermochemistry of a Gas-Phase Peptide.  

PubMed

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

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

2014-10-16

23

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

24

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

SciTech Connect

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

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

2010-11-17

25

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...

26

Single and Multicomponent Gas Phase Diffusion in a Porous Media: Modeling and Laboratory Measurements  

Microsoft Academic Search

Subsurface vapor migration of volatile chemicals may impact ambient and indoor air quality, increasing the importance to investigate the fate and transport of these chemicals. This project involved both modeling and experimental work to study the vapor phase transport behavior of single, binary, and tertiary component systems present in the gas phase. The experimental phase resulted in the development of

G. P. Partridge; Kevin S. McLeary; Tonia R. Showers; R. Scott Huebner; H. A. Elliott

2002-01-01

27

The interstellar gas phase production of highly complex hydrocarbons: construction of a model  

Microsoft Academic Search

Our current gas phase models of the chemistry of interstellar clouds have been extended to produce molecules as complex as fullerenes. Interstellar fullerenes are formed via an ion\\/molecule synthesis in which linear carbon chains grow until they spontaneously convert into monocyclic rings, which then undergo condensation reactions to form tricyclic rings. The tricyclic rings are converted to fullerenes by collisional

R. P. A. Bettens; Eric Herbst

1995-01-01

28

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

E-print Network

Steady-State and Dynamic Modeling of Gas-Phase Polypropylene Processes Using Stirred-Bed Reactors for the continuous gas-phase synthesis of polypropylene using stirred-bed reactors. The model considers the important- terization, and reactor residence time, in addition to the traditional Ziegler-Natta polymerization kinetics

Liu, Y. A.

29

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

E-print Network

From Solution to the Gas Phase: Stepwise Dehydration and Kinetic Trapping of Substance P Reveals+ , the results demonstrate that a compact dehydrated conformer population can be kinetically trapped on the time

Clemmer, David E.

30

Review of OCS gas-phase reactions in dark cloud chemical models  

E-print Network

The association reaction S + CO {\\to} OCS + hnu has been identified as being particularly important for the prediction of gas-phase OCS abundances by chemical models of dark clouds. We performed detailed ab-initio calculations for this process in addition to undertaking an extensive review of the neutral-neutral reactions involving this species which might be important in such environments. The rate constant for this association reaction was estimated to be several orders of magnitude smaller than the one present in current astrochemical databases. The new rate for this reaction and the introduction of other processes, notably OH + CS {\\to} OCS + H and C + OCS {\\to} CO + CS, dramatically changes the OCS gas-phase abundance predicted by chemical models for dark clouds. The disagreement with observations in TMC-1 (CP) and L134N (N), suggests that OCS may be formed on grain surfaces as is the case for methanol. The observation of solid OCS on interstellar ices supports this hypothesis.

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

2012-01-01

31

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

32

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

SciTech Connect

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

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

1992-01-01

33

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

PubMed Central

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

Fadda, Elisa; Woods, Robert J.

2014-01-01

34

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

E-print Network

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

Zachariah, Michael R.

35

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

PubMed

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

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

2014-11-01

36

CCSD(T), W1, and other model chemistry predictions for gas-phase deprotonation reactions  

NASA Astrophysics Data System (ADS)

A series of CCSD(T) single-point calculations on MP4(SDQ) geometries and the W1 model chemistry method have been used to calculate ?H° and ?G° values for the deprotonation of 17 gas-phase reactions where the experimental values have reported accuracies within 1 kcal/mol. These values have been compared with previous calculations using the G3 and CBS model chemistries and two DFT methods. The most accurate CCSD(T) method uses the aug-cc-pVQZ basis set. Extrapolation of the aug-cc-pVTZ and aug-cc-pVQZ results yields the most accurate agreement with experiment, with a standard deviation of 0.58 kcal/mol for ?G° and 0.70 kcal/mol for ?H°. Standard deviations from experiment for ?G° and ?H° for the W1 method are 0.95 and 0.83 kcal/mol, respectively. The G3 and CBS-APNO results are competitive with W1 and are much less expensive. Any of the model chemistry methods or the CCSD(T)/aug-cc-pVQZ method can serve as a valuable check on the accuracy of experimental data reported in the National Institutes of Standards and Technology (NIST) database.

Iv, Frank C. Pickard; Griffith, Daniel R.; Ferrara, Skylar J.; Liptak, Matthew D.; Kirschner, Karl N.; Shields, George C.

37

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

38

Theoretical study of through-space and through-bond electron transfer within positively charged peptides in the gas phase  

NASA Astrophysics Data System (ADS)

As part of an on-going effort to probe mechanisms for disulfide and backbone N-C[alpha] cleavage under electron capture or electron-transfer dissociation mass spectroscopy conditions, theoretical simulations have been carried out to consider the probabilities that a. an electron initially attached to a protonated amine site on a side chain can migrate (through-bond or through-space) to an S-S [sigma]* orbital and thus cause disulfide cleavage; b. an electron initially attached to a protonated site might be transferred (through-bond or through-space) to another protonated site or to a fixed-charge positive site thus allowing the electron to migrate throughout charged sites in a multiply charged peptide. The primary findings of this work include: c. charged-site to S-S [sigma]* orbital through-bond electron transfer can occur at significant probabilities but only over ca. 5 intervening bonds covering up to ca. 15 Å; d. through-space electron transfer from protonated sites to protonated sites or from fixed-charge sites to fixed-charge sites can be facile, but between protonated and fixed-charge sites transfer is very slow; to effect the transfers between equivalent sites, the two sites must come within ca. 5 Å of one another; e. through-space electron transfer from a protonated or fixed-charge site to an S-S [sigma]* orbital can occur with reasonable probability but if the two sites come within ca. 5 Å of one another. Based on these findings, speculation is offered both to interpret recent findings of the McLuckey group on flexible, triply charged peptides and earlier data from the Marshall group on more rigid, helical, doubly charged peptides, both of which contain disulfide linkages that experiments find to be readily cleaved.

Sobczyk, Monika; Neff, Diane; Simons, Jack

2008-02-01

39

Experimental and gas phase modeling of nanocrystalline diamond films grown on titanium alloys for biomedical applications  

Microsoft Academic Search

For biomedical applications, it is highly desirable to be able to deposit smooth adherent diamond films on various complex-shaped substrates using the hot filament chemical vapor deposition technique (HFCVD). The properties of these films are affected profoundly by process parameters such as filament temperature, gas composition, and pressure. In this study, we present an insight into the gas phase chemistry

M. J. Jackson; A. N. Jones; W. Ahmed

2005-01-01

40

Experimental and gas phase modeling of nanocrystalline diamond films grown on titanium alloys for biomedical applications  

Microsoft Academic Search

For biomedical applications, it is highly desirable to be able to deposit smooth adherent diamond films on various complex-shaped\\u000a substrates using the hot filament chemical vapor deposition technique (HFCVD). The properties of these films are affected\\u000a profoundly by process parameters such as filament temperature, gas composition, and pressure. In this study, we present an\\u000a insight into the gas phase chemistry

M. J. Jackson; A. N. Jones; W. Ahmed

2005-01-01

41

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

Microsoft Academic Search

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

Robert W. Barber; David R. Emerson

2006-01-01

42

Model of continuous dispersive flow with interactive deadwater and application to gas-phase flow in rotary calciners  

SciTech Connect

A continuous flow model is developed which describes flow through a vessel in which the fluid undergoes axial dispersed plug flow and some of the fluid is held back in a deadwater zone. The first three moments of the concentration-time curve are related to three parameters of the model, and an equation is presented to predict the outlet concentration from the vessel as a function of time for an impulse input. The model is used to analyze experimental gas-phase residence-time distribution data collected from a small rotary calciner operated at room temperature. These data are well represented by the model. 11 references, 9 figures, 1 table.

Spencer, B.B. (Oak Ridge National Lab., TN); Whatley, M.E.; Watson, J.S.

1983-05-01

43

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 ...

44

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

45

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

46

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

PubMed

The approach of Bates to the determination of neutral product branching ratios in ion-electron dissociative recombination reactions has been utilised in conjunction with quantum chemical techniques to redetermine branching ratios for a wide variety of important reactions of this class in dense interstellar clouds. The branching ratios have then been used in a pseudo time-dependent model calculation of the gas phase chemistry of a dark cloud resembling TMC-1 and the results compared with an analogous model containing previously used branching ratios. In general, the changes in branching ratios lead to stronger effects on calculated molecular abundances at steady state than at earlier times and often lead to reductions in the calculated abundances of complex molecules. However, at the so-called "early time" when complex molecule synthesis is most efficient, the abundances of complex molecules are hardly affected by the newly used branching ratios. PMID:11538328

Millar, T J; DeFrees, D J; McLean, A D; Herbst, E

1988-01-01

47

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

48

Simplified Combustion Modeling of Double Base Propellant: Gas Phase Chain Reaction Vs. Thermal Decomposition  

Microsoft Academic Search

Simplified combustion modeling of nitrocellulose (NC), nitroglycerin (NG) double base propellant is considered. Two models with simple but rational chemistry are compared: the classical thermal decomposition, high gas activation energy (Eg\\/RT> > 1) Denison-Baum-Williams (DBW) model, and a new chain reaction, low gas activation energy (Eg\\/RT < < 1) model recently proposed by Ward, Son, and Brewster (WSB). Both models

M. Q. BREWSTER; M. J. WARD; S. F. SON

2000-01-01

49

Different hydrodynamic model for gas-phase propylene polymerization in a catalytic fluidized bed reactor  

Microsoft Academic Search

A comparative simulation study was carried out using the improved well-mixed, constant bubble size and well mixed models. These fluidized bed reactor models, combined with comprehensive kinetics for propylene homopolymerization in the presence of a multiple active site Ziegler-Natta catalyst. In the improved model, the effect of the presence of particles in the bubbles and the excess gas in the

Ahmad Shamiri; H. Mohamed Azlan; S. M. Farouq; N. Mostoufi

2010-01-01

50

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

Microsoft Academic Search

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

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

2011-01-01

51

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

52

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

Microsoft Academic Search

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

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

2010-01-01

53

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

EPA Science Inventory

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

54

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

55

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

PubMed

Monomeric ZnOH has been studied for the first time using millimeter and microwave gas-phase spectroscopy. ZnOH is important in surface processes and at the active site of the enzyme carbonic anhydrase. In the millimeter-wave direct-absorption experiments, ZnOH was synthesized by reacting zinc vapor, produced in a Broida-type oven, with water. In the Fourier-transform microwave measurements, ZnOH was produced in a supersonic jet expansion of CH(3)OH and zinc vapor, created by laser ablation. Multiple rotational transitions of six ZnOH isotopologues in their X(2)A' ground states were measured over the frequency range of 22-482 GHz, and splittings due to fine and hyperfine structure were resolved. An asymmetric top pattern was observed in the spectra, showing that ZnOH is bent, indicative of covalent bonding. From these data, spectroscopic constants and an accurate structure were determined. The Zn-O bond length was found to be similar to that in carbonic anhydrase and other model enzyme systems. PMID:22224369

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

2012-02-16

56

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

57

Modeling the high-temperature catalytic partial oxidation of methane over platinum gauze: Detailed gas-phase and surface chemistries coupled with 3D flow field simulations  

Microsoft Academic Search

The high-temperature catalytic partial oxidation (CPO) of methane over a platinum gauze reactor was modeled by three-dimensional numerical simulations of the flow field coupled with heat transport as well as detailed gas-phase and surface reaction mechanisms. Model results agree well with data of CPO experiments over Pt-gauzes in the literature, confirming the presence of strong mass and heat-transport limitations. The

Raúl Quiceno; Javier Pérez-Ramírez; Jürgen Warnatz; Olaf Deutschmann

2006-01-01

58

Impact of gas-phase mechanisms on Weather Research Forecasting Model with Chemistry (WRF/Chem) predictions: Mechanism implementation and comparative evaluation  

NASA Astrophysics Data System (ADS)

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 conducted over the continental United States for July 2001, with three different gas-phase mechanisms, a default one (i.e., CBM-Z) and two newly implemented ones (i.e., CB05 and SAPRC-99). Simulation results are evaluated against available surface observations, satellite data, and reanalysis data. The model with these three gas-phase mechanisms gives similar predictions of most meteorological variables in terms of spatial distribution and statistics, but large differences exist in shortwave radiation and temperature and relative humidity at 2 m at individual sites under cloudy conditions, indicating the importance of aerosol semi-direct and indirect effects on these variables. Large biases exist in the simulated wind speed at 10 m, cloud water path, cloud optical thickness, and precipitation, due to uncertainties in current cloud microphysics and surface layer parameterizations. Simulations with all three gas-phase mechanisms well reproduce surface concentrations of O3, CO, NO2, and PM2.5, and column NO2. Larger biases exist in the surface concentrations of nitrate and organic matter (OM) and in the spatial distribution of column CO, tropospheric ozone residual, and aerosol optical depth, due to uncertainties in primary OM emissions, limitations in model representations of chemical transport, and radiative processes. Different gas-phase mechanisms lead to different predictions of mass concentrations of O3 (up to 5 ppb), PM2.5 (up to 0.5 ?g m-3), secondary inorganic PM2.5 species (up to 1.1 ?g m-3), organic PM (up to 1.8 ?g m-3), and number concentration of PM2.5 (up to 2 × 104 cm-3). Differences in aerosol mass and number concentrations further lead to sizeable differences in simulated cloud condensation nuclei (CCN) and cloud droplet number concentration (CDNC) due to the feedback mechanisms among H2SO4 vapor, PM2.5 number, CCN, and CDNC through gas-phase chemistry, new particle formation via homogeneous nucleation, aerosol growth, and aerosol activation by cloud droplets. This study illustrates the important impact of gas-phase mechanisms on chemical and aerosol predictions, their subsequent effects on meteorological predictions, and a need for an accurate representation of such feedbacks through various atmospheric processes in the model. The online-coupled models that simulate feedbacks between meteorological variables and chemical species may provide more accurate representations of the real atmosphere for regulatory applications and can be applied to simulate chemistry-climate feedbacks over a longer period of time.

Zhang, Yang; Chen, Yaosheng; Sarwar, Golam; Schere, Kenneth

2012-01-01

59

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

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

2013-03-01

60

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

61

Reactive species output of a plasma jet with a shielding gas device—combination of FTIR absorption spectroscopy and gas phase modelling  

NASA Astrophysics Data System (ADS)

In this work, a simple modelling approach combined with absorption spectroscopy of long living species generated by a cold atmospheric plasma jet yields insight into relevant gas phase chemistry. The reactive species output of the plasma jet is controlled using a shielding gas device. The shielding gas is varied using mixtures of oxygen and nitrogen at various humidity levels. Through the combination of Fourier transform infrared (FTIR) spectroscopy, computational fluid dynamics (CFD) simulations and zero dimensional kinetic modelling of the gas phase chemistry, insight into the underlying reaction mechanisms is gained. While the FTIR measurements yield absolute densities of ozone and nitrogen dioxide in the far field of the jet, the kinetic simulations give additional information on reaction pathways. The simulation is fitted to the experimentally obtained data, using the CFD simulations of the experimental setup to estimate the correct evaluation time for the kinetic simulation. It is shown that the ozone production of the plasma jet continuously rises with the oxygen content in the shielding gas, while it significantly drops as humidity is increased. The production of nitrogen dioxide reaches its maximum at about 30% oxygen content in the shielding gas. The underlying mechanisms are discussed based on the simulation results.

Schmidt-Bleker, A.; Winter, J.; Iseni, S.; Dünnbier, M.; Weltmann, K.-D.; Reuter, S.

2014-04-01

62

Structural Determination and Gas-Phase Synthesis of Monomeric, Unsolvated IZnCH3 (X?(1)A1): A Model Organozinc Halide.  

PubMed

The first experimental structure of a monomeric organozinc halide, IZnCH3, has been measured using millimeter-wave direct absorption spectroscopy in the frequency range 256-293 GHz. IZnCH3 is a model compound for organozinc halides, widely used in cross-coupling reactions. The species was produced in the gas phase by reaction of zinc vapor with iodomethane in the presence of a dc discharge. IZnCH3 was identified on the basis of its pure rotational spectrum as well as those of the isotopically substituted species I(66)ZnCH3, I(64)Zn(13)CH3, and I(64)ZnCD3. IZnCH3 is unmistakably a symmetric top molecule (X?(1)A1) belonging to the C3v point group, in agreement with DFT calculations, with the following experimentally determined structural parameters: rIZn = 2.4076(2) Å, rZnC = 1.9201(2) Å, rCH = 1.105(9) Å, and ?H-C-H = 108.7(5)°. The basic methyl group geometry is not significantly altered in this molecule. Experimental observations suggest that IZnCH3 is synthesized in the gas phase by direct insertion of activated atomic zinc into the carbon-iodine bond of iodomethane. PMID:25424558

Bucchino, Matthew P; Young, Justin P; Sheridan, Phillip M; Ziurys, Lucy M

2014-11-26

63

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

64

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

65

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...

66

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

67

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

68

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

SciTech Connect

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

Sant, S. P.; Nelson, C. T.; Overzet, L. J.; Goeckner, M. J. [Electrical Engineering, University of Texas at Dallas, 800 W Campbell, Richardson, Texas 75080 (United States)

2009-07-15

69

Monitoring CO2 gas-phase injection in a shallow sand aquifer using cross borehole GPR and modeled with T2VOC multi-phase code  

NASA Astrophysics Data System (ADS)

Risk assessment of potential leakage is an important issue that needs attention in designing effective storage schemes for CO2 storage. Leaking gas may threat groundwater resources and be a liability if pooled up in buildings. We have designed an experiment where we were track the movement of an injected CO2 gas-phase using cross borehole GPR in an unconfined sandy aquifer located in the southwestern part of Denmark. The geology at the field site has been determined using GPR- data, natural gamma ray logging in boreholes, cores sampled with a Geoprobe soil-sampling tool and grain size analysis of the cores. From these measurements the field site geology can be divided into three geological zones. The first zone is an approximately 4 m fine aeolian sand; the second zone is poorly sorted glacial deposits dominated by sand down to 9 m; and the the last zone from 9 m and down consist of well-sorted medium melt water sand. In total we conducted four short injection experiments all of them producing very similar results. The screen of the injection well was 10 m below ground level or 8 m below the water table. An array of six GPR boreholes was installed around the injection well and downwards of dominating gas flow direction. GPR-data were acquired in zero-offset (1D) and multiple-offset (2D) configurations prior and during the injection. All sets of GPR data showed that a plume developed at the depth of the injection screen and that the injected gas primarily spread towards South-East and never breach a barrier around 5 m depth. This corresponded very well with the natural gamma logs, which resulted in higher readings from 4-6.5 m depth. The grain size analyses confirmed that there is a fine sediment layer throughout the area at 4-6 meters depth. We guesstimated van Genucthen parameters from the grain size analysis and used as input to the numerical model and GPR data were used for calibration. The numerical model enabled us to test minimum entry pressure required for the fine sediment layer to function as a barrier and the 'leakage' rate required for the gas phase to breach the barrier.

Lassen, R. N.; Jensen, K.; Looms, M. C.; Sonnenborg, T.; Gudbjerg, J.

2013-12-01

70

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

PubMed

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

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

2008-11-20

71

Published in Journal de Physique IV, vol 11, pp. Pr3-101 ---Pr3-108 Kinetic modelling of gas-phase decomposition of propane : correlation with pyrocarbon deposition  

E-print Network

-phase decomposition of propane : correlation with pyrocarbon deposition Cédric Descamps, Gerard L. Vignoles , Olivier : A chemical kinetic model for gas-phase pyrolysis of propane has been set up, partially reduced, and validated the notion of "maturation" from propane to lighter hydrocarbons, then to aromatic compounds and PAHs. The gas

Boyer, Edmond

72

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

NASA Technical Reports Server (NTRS)

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

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

1980-01-01

73

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

74

Gas Phase Anodization of Tantalum.  

National Technical Information Service (NTIS)

The anodic oxidation of tantalum in the gas phase was studied using an electromagnetic ion cathode. The anodic films were prepared at constant current densities of 1.0 and 2.0 ma/sq cm. The growth characteristics of anodic tantalum oxide films, in the gas...

T. A. Jennings, W. McNeill, R. E. Salomon

1967-01-01

75

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

E-print Network

representation of an Ion Mobility-o-TOF MS............................ 6 3 Partial mass spectra of protonated GlyGlyHis reacted with deuterated methanol. Reaction times ranging from 1 ? 120 seconds.......................... 10 4 Temporal plot for gas...-phase H/D exchange of protonated GlyGlyHis with deuterated methanol at ~1.4 E-7 torr .......................................................... 11 5 Schematic representation of a typical cubic cell......................................... 16 6...

Marini, Joseph Thomas

2004-09-30

76

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

NASA Astrophysics Data System (ADS)

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

Wang, Kai; Zhang, Yang

2014-12-01

77

Spectroscopic studies of cold, gas-phase biomolecular ions  

NASA Astrophysics Data System (ADS)

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

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

78

Fission and Nuclear Liquid-Gas Phase Transition  

E-print Network

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

E. A. Cherepanov; V. A. Karnaukhov

2007-03-30

79

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

PubMed Central

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

Garcia-Sosa, Alfonso T.; Langel, Ulo

2014-01-01

80

Peptides  

SciTech Connect

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

Blackburn, S.

1986-01-01

81

Rate processes in gas phase  

NASA Technical Reports Server (NTRS)

Reaction-rate theory and experiment are given a critical review from the engineers' point of view. Rates of heavy-particle, collision-induced reaction in gas phase are formulated in terms of the cross sections and activation energies for reaction. The effect of cross section function shape and of excited state contributions to reaction both cause the slope of Arrhenius plots to differ from the true activation energy, except at low temperature. The master equations for chemically reacting gases are introduced, and dissociation and ionization reactions are shown to proceed primarily from excited states about kT from the dissociation or ionization limit. Collision-induced vibration, vibration-rotation, and pure rotation transitions are treated, including three-dimensional effects and conservation of energy, which have usually been ignored. The quantum theory of transitions at potential surface crossing is derived, and results are found to be in fair agreement with experiment in spite of some questionable approximations involved.

Hansen, C. F.

1983-01-01

82

Stabilized enzymes in continuous gas phase reactions  

SciTech Connect

We are assessing the utility of enzymes to catalyze reactions in a continuous gas phase reactor. First, alcohol dehydrogenase has been used to oxidize an unsaturated alcohol, 3-methyl-2-buten-1-ol (UOL), to the corresponding unsaturated aldehyde, 3-methyl-2-butenal (UAL). Cofactor NAD{sup +} was regenerated by concomitant acetone reduction to isopropyl alcohol. Second, organophosphorus hydrolase (OPH) has been used to hydrolyze pesticide vapors. In order to control enzyme hydration level, enzyme water adsorption isotherms at different temperature have been studied. Huttig`s isotherm model has been found suitable to describe adsorption behavior. The influence of enzyme hydration level, enzyme loading on glass beads, reaction temperature and flow rate on enzymatic reaction rate and biocatalyst stability were investigated. Reaction kinetics were studied and a kinetic model was proposed. We will also report our attempts to further stabilize enzymes for use in gas reactions by incorporating them into polymer matrices.

Yang, Fangxiao; LeJeune, K.; Yang, Zhen [Univ. of Pittsburgh, PA (United States)] [and others

1995-12-01

83

[Biological activity of regulatory peptides in model experiments in vitro].  

PubMed

Biological effects of short regulatory peptides, pinealon, vesugen, vilon and epitalon were studied in model experiments in vitro. These peptides were found not to demonstrate direct antioxidant activity but be able to restrict lipid peroxidation of human lipoproteins by modification of their structure. The short peptides increase stability of red blood cell membranes toward osmotic hemolysis. They also elevate the stationary level of intracellular reactive oxygen species and at the same time decrease (all excepting epitalon) percent of dead cells in neuronal population. The suggestion was made that under in vivo conditions, short peptides may participate in apoptosis/necrosis regulation. PMID:18546826

Kozina, L S; Arutiunian, A V; Stvolinski?, S L; Khavinson, V Kh

2008-01-01

84

Gas-Phase Spectroscopy of Biomolecular  

E-print Network

Republic, 166 10 Prague 6, Czech Republic; email: pavel.hobza@uochb.cas.cz Annu. Rev. Phys. Chem. 2007. 58 biomolecules into the gas phase intact has largely been solved, making a rich tool chest of gas

de Vries, Mattanjah S.

85

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.

86

Artificial neural network modeling of peptide mobility and peptide mapping in capillary zone electrophoresis  

Microsoft Academic Search

Recently, we have developed an artificial neural network model, which was able to predict accurately the electrophoretic mobilities of relatively small peptides. To examine the robustness of this methodology, a 3-3-1 back-propagation artificial neural network (BP-ANN) model was developed using the same inputs as the previous model, which were the Offord's charge over mass term (Q\\/M2\\/3), corrected steric substituent constant

Mehdi Jalali-Heravi; Yang Shen; Mostafa Hassanisadi; Morteza G Khaledi

2005-01-01

87

Liquid-gas phase transition in nuclear matter including strangeness  

SciTech Connect

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

Wang, P.; Leinweber, D.B.; Williams, A.G. [Special Research Center for the Subatomic Structure of Matter (CSSM) and Department of Physics, University of Adelaide, Adelaide 5005 (Australia); Thomas, A.W. [Special Research Center for the Subatomic Structure of Matter (CSSM) and Department of Physics, University of Adelaide, Adelaide 5005 (Australia); Jefferson Laboratory, 12000 Jefferson Avenue, Newport News, Virginia 23606 (United States)

2004-11-01

88

Molecular Tagging Velocimetry (MTV) measurements in gas phase flows  

NASA Astrophysics Data System (ADS)

Recent developments in Molecular Tagging Velocimetry (MTV) using the phosphorescence of biacetyl are described for gas-phase flows. With improvements in tagging, detection, and processing schemes, whole-field measurements of two components of the velocity vector are obtained simultaneously, typically at more than 300 points over a plane. Application of this measurement approach is demonstrated in mapping the velocity and vorticity fields of the intake flow into a ``steady flow rig'' model of an internal combustion engine.

Stier, B.; Koochesfahani, M. M.

89

pH-dependent coarse-grained model of peptides  

E-print Network

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

Enciso, Marta; Site, Luigi Delle

2012-01-01

90

Continuous-Flow Gas-Phase Bioreactors  

NASA Technical Reports Server (NTRS)

Continuous-flow gas-phase bioreactors proposed for biochemical, food-processing, and related industries. Reactor contains one or more selected enzymes dehydrated or otherwise immobilized on solid carrier. Selected reactant gases fed into reactor, wherein chemical reactions catalyzed by enzyme(s) yield product biochemicals. Concept based on discovery that enzymes not necessarily placed in traditional aqueous environments to function as biocatalysts.

Wise, Donald L.; Trantolo, Debra J.

1994-01-01

91

In-canopy gas-phase chemistry during CABINEX 2009: sensitivity of a 1-D canopy model to vertical mixing and isoprene chemistry  

NASA Astrophysics Data System (ADS)

Vegetation emits large quantities of biogenic volatile organic compounds (BVOC). At remote sites, these compounds are the dominant precursors to ozone and secondary organic aerosol (SOA) production, yet current field studies show that atmospheric models have difficulty in capturing the observed HOx cycle and concentrations of BVOC oxidation products. In this manuscript, we simulate BVOC chemistry within a forest canopy using a one-dimensional canopy-chemistry model (Canopy Atmospheric CHemistry Emission model; CACHE) for a mixed deciduous forest in northern Michigan during the CABINEX 2009 campaign. We find that the base-case model, using fully-parameterized mixing and the simplified biogenic chemistry of the Regional Atmospheric Chemistry Model (RACM), underestimates daytime in-canopy vertical mixing by 50-70% and by an order of magnitude at night, leading to discrepancies in the diurnal evolution of HOx, BVOC, and BVOC oxidation products. Implementing observed micrometeorological data from above and within the canopy substantially improves the diurnal cycle of modeled BVOC, particularly at the end of the day, and also improves the observation-model agreement for some BVOC oxidation products and OH reactivity. We compare the RACM mechanism to a version that includes the Mainz isoprene mechanism (RACM-MIM) to test the model sensitivity to enhanced isoprene degradation. RACM-MIM simulates higher concentrations of both primary BVOC (isoprene and monoterpenes) and oxidation products (HCHO, MACR+MVK) compared with RACM simulations. Additionally, the revised mechanism alters the OH concentrations and increases HO2. These changes generally improve agreement with HOx observations yet overestimate BVOC oxidation products, indicating that this isoprene mechanism does not improve the representation of local chemistry at the site. Overall, the revised mechanism yields smaller changes in BVOC and BVOC oxidation product concentrations and gradients than improving the parameterization of vertical mixing with observations, suggesting that uncertainties in vertical mixing parameterizations are an important component in understanding observed BVOC chemistry.

Bryan, A. M.; Bertman, S. B.; Carroll, M. A.; Dusanter, S.; Edwards, G. D.; Forkel, R.; Griffith, S.; Guenther, A. B.; Hansen, R. F.; Helmig, D.; Jobson, B. T.; Keutsch, F. N.; Lefer, B. L.; Pressley, S. N.; Shepson, P. B.; Stevens, P. S.; Steiner, A. L.

2012-09-01

92

In-canopy gas-phase chemistry during CABINEX 2009: sensitivity of a 1-D canopy model to vertical mixing and isoprene chemistry  

NASA Astrophysics Data System (ADS)

Vegetation emits large quantities of biogenic volatile organic compounds (BVOC). At remote sites, these compounds are the dominant precursors to ozone and secondary organic aerosol (SOA) production, yet current field studies show that atmospheric models have difficulty in capturing the observed HOx cycle and concentrations of BVOC oxidation products. In this manuscript, we simulate BVOC chemistry within a forest canopy using a one-dimensional canopy-chemistry model (Canopy Atmospheric CHemistry Emission model; CACHE) for a mixed deciduous forest in northern Michigan during the CABINEX 2009 campaign. We find that the base-case model, using fully-parameterized mixing and the simplified biogenic chemistry of the Regional Atmospheric Chemistry Model (RACM), underestimates daytime in-canopy vertical mixing by 50-70% and by an order of magnitude at night, leading to discrepancies in the diurnal evolution of HOx, BVOC, and BVOC oxidation products. Implementing observed micrometeorological data from above and within the canopy substantially improves the diurnal cycle of modeled BVOC, particularly at the end of the day, and also improves the observation-model agreement for some BVOC oxidation products and OH reactivity. We compare the RACM mechanism to a version that includes the Mainz isoprene mechanism (RACM-MIM) to test the model sensitivity to enhanced isoprene degradation. RACM-MIM simulates higher concentrations of both primary BVOC (isoprene and monoterpenes) and oxidation products (HCHO, MACR + MVK) compared with RACM simulations. Additionally, the revised mechanism alters the OH concentrations and increases HO2. These changes generally improve agreement with HOx observations yet overestimate BVOC oxidation products, indicating that this isoprene mechanism does not improve the representation of local chemistry at the site. Overall, the revised mechanism yields smaller changes in BVOC and BVOC oxidation product concentrations and gradients than improving the parameterization of vertical mixing with observations, suggesting that uncertainties in vertical mixing parameterizations are an important component in understanding observed BVOC chemistry.

Bryan, A. M.; Bertman, S. B.; Carroll, M. A.; Dusanter, S.; Edwards, G. D.; Forkel, R.; Griffith, S.; Guenther, A. B.; Hansen, R. F.; Helmig, D.; Jobson, B. T.; Keutsch, F. N.; Lefer, B. L.; Pressley, S. N.; Shepson, P. B.; Stevens, P. S.; Steiner, A. L.

2012-05-01

93

Factors Affecting the Fragmentation of Peptide Ions: Metal Cationization and Fragmentation Timescale  

E-print Network

in the gas-phase is particularly interesting. Herein, a comparison of fragmentation patterns of a model peptide series with various charge carriers (H+, Li+, Na+, K+, and Cu+) will assist in determining the location of the preferred binding site of the metal...

Kmiec, Kevin

2012-10-19

94

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

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

95

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

96

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

E-print Network

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

Aluffi, Paolo

97

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.

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

2014-01-01

98

Gas-phase optically pumped infrared lasers  

Microsoft Academic Search

This experimental research program is designed to assess the possibility of using gas-phase optically pumped lasers (OPL) as efficient, frequency-agile mid-infrared sources. The eventual goal will be to incorporate efficient diode lasers into the pumping step, either by direct frequency stabilized diode pumping or by pumping with diode-pumped solid state lasers. In this paper, we discuss experiments on a optically

Harold C. Miller; Dan T. Radzykewycz; Gordon D. Hager; William J. Kessler; Steven J. Davis

1993-01-01

99

Gas-Phase Protonation Thermochemistry of Adenosine  

Microsoft Academic Search

The goal of this work was to obtain a detailed insight on the gas-phase protonation energetic of adenosine using both mass spectrometric experiments and quantum chemical calculations. The experimental approach used the extended kinetic method with nanoelectrospray ionization and collision-induced dissociation tandem mass spectrometry. This method provides experimental values for proton affinity, PA(adenosine) ) 979 ( 1 kJ ·mol-1, and

David Touboul; Guy Bouchoux; Renato Zenobi

2008-01-01

100

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

101

Oxidation of Methionine Residues in Polypeptide Ions Via Gas-Phase Ion/Ion Chemistry  

NASA Astrophysics Data System (ADS)

The gas-phase oxidation of methionine residues is demonstrated here using ion/ion reactions with periodate anions. Periodate anions are observed to attach in varying degrees to all polypeptide ions irrespective of amino acid composition. Direct proton transfer yielding a charge-reduced peptide ion is also observed. In the case of methionine and, to a much lesser degree, tryptophan-containing peptide ions, collisional activation of the complex ion generated by periodate attachment yields an oxidized peptide product (i.e., [M + H + O]+), in addition to periodic acid detachment. Detachment of periodic acid takes place exclusively for peptides that do not contain either a methionine or tryptophan side chain. In the case of methionine-containing peptides, the [M + H + O]+ product is observed at a much greater abundance than the proton transfer product (viz., [M + H]+). Collisional activation of oxidized Met-containing peptides yields a signature loss of 64 Da from the precursor and/or product ions. This unique loss corresponds to the ejection of methanesulfenic acid from the oxidized methionine side chain and is commonly used in solution-phase proteomics studies to determine the presence of oxidized methionine residues. The present work shows that periodate anions can be used to `label' methionine residues in polypeptides in the gas phase. The selectivity of the periodate anion for the methionine side chain suggests several applications including identification and location of methionine residues in sequencing applications.

Pilo, Alice L.; McLuckey, Scott A.

2014-06-01

102

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

103

UV damage of collagen: insights from model collagen peptides.  

PubMed

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 T(m) 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

2012-03-01

104

Mechanism of unfolding of a model helical peptide.  

PubMed

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

Pastrana-Rios, B

2001-08-01

105

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

Microsoft Academic Search

We have explored the utility of gas-phase fractionation by mass spectrometry (MS) in the mass-to-charge (m\\/z) dimension (GPFm\\/z) for increasing the effective number of protein identifications in cases where sample quantity limits the use of multi-dimensional chromatographic fractionation. A peptide digestate from proteins isolated from the membrane fraction of natural killer (NK) cells was analyzed by microcapillary reversed-phase liquid chromatography

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

2004-01-01

106

Molecular Modeling of Geometries, Charge Distributions, and Binding Energies of Small, Drug-Like Molecules Containing Nitrogen Heterocycles and Exocyclic Amino Groups in the Gas Phase and Aqueous Solution  

PubMed Central

We have tested a variety of approximate methods for modeling 30 systems containing mixtures of nitrogen heterocycles and exocyclic amines, each of which is studied with up to 31 methods in one or two phases (gaseous and aqueous). Fifteen of the systems are protonated, and 15 are not. We consider a data set consisting of geometric parameters, partial atomic charges, and water binding energies for the methotrexate fragments 2-(aminomethyl)pyrazine and 2,4-diaminopyrimidine, as well as their cationic forms 1H-2-(aminomethyl)pyrazine and 1H-2,4-diaminopyrimidine. We first evaluated the suitability of several density functionals with the 6-31+G(d,p) basis set to serve as a benchmark by comparing calculated molecular geometries to results obtained from coupled-cluster [CCSD/6-31+G(d,p)] wave function theory (WFT). We found that the M05-2X density functional can be used to obtain reliable geometries for our data set. To accurately model partial charges in our molecules, we elected to utilize the well-validated Charge Model 4 (CM4). In the process of establishing benchmark values, we consider gas-phase coupled cluster and density functional theory (DFT) calculations followed by aqueous-phase DFT calculations, where the effect of solvent is treated by the SM6 quantum mechanical implicit solvation model. The resulting benchmarks were used to test several widely available and economical semiempirical molecular orbital (SE-MO) methods and molecular mechanical (MM) force fields for their ability to accurately predict the partial charges, binding energies to a water molecule, and molecular geometries of representative fragments of methotrexate in the gaseous and aqueous phases, where effects of water were simulated by the SM5.4 and SM5.42 quantum mechanical implicit solvation models for SE-MO and explicit solvation used for MM. In addition, we substituted CM4 charges into the MM force fields tested to observe the effect of improved charge assignment on geometric and energetic modeling. The most accurate MM force fields (with or without CM4 charges substituted) were validated against gas-phase and aqueous-phase geometries and charge distributions of a larger set of 16 drug-like ligands, both neutral and cationic. This process showed that the Merck Molecular Force Field (MMFF94) with or without CM4 charges substituted, is, on average, the most accurate force field for geometries of molecules containing nitrogen heterocycles and exocyclic amino groups, both protonated and unprotonated. This force field was then applied to the complete methotrexate molecule, in an effort to systematically explore its accuracy for trends in geometries and charge distributions. The most accurate force fields for the binding energies of nitrogen heterocycles to a water molecule are OPLS2005 and AMBER. PMID:23700392

White, Brian R.; Wagner, Carston R.; Truhlar, Donald G.; Amin, Elizabeth A.

2013-01-01

107

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

108

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

109

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

110

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

111

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

E-print Network

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

Ghosh, Indraneel

112

Predicting immunogenicity of HIV peptides using a CD8 T cell repertoire model  

E-print Network

Predicting immunogenicity of HIV peptides using a CD8 T cell repertoire model Johannes Textor, TBB. 3 For each HIV peptide, determine the precursor frequency in the artificial repertoire. 4 Use this quantity to predict which peptides elicit responses by real T cells in real immune systems. (We know

Utrecht, Universiteit

113

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

PubMed Central

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

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

2008-01-01

114

Gas-phase fragmentation of polyoxotungstate anions.  

PubMed

A series of phospho-polyoxotungstate anions was transferred to the gas phase via electrospray ionization (ESI), and the anions' fragmentation was examined by collision-induced dissociation (CID). The anions included [PW12O40]3-, [P2W18O62]6-, and {Co4(H2O)2][PW9O34]2}10- as well as lacunary and metal-substituted derivatives such as [PW11O39]7- and [MPW11O39]5- (M = Co(II), Ni(II), Cu(II)). Common species observed in the mass spectra arose from protonation and alkali metal cationization of the precursor ions. Additional species arising from the formal loss of oxide from the precursor species were also observed, presumably formed via protonation and the loss of an oxo ligand as water. These processes of protonation/cationization and the loss of water both led to species with reduced gas-phase anionic charges, and their formation appears to be driven by the enhanced effects of Coulombic repulsion in the desolvated species generated during transfer to the gas phase via ESI. Fragmentation of selected species was examined by multistage mass spectrometry experiments employing CID. Fragmentation occurred via multiple reaction channels, leading to pairs of complementary product anions whose total stoichiometry and charge matched those of the precursor anion. For example, [PW12O40]3- fragmented to give pairs of product ions of general formulas [W(x)O(3x+1)]2- and [PW(12-x)O(39-3x)]- (x = 6-9), with the most intense pair being [W6O19]2- and [PW6O21]-. Similar ions were also observed for fragmentation of [P2W18O61]4- (derived from the loss of water from [P2W18O62]6-). The lacunary and M(II)-substituted lacunary systems fragmented via related pathways, with the latter generating additional fragment ions due to the presence of M(II). These results highlight the usefulness of ESI-MS in the characterization of complex polyoxometalate anion clusters. PMID:19072590

Ma, Michelle T; Waters, Tom; Beyer, Karin; Palamarczuk, Rosemary; Richardt, Peter J S; O'Hair, Richard A J; Wedd, Anthony G

2009-01-19

115

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

116

Advanced QSRR modeling of peptides behavior in RPLC.  

PubMed

In QSRR the retention is modeled as a function of structural or molecular descriptors. Since the structural datasets can be very large a selection of informative variables is often required. But beside the question which subset of variables (descriptors) produces optimum predictions one should answer the question: can good prediction be used in the QSRR community even if the physical meaning of applied descriptors is hard to interpret? The main focus in this paper is put on different modeling methodologies applied and molecular descriptors used in the QSRR approaches. Besides the widely used multiple linear regression (MLR), these methodologies include partial least squares (PLS), uninformative variable elimination partial least squares (UVE-PLS), genetic algorithms (GA) prior to MLR or PLS. The comparison will focus on the predictive performance but also on the descriptors found to be most important for the chromatographic retention prediction of peptides. The results of this study showed that stepwise-MLR and UVE-PLS are producing better predictions than the rest of the studied methodologies. From the variables selected by various methodologies one can see that the important information for the retention mechanism of RPLC was given by 2D-, 3D-descriptors and descriptors from the empirical QSRR equations, which bring the information about hydrogen-bonding properties, molecular size, and complexity. Overall, for the considered data set the empirical QSRR models were predicting the peptides retention best. PMID:20441962

Bodzioch, K; Durand, A; Kaliszan, R; Baczek, T; Vander Heyden, Y

2010-06-15

117

Dynamics of particle growth and overheating in gas-phase polymerization reactors  

Microsoft Academic Search

The particle overheating is an important problem in the industrial catalytic gas-phase olefin polymerization reactors. It has been first investigated with a pseudo-stationary model of a single polymer particle by Hutchinson and Ray (J. Appl. Poly. Sci. 34 (1987) 657). A systematic study of overheating of polymer particle with models based on Fick's and dusty gas model (DGM) transport described

J. Kosek; Z. Grof; A. ák; F. Št?pánek; M. Marek

2001-01-01

118

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

119

Sub-angstrom modeling of complexes between flexible peptides and globular proteins.  

PubMed

A wide range of regulatory processes in the cell are mediated by flexible peptides that fold upon binding to globular proteins. Computational efforts to model these interactions are hindered by the large number of rotatable bonds in flexible peptides relative to typical ligand molecules, and the fact that different peptides assume different backbone conformations within the same binding site. In this study, we present Rosetta FlexPepDock, a novel tool for refining coarse peptide-protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark that is based on a large nonredundant dataset of 89 peptide-protein interactions. Importantly, side chains of known binding motifs are modeled particularly well, typically with atomic accuracy. In addition, our protocol has improved modeling quality for the important application of cross docking to PDZ domains. We anticipate that the ability to create high resolution models for a wide range of peptide-protein complexes will have significant impact on structure-based functional characterization, controlled manipulation of peptide interactions, and on peptide-based drug design. PMID:20455260

Raveh, Barak; London, Nir; Schueler-Furman, Ora

2010-07-01

120

Anti-inflammatory effect of a retrovirus-derived immunosuppressive peptide in mouse models  

PubMed Central

Background Short dimeric or mulitmeric peptides derived from a highly conserved stretch of amino acids from gammaretroviral envelope proteins has been found to have immunosuppressive properties in vitro. Here we test the hypothesis that such immunosuppressive peptides may serve as immunomodulatory reagents for treatment of inflammatory disorders. Results The anti-inflammatory effect of a synthetic retrovirus-derived immunosuppressive peptide of 17 amino acids was tested in two murine skin inflammation models, a TPA-induced acute toxic contact eczema model and an oxazolone-induced allergic contact dermatitis. Overall, mice (n?=?24) treated with a topically applied cream containing the dimeric immunosuppressive peptide exhibited a reduction of 28.8% in ear thickness (range 20.1-42.5), whereas the application of a scrambled peptide dimer or a monomer of the immunosuppressive peptide remained without effect (p?=?0.028). Furthermore, ear biopsies from mice treated with the dimeric immunosuppressive peptide showed a significant reduction in mRNA of the pro-inflammatory cytokines TNF-?, IL-17C, and IL-6 as well as the chemokine CXCL2 compared to mice treated with control peptides. Conclusion Using two murine skin inflammation models, we show that an immunosuppressive retroviral peptide is capable of reducing inflammatory disorders. The results indicate that virus-derived immunosuppressive peptides capable of down-regulating several proinflammatory cytokines may represent a novel class of drugs for the treatment of excess inflammation. PMID:24245569

2013-01-01

121

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

122

Dynamic evolution of the particle size distribution in gas-phase olefin polymerization fluidized bed reactors  

Microsoft Academic Search

In the present study, a comprehensive mathematical model is developed to predict the evolution of particle size distribution (PSD) in a gas-phase olefin polymerization fluidized bed reactor (FBR). To calculate the particle growth and the spatial monomer and temperature profiles in a particle, the random pore polymeric flow model (RPPFM) is employed. The RPPFM is solved together with a dynamic

Georgios Dompazis; Vassileios Kanellopoulos; Haris Yiannoulakis; Athanasios Yiagopoulos; Costas Kiparissides

2004-01-01

123

Mass Spectrometry Analysis of Hepcidin Peptides in Experimental Mouse Models  

PubMed Central

The mouse is a valuable model for unravelling the role of hepcidin in iron homeostasis, however, such studies still report hepcidin mRNA levels as a surrogate marker for bioactive hepcidin in its pivotal function to block ferroportin-mediated iron transport. Here, we aimed to assess bioactive mouse Hepcidin-1 (Hep-1) and its paralogue Hepcidin-2 (Hep-2) at the peptide level. To this purpose, fourier transform ion cyclotron resonance (FTICR) and tandem-MS was used for hepcidin identification, after which a time-of-flight (TOF) MS-based methodology was exploited to routinely determine Hep-1 and -2 levels in mouse serum and urine. This method was biologically validated by hepcidin assessment in: i) 3 mouse strains (C57Bl/6; DBA/2 and BABL/c) upon stimulation with intravenous iron and LPS, ii) homozygous Hfe knock out, homozygous transferrin receptor 2 (Y245X) mutated mice and double affected mice, and iii) mice treated with a sublethal hepatotoxic dose of paracetamol. The results showed that detection of Hep-1 was restricted to serum, whereas Hep-2 and its presumed isoforms were predominantly present in urine. Elevations in serum Hep-1 and urine Hep-2 upon intravenous iron or LPS were only moderate and varied considerably between mouse strains. Serum Hep-1 was decreased in all three hemochromatosis models, being lowest in the double affected mice. Serum Hep-1 levels correlated with liver hepcidin-1 gene expression, while acute liver damage by paracetamol depleted Hep-1 from serum. Furthermore, serum Hep-1 appeared to be an excellent indicator of splenic iron accumulation. In conclusion, Hep-1 and Hep-2 peptide responses in experimental mouse agree with the known biology of hepcidin mRNA regulators, and their measurement can now be implemented in experimental mouse models to provide novel insights in post-transcriptional regulation, hepcidin function, and kinetics. PMID:21408141

van Swelm, Rachel P. L.; Theurl, Milan; Theurl, Igor; Kemna, Erwin H.; van der Burgt, Yuri E. M.; Venselaar, Hanka; Dutilh, Bas E.; Russel, Frans G. M.; Weiss, Gunter; Masereeuw, Rosalinde; Fleming, Robert E.; Swinkels, Dorine W.

2011-01-01

124

Gas-Phase Infrared Spectrum of the Coronene Cation  

NASA Astrophysics Data System (ADS)

The gas-phase infrared spectrum of the coronene cation in the 700-1700 cm-1 range is presented. The spectrum is obtained via multiphoton dissociation spectroscopy of ionic coronene stored in a quadrupole ion trap using the intense and narrowband infrared radiation of a free electron laser. The spectrum shows main absorption peaks at 849, 1327, and 1533 cm-1 along with some weak and barely resolved features, in good agreement with density functional calculations if the effects of vibrational anharmonicity are accounted for. Relative line intensities show remarkable differences with respect to matrix isolation data. The novel experimental technique applied here leads in a natural way to an absorption spectrum of highly excited species. Hence, measured absorption spectra can be compared rather directly to interstellar emission spectra, negating to some extent the need for detailed model calculations.

Oomens, Jos; Sartakov, Boris G.; Tielens, A. G. G. M.; Meijer, Gerard; von Helden, Gert

2001-10-01

125

Regenerable Air Purification System for Gas-Phase Contaminant Control  

NASA Technical Reports Server (NTRS)

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

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

2000-01-01

126

Gas-phase reactions of halogen species of atmospheric importance  

NASA Astrophysics Data System (ADS)

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

Heard, Anne C.

127

Liquid-gas Phase Transition in Strange Hadronic Matter with Weak Y-Y Interaction  

E-print Network

The liquid-gas phase transition in strange hadronic matter is reexamined by using the new parameters about the $\\Lambda - \\Lambda$ interaction deduced from recent observation of $^{6}_{\\Lambda\\Lambda}He$ double hypernucleus. The extended Furnstahl-Serot-Tang model with nucleons and hyperons is utilized. The binodal surface, the limit pressure, the entropy, the specific heat capacity and the Caloric curves are addressed. We find that the liquid-gas phase transition can occur more easily in strange hadronic matter with weak Y-Y interaction than that of the strong Y-Y interaction.

Li Yang; Shao Yu Yin; Wei Liang Qian; Ru-keng Su

2005-06-19

128

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

129

Fragmentation of peptide negative molecular ions induced by resonance electron capture  

SciTech Connect

A simple robust method to study resonance gas-phase reactions between neutral peptides of low volatility and free electrons has been designed and implemented. Resonance electron capture (REC) experiments were performed by several neutral model peptides and two naturally occurring peptides. The assignment of negative ions (NIs) formed in these gas-phase reactions was based on high mass-resolving power experiments. From these accurate mass measurements, it was concluded that fragment NIs formed by low (1-2 eV) energy REC are of the same types as those observed in electron capture/transfer dissociation, where the positive charge is a factor. The main feature resulting from these REC experiments by peptides is the occurrence of z{sub n}-1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M-H]{sup -} NIs presumably the carboxylate anion structure dominate the REC spectra of smaller peptides. There was no evidence for the occurrence of the complementary reaction, i.e., the formations of c{sub n}+1 ions. Instead, c{sub n} ions arose without hydrogen/proton transfer albeit with lower abundances than that observed for z{sub n}-1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the c{sub n} ions than for the z{sub n}-1 ions. The mechanisms for the N-C{sub {alpha}} bond cleavage are discussed.

Vasil'ev, Yury V. [Department of Chemistry, Oregon State University, Corvallis, Oregon 97331 (United States); Department of Physics, Bashkir State Agriculture University, Ufa 450001 (Russian Federation); Figard, Benjamin J. [Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331 (United States); Morre, Jeff [Environmental Health Science Center, Oregon State University, Corvallis, Oregon 97331 (United States); Deinzer, Max L. [Department of Chemistry, Oregon State University, Corvallis, Oregon 97331 (United States); Environmental Health Science Center, Oregon State University, Corvallis, Oregon 97331 (United States)

2009-07-28

130

A Molecular Model of Alzheimer Amyloid beta Peptide Fibril Formation  

Microsoft Academic Search

Polymerization of the amyloid beta (Ab) peptide into protease-resistant fibrils is a significant step in the pathogenesis of Alzheimer's disease. It has not been pos- sible to obtain detailed structural information about this process with conventional techniques because the peptide has limited solubility and does not form crys- tals. In this work, we present experimental results lead- ing to a

Lars O. Tjernberg; David J. E. Callaway; Agneta Tjernbergi; Solveig Hahne; Christina Lilliehook; Lars Terenius; Johan Thyberg; Christer Nordstedt

1999-01-01

131

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

PubMed Central

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

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

2012-01-01

132

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

E-print Network

by a model of the important gas phase chemical reactions, which recognizes the very different gas temperature diamond grown by chemical vapor deposition CVD have led to interest in such films for use in electronic-containing gases such as diborane to the standard CVD gas mixture 1% CH4 /H2 .3 Such films find use in UV detectors

Bristol, University of

133

Gas Phase 11 Electronic Spectra of Polyacetylenes HC2nH, n ) 5-7  

E-print Network

in the gas phase. The UV absorption spectra of these chains were recorded using the resonant two-color two to better understand the chemical processes that eventually led to the origin of life on earth.7 The other surface. Several photochemical models8-10 have been developed to gain insight into the various pathways

Maier, John Paul

134

Gas phase reactions and rate coefficients for use in astrochemistry - The UMIST ratefile  

Microsoft Academic Search

The rate coefficients of 2880 gas-phase reactions among 313 species involving 12 elements are presented for use in astrochemical models. The motivation behind this work and the caveats which attach to the data are discussed. The permanent electric dipole moments of nearly all the 112 neutral molecules contained in the data set are given, so that rate coefficients can be

T. J. Millar; A. Bennett; J. M. C. Rawlings; P. D. Brown; S. B. Charnley

1991-01-01

135

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

E-print Network

Universal correlations of one­dimensional interacting electrons in the gas phase F. G¨ohmann and V electrons in one dimension at finite temperature. Below a critical value of the chemical potential temperature thermodynamics is that of an ideal gas. We identify the impenetrable electron gas model

136

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

PubMed Central

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

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

2012-01-01

137

Gas phase precursors to anthropogenic secondary organic aerosol: detailed observations of 1,3,5-trimethylbenzene photooxidation  

Microsoft Academic Search

A series of photooxidation experiments were conducted in an atmospheric simulation chamber in order to investigate the oxidation mechanism and secondary organic aerosol (SOA) formation potential of the model anthropogenic gas phase precursor, 1,3,5-trimethylbenzene. Alongside specific aerosol measurements, comprehensive gas phase measurements, primarily by Chemical Ionisation Reaction Time-of-Flight Mass Spectrometry (CIR-TOF-MS), were carried out to provide detailed insight into the

K. P. Wyche; P. S. Monks; A. M. Ellis; R. L. Cordell; A. E. Parker; C. Whyte; A. Metzger; J. Dommen; J. Duplissy; A. S. H. Prevot; U. Baltensperger; A. R. Rickard; F. Wulfert

2009-01-01

138

TAP-binding peptides prediction by QSAR modeling based on amino acid structural information.  

PubMed

The transporter associated with antigen processing (TAP) is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on a major histocompatibility complex (MHC) I molecules and form peptide-MHC complex. The peptide-MHC leaves the ER and displays their antigenic cargo on the cell surface to cytotoxic T cells. In this study, 89 physicochemical properties of amino acid were collected from AAIndex database, and used to characterize the peptides which were binding to TAP. Then, the stepwise regression (STR) was used to optimize the parameters which characterized the TAP binding peptides, and the multiple linear regression (MLR) was used to construct the quantitative structural activity relationship (QSAR) model based on optimized parameters. The quantitative models had good reliability and predictive ability: the Q² of "leave one out" validation is 0.676 and R² of test dataset is 0.722 respectively. Additionally, the standardized coefficients of the models could demonstrate the attributions for each position of epitope and determine which special amino acid is suitable at any position of the peptide. Therefore, the QSAR model constructed by STR-MLR has many advantages, such as, easier calculation and explanation, good performance, and definite physiochemical indication, which could be used to guide the design and modification of the TAP binding peptide. PMID:21692742

Wang, Yuanqing; Cheng, Xiaoming; Lin, Yong; Wen, Haixia; Wang, Li; Xia, Qingyou; Lin, Zhihua

2012-03-01

139

Coordination of two high-affinity hexamer peptides to copper(II) and palladium(II) models of the peptide-metal chelation site on IMAC resins  

Microsoft Academic Search

The coordination of peptides Ser-Pro-His-His-Gly-Gly (SPHHGG) and (His) (HHHHHH) to [Pd{sup II}(mida)(DO)] (mida² = N-methyliminodiacetate) was studied by ¹H NMR as model reactions for Cu{sup II}(iminodiacetate)-immobilized metal affinity chromatography (IMAC) sites. This is the first direct physical description of peptide coordination for IMAC. A three-site coordination is observed which involves the first, third, and fourth residues along the peptide chain.

Ya Chen; Richard Pasquinelli; Mohammed Ataai; Richard R. Koepsel; Richard A. Kortes; Rex E. Shepherd

2000-01-01

140

The cooperative behaviour of antimicrobial peptides in model membranes.  

PubMed

A systematic analysis of the hypothesis of the antimicrobial peptides' (AMPs) cooperative action is performed by means of full atomistic molecular dynamics simulations accompanied by circular dichroism experiments. Several AMPs from the aurein family (2.5,2.6, 3.1), have a similar sequence in the first ten amino acids, are investigated in different environments including aqueous solution, trifluoroethanol (TFE), palmitoyloleoylphosphatidylethanolamine (POPE), and palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayers. It is found that the cooperative effect is stronger in aqueous solution and weaker in TFE. Moreover, in the presence of membranes, the cooperative effect plays an important role in the peptide/lipid bilayer interaction. The action of AMPs is a competition of the hydrophobic interactions between the side chains of the peptides and the hydrophobic region of lipid molecules, as well as the intra peptide interaction. The aureins 2.5-COOH and 2.6-COOH form a hydrophobic aggregate to minimize the interaction between the hydrophobic group and the water. Once that the peptides reach the water/lipid interface the hydrophobic aggregate becomes smaller and the peptides start to penetrate into the membrane. In contrast, aurein 3.1-COOH forms only a transient aggregate which disintegrates once the peptides reached the membrane, and it shows no cooperativity in membrane penetration. PMID:25046254

Wang, Jianping; Mura, Manuela; Zhou, Yuhua; Pinna, Marco; Zvelindovsky, Andrei V; Dennison, Sarah R; Phoenix, David A

2014-11-01

141

Gas-Phase Spectroscopy of Biomolecular Building Blocks  

NASA Astrophysics Data System (ADS)

Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.

de Vries, Mattanjah S.; Hobza, Pavel

2007-05-01

142

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

143

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

144

Alteration of gas phase ion polarizabilities upon hydration in high dielectric liquids  

E-print Network

We investigate the modification of gas phase ion polarizabilities upon solvation in polar solvents and ionic liquids. To this aim, we develop a classical electrostatic theory of charged liquids composed of solvent molecules modeled as finite size dipoles, and embedding polarizable ions that consist of Drude oscillators. In qualitative agreement with ab-initio calculations of polar solvents and ionic liquids, the hydration energy of a polarizable ion in both type of dielectric liquid is shown to favor the expansion of its electronic cloud. Namely, the ion carrying no dipole moment in the gas phase acquires a dipole moment in the liquid environment, but its electron cloud also reaches an enhanced rigidity. We find that the overall effect is an increase of the gas phase polarizability upon hydration. In the specific case of ionic liquids, it is shown that this hydration process is driven by a collective solvation mechanism where the dipole moment of a polarizable ion induced by its interaction with surrounding ions self-consistently adds to the polarization of the liquid, thereby amplifying the dielectric permittivity of the medium in a substantial way. We propose this self-consistent hydration as the underlying mechanism behind the high dielectric permittivities of ionic liquids composed of small charges with negligible gas phase dipole moment. Hydration being a correlation effect, the emerging picture indicates that electrostatic correlations cannot be neglected in polarizable liquids.

Sahin Buyukdagli; Tapio Ala-Nissila

2013-04-23

145

Quantification of Isotopically Overlapping Deamidated and 18O Labeled Peptides Using Isotopic Envelope Mixture Modeling  

PubMed Central

A robust peptide quantification method was developed where overlapping peptide isotopic distributions were fit with predicted peptide isotopic envelope mixture models (IEMM). Application to two difficult quantitative problems was demonstrated. The first was the quantification of deamidation, where masses of isotopic peaks differ by a single Da, and the second, 18O labeling, where the isotopic peaks are shifted 2 and 4 Da. In both cases, peptide quantification cannot be performed by simple integration of extracted ion chromatograms, because the isotopic envelopes of mass shifted peptides are normally not resolved. To test the methodology for quantification of deamidation, several synthetic peptides and their corresponding deamidated forms were mixed at various ratios (1:0, 1:2, 2:1, 4:1, 10:1 and 20:1) and analyzed using the IEMM method, resulting in a high correlation (R2=0.96) between measured and known percentages of deamidation. The IEMM method was then incorporated into a workflow for deamidation quantification in a large-scale proteomics experiment. A series of normal (3-day, 2-year, 35-year, and 70-year) and cataractous (93-year) human lenses were analyzed using two-dimensional liquid chromatography tandem mass spectrometry and deamidation quantities of several ?S-crystallin peptides ([N14-Q16], N53, [Q63–Q70], and N143) were determined. Two peptides (N53 and [Q63–Q70]) had more extensive deamidation in the water-insoluble portions of normal lens samples, and deamidation at N143 was more extensive in the 93-year water-insoluble cataractous sample. The utility of the technique for analysis of 18O-labeled peptides was examined using mixtures of labeled BSA peptides in known 16O to 18O ratios (10:1, 4:1, 1:1, 1:4, and 1:10). The methodology allowed accurate measurements of ratios of 16O/18O peptides over the wide range of relative abundances. PMID:19173613

Dasari, Surendra; Wilmarth, Phillip A.; Reddy, Ashok P.; Robertson, Lucinda J. G.; Nagalla, Srinivasa R.; David, Larry L.

2009-01-01

146

Short cell-penetrating peptides: a model of interactions with gene promoter sites.  

PubMed

Analysis of the main parameters of molecular mechanics (number of hydrogen bonds, hydrophobic and electrostatic interactions, DNA-peptide complex minimization energy) provided the data to validate the previously proposed qualitative models of peptide-DNA interactions and to evaluate their quantitative characteristics. Based on these estimations, a three-dimensional model of Lys-Glu and Ala-Glu-Asp-Gly peptide interactions with DNA sites (GCAG and ATTTC) located in the promoter zones of genes encoding CD5, IL-2, MMP2, and Tram1 signal molecules. PMID:23484211

Khavinson, V Kh; Tarnovskaya, S I; Linkova, N S; Pronyaeva, V E; Shataeva, L K; Yakutseni, P P

2013-01-01

147

"Best Match" Model and Effect of Na+/H+ Exchange on Anion Attachment to Peptides and Stability of Formed Adducts in Negative Ion Electrospray Mass Spectrometry  

NASA Astrophysics Data System (ADS)

The "Best Match" model has been extended to account for the role that Na+/H+ exchange plays on anion attachment in negative ion electrospray. Without any Na+/H+ exchange on (Glu) fibrinopeptide B, the higher basicity anions F- and CH3COO- can hardly form observable adducts; however, after multiple Na+/H+ exchanges, adduct formation is enabled. Moreover, dissociation pathways of CF3COO- adducts with singly deprotonated peptides that have undergone 0 to 3 Na+/H+ exchanges exhibit a shift in CID product ions from losing predominately CF3COOH (case of 0 Na+/H+ exchanges) to losing predominately CF3COO- (case of 3 Na+/H+ exchanges). These phenomena can be rationalized by considering that Na+ cations exchange at, and serve to "block", the most acidic sites, thereby forcing implicated anions to attach to lower acidity protons. In addition to forming ion pairs with carboxylate groups, Na+ also participates in formation of tri-atomic ions of the form ANaA- during adduct dissociation. The fact that low gas-phase basicity (GB) anions preferentially form ANaA- species, even though high GB anions form more stable tri-atomic species, indicates that the monatomic ions were not in close contact in the initial adduct. The propensity for formation of stable anionic adducts is dependent on the degree of matching between anion GBs and GBapp of deprotonated sites on the peptide. The GBapp is raised dramatically as the charge state of the peptide increases via a through-space effect. The presence of Na+ on carboxylate sites substantially decreases the GBapp by neutralizing these sites, while slightly increasing the intrinsic GBs by an inductive effect.

Liu, Xiaohua; Cole, Richard B.

2013-12-01

148

Gas-Phase Reactions of Halogen Species of Atmospheric Importance.  

NASA Astrophysics Data System (ADS)

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

Heard, Anne C.

149

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

150

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

PubMed Central

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

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

1996-01-01

151

Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling.  

PubMed

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

Rand, Kasper D; Zehl, Martin; Jørgensen, Thomas J D

2014-10-21

152

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

153

Assembling gas-phase reaction mechanisms for high temperature inorganic systems based on quantum chemistry calculations and reaction rate theories  

NASA Astrophysics Data System (ADS)

Detailed chemical kinetic modeling based on computational quantum chemistry has been quite successful in making quantitative predictions about some systems, particularly the combustion of small hydrocarbons and certain areas of atmospheric chemistry. The gas phase chemistry of many processes in high-temperature inorganic systems, from materials synthesis to propulsion to waste incineration, could in principle be modeled with equal or greater success using detailed chemical kinetic modeling. This contribution provides examples from our own work of how computational quantum chemistry can be used in developing gas phase reaction mechanisms for modeling of high temperature materials processing. In the context of CVD of silicon from dichlorosilane, CVD of alumina from AlCl3/H2/CO2 mixtures, and particle nucleation from silane, this detailed chemical kinetic modeling has given us insight into gas phase reaction pathways that we would not likely have gained by other means.

Swihart, Mark T.

2005-02-01

154

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

E-print Network

to be unaffected by the antibiotic resistance that renders small drug molecules 0196-9781/$ ­ see front matter nearly everything in between. These naturally occurring peptides have been preserved through evolution species. They have been favored through evolution for their small size and their high potency [7

Minnesota, University of

155

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

PubMed

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

Christensen, Anders S; Hamelryck, Thomas; Jensen, Jan H

2014-01-01

156

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

PubMed Central

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

Hamelryck, Thomas; Jensen, Jan H.

2014-01-01

157

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

PubMed Central

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

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2011-01-01

158

Gas-phase observation of multiply charged C60 anions.  

PubMed

Gas-phase observation of C60(1-), C60(3-), and C60(4-) anions generated at platinum and gold electrodes and detected by electrochemical/electrospray mass spectrometry is reported. The anions were electrochemically generated from solutions of C60 dissolved in toluene/acetonitrile as well as from reduction of C60 films on gold electrode surfaces. The gas-phase observation of C60(3-) and C60(4-), despite the fact that they have negative electron affinities, is a result of a Coulombic barrier to electron loss. The fact that C60(2-) was not detected in these experiments is ascribed to its limited solubility under the reaction conditions. These studies, which demonstrate the gas-phase kinetic stability of C60(3-) and C60(4-), illustrate the promise of electrochemical/electrospray mass spectrometry for the study of metastable anions. PMID:16833589

Cammarata, Vince; Guo, Tan; Illies, Andreas; Li, Lidong; Shevlin, Philip

2005-03-31

159

Deamidation, acylation and proteolysis of a model peptide in PLGA films.  

PubMed

The relative rates of deamidation, acylation and proteolysis (i.e. amide bond cleavage) were determined for a model peptide (VYPNGA) in poly (dl-lactide-co-glycolide) films. Films were stored at 70 degrees C and either 95%, 75%, 60%, 45%, 28%, or approximately 0% relative humidity and at 37 degrees C and 95% relative humidity. Peptide degradation products were identified by ESI+MS/MS and quantitated by LC/MS/MS. Extensive overlap of degradation mechanisms occurred, producing a complex mixture of products. Acylation was the dominant peptide degradation reaction (10-20% of total peptide) at early stages of PLGA hydrolysis and at intermediate relative humidity (60-45% RH). Deamidation and proteolysis were dominant (25-50% and 20-40% of total peptide, respectively) at later stages and at high relative humidity (95-75% RH). Understanding the relative rates of each peptide degradation reaction will allow for improved design of PLGA formulations that preserve the stability of peptide and protein drugs. PMID:16529840

Houchin, M L; Heppert, K; Topp, E M

2006-05-01

160

Gas phase acetaldehyde production in a continuous bioreactor  

SciTech Connect

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

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

1993-08-20

161

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

PubMed

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

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

2005-07-01

162

Using gas-phase nitric acid as an indicator of PSC composition  

NASA Astrophysics Data System (ADS)

The composition of polar stratospheric cloud particles is investigated using data from several remote sensing instruments: gas-phase HNO3 measured by the Airborne Submillimeter Radiometer (ASUR), temperature measured by the Airborne Raman Ozone, Temperature and Aerosol Lidar (AROTEL), and aerosol backscatter wavelength dependence and depolarization measured by the UV Differential Absorption Lidar (DIAL). All three instruments have been operated onboard the NASA DC-8 during the SOLVE winter 1999/2000. A simple thermodynamical model is used to calculate the gas-phase amount of HNO3 in the presence of polar stratospheric clouds (PSCs) along the flight track of the DC-8 for one flight into the polar vortex on 7 December 1999. Three types of PSCs are considered in the model: nitric acid trihydrate (NAT), nitric acid dihydrate (NAD), and supercooled ternary solutions (STS). The comparison of the modeled and measured gas-phase HNO3 in the presence of PSCs shows a very good agreement if a NAT composition of the particles is assumed. However, sensitivity studies show that while the PSCs observed on this flight are not in agreement with a STS composition, the model is very sensitive to temperature, and a NAD composition of the PSC cannot be ruled out.

von König, Miriam; Bremer, Holger; Kleinböhl, Armin; Küllmann, Harry; Künzi, Klaus F.; Goede, Albert P. H.; Browell, Edward V.; Grant, William B.; Burris, John F.; McGee, Thomas J.; Twigg, Laurence

2002-08-01

163

Reacting Flow in the Entrance to a Channel with Surface and Gas-Phase Kinetics  

NASA Astrophysics Data System (ADS)

In many catalytic reactors the conversion process is most intense at the very beginning of the channel where the flow is not yet fully developed; hence there will be important interactions between the developing flow field and reaction. To study this problem we have written an object-oriented code for the analysis of reacting flow in the entrance of a channel where both surface reaction and gas-phase reaction are modeled with detailed kinetics. Fluid mechanical momentum and energy equations are modeled by parabolic ``boundary layer''-type equations where streamwise gradient terms are small and the pressure is constant in the transverse direction. Transport properties are modeled with mixture-averaging and the chemical kinetic sources terms are evaluated using Cantera. Numerical integration is done with Matlab using the function pdepe. Calculations were completed using mixtures of methane and air flowing through a channel with platinum walls held at a fixed temperature. GRI-Mech 3.0 was used to describe the gas-phase chemistry and Deutchmann's methane-air-platinum model was used for the surface chemistry. Ignition in the gas phase is predicted for high enough wall temperatures. A hot spot forms away from the walls just before ignition that is fed by radicals produced at the surface.

Mikolaitis, David; Griffen, Patrick

2006-11-01

164

Probing the Lipid-Protein Interface Using Model Transmembrane Peptides with a Covalently Linked Acyl Chain  

PubMed Central

The aim of this study was to gain insight into how interactions between proteins and lipids in membranes are sensed at the protein-lipid interface. As a probe to analyze this interface, we used deuterium-labeled acyl chains that were covalently linked to a model transmembrane peptide. First, a perdeuterated palmitoyl chain was coupled to the Trp-flanked peptide WALP23 (Ac-CGWW(LA)8LWWA-NH2), and the deuterium NMR spectrum was analyzed in di-C18:1-phosphatidylcholine (PC) bilayers. We found that the chain order of this peptide-linked chain is rather similar to that of a noncovalently coupled perdeuterated palmitoyl chain, except that it exhibits a slightly lower order. Similar results were obtained when site-specific deuterium labels were used and when the palmitoyl chain was attached to the more-hydrophobic model peptide WLP23 (Ac-CGWWL17WWA-NH2) or to the Lys-flanked peptide KALP23 (Ac-CGKK(LA)8LKKA-NH2). The experiments showed that the order of both the peptide-linked chains and the noncovalently coupled palmitoyl chains in the phospholipid bilayer increases in the order KALP23 < WALP23 < WLP23. Furthermore, changes in the bulk lipid bilayer thickness caused by varying the lipid composition from di-C14:1-PC to di-C18:1-PC or by including cholesterol were sensed rather similarly by the covalently coupled chain and the noncovalently coupled palmitoyl chains. The results indicate that the properties of lipids adjacent to transmembrane peptides mostly reflect the properties of the surrounding lipid bilayer, and hence that (at least for the single-span model peptides used in this study) annular lipids do not play a highly specific role in protein-lipid interactions. PMID:22004750

Nyholm, Thomas K.M.; van Duyl, Bianca; Rijkers, Dirk T.S.; Liskamp, Rob M.J.; Killian, J. Antoinette

2011-01-01

165

Numerical Analysis of an Impinging Jet Reactor for the CVD and Gas-Phase Nucleation of Titania  

NASA Technical Reports Server (NTRS)

We model a cold-wall atmospheric pressure impinging jet reactor to study the CVD and gas-phase nucleation of TiO2 from a titanium tetra-iso-propoxide (TTIP)/oxygen dilute source gas mixture in nitrogen. The mathematical model uses the computational code FIDAP and complements our recent asymptotic theory for high activation energy gas-phase reactions in thin chemically reacting sublayers. The numerical predictions highlight deviations from ideality in various regions inside the experimental reactor. Model predictions of deposition rates and the onset of gas-phase nucleation compare favorably with experiments. Although variable property effects on deposition rates are not significant (approximately 11 percent at 1000 K), the reduction rates due to Soret transport is substantial (approximately 75 percent at 1000 K).

Gokoglu, Suleyman A.; Stewart, Gregory D.; Collins, Joshua; Rosner, Daniel E.

1994-01-01

166

Tropospheric Gas-phase Composition Reanalyses in GEMS and MACC (Invited)  

Microsoft Academic Search

Chemically reactive gas-phase compounds in the troposphere are important players in regional air quality, long-range transport of air pollution and climate change. In-situ and remote measurements provide important information on the geographical distribution and temporal variability of tropospheric ozone and its precursor species, sulphur dioxide, methane and other species, but only the combination of measurements with numerical models can give

M. G. Schultz; O. Stein; A. Agusti-Panareda; A. Benedetti; R. J. Engelen; J. Flemming; A. Inness; A. Simmons; C. Granier; F. Khokar; K. Law; H. Eskes; V. Huijnen; E. Katragkou; C. S. Zerefos; J. Leitao; A. Richter; J. Cammas; N. Elguindi; V. Thouret

2010-01-01

167

A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet.  

PubMed

PeptideProphet is a post-processing algorithm designed to evaluate the confidence in identifications of MS/MS spectra returned by a database search. In this manuscript we describe the "what and how" of PeptideProphet in a manner aimed at statisticians and life scientists who would like to gain a more in-depth understanding of the underlying statistical modeling. The theory and rationale behind the mixture-modeling approach taken by PeptideProphet is discussed from a statistical model-building perspective followed by a description of how a model can be used to express confidence in the identification of individual peptides or sets of peptides. We also demonstrate how to evaluate the quality of model fit and select an appropriate model from several available alternatives. We illustrate the use of PeptideProphet in association with the Trans-Proteomic Pipeline, a free suite of software used for protein identification. PMID:23176103

Ma, Kelvin; Vitek, Olga; Nesvizhskii, Alexey I

2012-01-01

168

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

SciTech Connect

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

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

2005-10-01

169

Gas Phase diagnostics of Protoplanetary disk extension  

E-print Network

We investigate the potential of using ratios of fine structure and near-infrared forbidden line transitions of atomic carbon to diagnose protoplanetary disk extension. Using results from 2D photoionisation and radiative transfer modeling of a realistic protoplanetary disk structure irradiated by X-rays from a T Tauri star, we obtain theoretical emission maps from which we construct radial distributions of the strongest emission lines produced in the disk. We show that ratios of fine structure to near-infrared forbidden line emission of atomic carbon are especially promising to constrain the minimum size of gaseous protoplanetary disks. While theoretically viable, the method presents a number of observational difficulties that are also discussed here.

B. Ercolano; J. J. Drake; C. J. Clarke

2008-11-21

170

Photodesorption of ices Releasing organic precursors into the gas phase  

Microsoft Academic Search

A long-standing problem in interstellar chemistry is how molecules can be maintained in the gas phase at the extremely low temperatures in space. Photodesorption has been suggested to explain the observed cold gas in cloud cores and disk mid-planes. We are studying the UV photodesorption of ices experimentally under ultra high vacuum and at astrochemically relevant temperatures (15 27 K)

Karin I. Öberg; Ewine F. van Dishoeck; Harold Linnartz

2008-01-01

171

INVESTIGATION OF GAS-PHASE OZONE AS A POTENTIAL BIOCIDE  

EPA Science Inventory

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

172

Oriented xenon hydride molecules in the gas phase  

Microsoft Academic Search

The production of the xenon hydride molecules HXeX with X = I and Cl in the gas phase is reviewed. These molecules are generated by the photolysis of the hydrogen halide HI and HCl molecules on the surface of large xenon Xen clusters. Molecular dynamics simulations show that the flexible H atoms react with the heavy XeX moiety and form

Udo Buck; Michal Fárník

2006-01-01

173

Experiments on gas-phase optically pumped infrared lasers  

Microsoft Academic Search

Population inversions in small gas-phase molecules are produced by optical pumping of vibrational overtone transitions. Efficient frequency down conversion of the pump radiation is obtained by lasing on the inverted transitions. The performance of the lasers is governed by kinetic relaxation and energy exchange processes. The effect of these processes on the ultimate scalability of this class of laser will

Harold C. Miller; Gordon D. Hager

1995-01-01

174

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

175

Stochastic Lindemann kinetics for unimolecular gas-phase reactions.  

PubMed

Lindemann, almost a century ago, proposed a schematic mechanism for unimolecular gas-phase reactions. Here, we present a new semiempirical method to calculate the effective rate constant in unimolecular gas-phase kinetics through a stochastic reformulation of Lindemann kinetics. Considering the rate constants for excitation and de-excitation steps in the Lindemann mechanism as temperature dependent empirical parameters, we construct and solve a chemical master equation for unimolecular gas-phase kinetics. The effective rate constant thus obtained shows excellent agreement with experimental data in the entire concentration range in which it is reported. The extrapolated values of the effective rate constant for very low and very high concentrations of inert gas molecules are in close agreement with values obtained using the Troe semiempirical method. Stochastic Lindemann kinetics, thus, provides a simple method to construct the full falloff curves and can be used as an alternative to the Troe semiempirical method of kinetic data analysis for unimolecular gas-phase reactions. PMID:23879409

Saha, Soma; Dua, Arti

2013-08-22

176

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

NASA Astrophysics Data System (ADS)

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

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

2010-05-01

177

Photodissociation dynamics of acetoxime in gas phase  

NASA Astrophysics Data System (ADS)

The dynamics of photodissociation of acetoxime at 193nm, leading to the formation of (CH3)2C?N and OH fragments, has been investigated. The nascent OH radicals, which are both rotationally and vibrationally excited, were probed by laser photolysis-laser induced fluorescence technique. OH fragments in both v?=1 and v?=0 vibrational states were detected with a ratio of population in the higher to lower level of 0.07±0.01. The rotational temperatures of v?=0 and 1 levels of OH radicals are 2650±150K and 1290±20K, respectively. More than 30% of the available energy, i.e., 115±21kJmol-1 is partitioned into the relative translational energy of the fragments. The results of excited electronic state and transition state calculations at the configuration interaction with single electronic excitation level suggest that the dissociation takes place with an exit barrier of ˜126kJmol-1 at the triplet state (T2) potential energy surface, formed by internal conversions/intersystem crossing from the initially populated S2 state. Using the calculated transition state geometry and its energy, the observed energy distribution pattern can be reproduced by the hybrid model within experimental uncertainties. The presence of an exit barrier is further supported by the observation of N-OH dissociation upon 248nm excitation, where the relative translational energy of the fragments is found to be ˜96kJmol-1. The photodissociation dynamics of acetoxime is compared with C-OH dissociation in enols and carboxylic acid and N-OH dissociation in nitrous acid. The observed emission (?max=430nm ) and the N-OH dissociation dynamics indicate crossing of the initially populated state to an emissive state of acetoxime, which is different from the dissociative state.

Dhanya, Suresh; Upadhyaya, Hari P.; Kumar, Awadhesh; Naik, Prakash D.; Saini, Rameshwar D.

2005-05-01

178

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

179

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

PubMed Central

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

Larsson, Per; Kasson, Peter M.

2013-01-01

180

Ultrafast dynamics and hydrogen-bond structure in aqueous solutions of model peptides.  

PubMed

The dynamics of water molecules in the hydration layers of proteins are critical for biological function. Here the molecular dynamics in aqueous solutions of model hydrophilic and amphiphilic dipeptides are studied as a function of concentration using the ultrafast optical Kerr effect (OKE). The OKE is a direct time-domain method which yields both picosecond time scale molecular dynamics and low-frequency (Terahertz) Raman spectra, which contain information on the hydrogen-bonded structure of aqueous solutions. Two distinct concentration regimes are identified, above and below 0.4 M peptide concentration. In the low-concentration regime the tetrahedral water structure is largely preserved but the structural dynamics in water are slowed significantly by interaction with the peptide. The slow down is more marked for the hydrophilic than the amphiphilic peptide. Suppression of water structural dynamics observed is greater than that reported for retardation of the water reorientation in NMR, reflecting the different dynamics probed by these different methods. Above 0.4 M the tetrahedral water structure is more strongly perturbed, a contribution to the THz Raman spectrum from the solvated peptide is observed, and structural dynamics in the solution are markedly slowed. This is assigned to slow relaxation within an H-bonded network of peptide molecules. The strong concentration dependence observed goes some way toward explaining disagreements between different measurements of the dynamics of peptide solvation which have appeared in the literature. PMID:20666567

Mazur, Kamila; Heisler, Ismael A; Meech, Stephen R

2010-08-19

181

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

PubMed Central

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

Price, William D.; Jockusch, Rebecca A.

2005-01-01

182

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

183

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. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd. 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

184

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

NASA Astrophysics Data System (ADS)

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

Weinkauf, Rainer; Lehrer, Florian

1998-12-01

185

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

PubMed Central

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

2012-01-01

186

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

PubMed

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

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

1992-01-01

187

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

188

Gas Phase Chiral Separations By Ion Mobility Spectrometry  

PubMed Central

This manuscript introduces the concept of Chiral Ion Mobility Spectrometry (CIMS) and presents examples demonstrating the gas phase separation of enantiomers of a wide range of racemates including pharmaceuticals, amino acids and carbohydrates. CIMS is similar to traditional ion mobility spectrometry (IMS), where gas phase ions, when subjected to a potential gradient are separated at atmospheric pressure due to differences in their shapes and sizes. In addition to size and shape, CIMS separates ions based on their stereospecific interaction with a chiral gas. In order to achieve chiral discrimination by CIMS, an asymmetric environment was provided by doping the drift gas with a volatile chiral reagent. In this study S-(+)-2-butanol was used as a chiral modifier to demonstrate enantiomeric separations of atenolol, serine, methionine, threonine, methyl-?-glucopyranoside, glucose, penicillamine, valinol, phenylalanine, and tryptophan from their respective racemic mixtures. PMID:17165808

Dwivedi, Prabha; Wu, Ching; Hill, Herbert H.

2013-01-01

189

Para-Hydrogen-Enhanced Gas-Phase Magnetic Resonance Imaging  

SciTech Connect

Herein, we demonstrate magnetic resonance imaging (MRI) inthe gas phase using para-hydrogen (p-H2)-induced polarization. A reactantmixture of H2 enriched in the paraspin state and propylene gas is flowedthrough a reactor cell containing a heterogenized catalyst, Wilkinson'scatalyst immobilized on modified silica gel. The hydrogenation product,propane gas, is transferred to the NMR magnet and is spin-polarized as aresult of the ALTADENA (adiabatic longitudinal transport and dissociationengenders net alignment) effect. A polarization enhancement factor of 300relative to thermally polarized gas was observed in 1D1H NMR spectra.Enhancement was also evident in the magnetic resonance images. This isthe first demonstration of imaging a hyperpolarized gaseous productformed in a hydrogenation reaction catalyzed by a supported catalyst.This result may lead to several important applications, includingflow-through porous materials, gas-phase reaction kinetics and adsorptionstudies, and MRI in low fields, all using catalyst-free polarizedfluids.

Bouchard, Louis-S.; Kovtunov, Kirill V.; Burt, Scott R.; Anwar,M. Sabieh; Koptyug, Igor V.; Sagdeev, Renad Z.; Pines, Alexander

2007-02-23

190

Nanoparticle collisions in the gas phase in the presence of singular contact potentials  

NASA Astrophysics Data System (ADS)

Collisional growth and ionization is commonplace for gas phase nanoparticles (i.e., in aerosols). Nanoparticle collisions in atmospheric pressure environments occur in the mass transfer transition regime, and further attractive singular contact potentials (which arise when modeling nanoparticles as condensed matter and for which the potential energy approaches -? when two entities contact) often have a non-negligible influence on collision processes. For these reasons collision rate calculations for nanoparticles in the gas phase are not straightforward. We use mean first passage time calculations to develop a simple relationship to determine the collision rate in the gas phase, accounting for the influences of both the transition regime and singular contact potentials (specifically the non-retarded van der Waals and image potentials). In the presented analysis, methods to determine the degree of enhancement in collision rate due to attractive singular potentials in the continuum (diffusive) regime, ?C, and the degree of enhancement in the free molecular (ballistic) regime, ?FM, are first reviewed. Accounting for these enhancement factors, with mean first passage time calculations it is found that the collision rate for gas phase nanoparticles with other gas phase entities can be determined from a relationship between the dimensionless collision rate coefficient, H, and the diffusive Knudsen number, KnD, i.e., the ratio of the mean collision persistence distance to the collision length scale. This coincides with the H(KnD) relationship found to appropriately describe collisions between entities interacting via a hard-sphere potential, but with ?C and ?FM incorporated into the definitions of both H and KnD, respectively. The H(KnD) relationship is compared to the predictions of flux matching theory, used prevalently in prior work for collision rate calculation, and through this comparison it is found that at high potential energy to thermal energy ratios, flux matching theory predictions underestimate the true collision rate. Finally, a series of experimental measurements of nanoparticle-nanoparticle collision rates are compared to the determined H(KnD) expression, considering that nanoparticles interact via non-retarded van der Waals potentials. Very good agreement is found with collision rates inferred from experiments, with almost all measured values from four separate studies within 25% of model predictions.

Ouyang, Hui; Gopalakrishnan, Ranganathan; Hogan, Christopher J.

2012-08-01

191

A multiwatt all gas-phase iodine laser (AGIL)  

Microsoft Academic Search

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(a1Delta) 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

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

2004-01-01

192

Gas phase chemical detection with an integrated chemical analysis system  

SciTech Connect

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

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

2000-04-12

193

Gas phase photocatalytic removal of toluene effluents on sulfated titania  

Microsoft Academic Search

Photocatalytic removal of toluene in the gas phase was carried out over UV-illuminated sulfated titania materials in a cylinder-like continuous reactor. A series of SO42?–TiO2 samples was obtained from the addition of H2SO4 on an amorphous titanium hydroxide gel synthesized according to a classical sol–gel procedure. The wide variety of materials led to varying photocatalytic behaviors depending strongly on the

Elodie Barraud; Florence Bosc; David Edwards; Nicolas Keller; Valérie Keller

2005-01-01

194

Molecular Tagging Velocimetry (MTV) measurements in gas phase flows  

Microsoft Academic Search

Recent developments in Molecular Tagging Velocimetry (MTV) using the phosphorescence of biacetyl are described for gas-phase flows. With improvements in tagging, detection, and processing\\u000a schemes, whole-field measurements of two components of the velocity vector are obtained simultaneously, typically at more\\u000a than 300 points over a plane. Application of this measurement approach is demonstrated in mapping the velocity and vorticity\\u000a fields

B. Stier; M. M. Koochesfahani

1999-01-01

195

Entropy effects in gas phase ion-molecule association reactions  

Microsoft Academic Search

The kinetics of gas phase reactions of the ions C5H5M+ (M=V, Co, Ni and Ru) with oxygen (Me2CO, Me2O, MeOH, Me2CHOH, H2O) and nitrogen (NH3, NH2Me, NHMe2, NMe3) donor ligands have been studied by Ion Trap Mass Spectrometry. The kinetic data confirm the previously found dependence of the log of the rate constants upon the ligand ionization energy. To get

Sandro Torroni; Andrea Maranzana

2001-01-01

196

Novel five-membered ring intermediates in gas phase reactions  

Microsoft Academic Search

This review considers the role of closed-ring intermediates in chemistry, in general, and focuses on recent experimental and\\u000a theoretical works that provide compelling evidence for a fivemembered ring intermediate in the gas phase. The reactions of\\u000a oxygen atoms with ethyl iodide and larger alkyl iodides produce HOI and a corresponding ethylenic compound via attack of the\\u000a oxygen atom at the

Richard A. Loomis; Stephen R. Leone; Mary K. Gilles

1998-01-01

197

FTIR Studies of Collagen Model Peptides: Complementary Experimental and Simulation Approaches to Conformation and Unfolding  

PubMed Central

X-ray crystallography of collagen model peptides has provided high resolution structures of the basic triple-helical conformation and its water-mediated hydration network. Vibrational spectroscopy provides a useful bridge for transferring the structural information from x-ray diffraction to collagen in its native environment. The vibrational mode most useful for this purpose is the Amide I mode (mostly peptide bond C=O stretch) near 1650 cm?1. The current study refines and extends the range of utility of a novel simulation method that accurately predicts the IR Amide I spectral contour from the three dimensional structure of a protein or peptide. The approach is demonstrated through accurate simulation of the experimental Amide I contour in solution for both a standard triple-helix, (Pro-Pro-Gly)10, and a second peptide with a Gly ? Ala substitution in the middle of the chain that models the effect of a mutation in the native collagen sequence. Monitoring the major Amide I peak as a function of temperature gives sharp thermal transitions for both peptides, similar to those obtained by circular dichroism spectroscopy, and the FTIR spectra of the unfolded states were compared with polyproline II. The simulation studies were extended to model early stages of thermal denaturation of (Pro-Pro-Gly)10. Dihedral angle changes suggested by molecular dynamics simulations were made in a stepwise fashion to generate peptide unwinding from each end, which emulates the effect of increasing temperature. Simulated bands from these new structures were then compared to the experimental bands obtained as temperature was increased. The similarity between the simulated and experimental IR spectra lends credence to the simulation method, and paves the way for a variety of applications. PMID:17550251

Bryan, Michael A.; Brauner, Joseph W.; Anderle, Gloria; Flach, Carol R.; Brodsky, Barbara; Mendelsohn, Richard

2008-01-01

198

Simulation Approach for Microscale Noncontinuum Gas-Phase Heat Transfer  

NASA Astrophysics Data System (ADS)

In microscale thermal actuators, gas-phase heat transfer from the heated beams to the adjacent unheated substrate is often the main energy-loss mechanism. Since the beam-substrate gap is comparable to the molecular mean free path, noncontinuum gas effects are important. A simulation approach is presented in which gas-phase heat transfer is described by Fourier's law in the bulk gas and by a wall boundary condition that equates the normal heat flux to the product of the gas-solid temperature difference and a heat transfer coefficient. The dimensionless parameters in this heat transfer coefficient are determined by comparison to Direct Simulation Monte Carlo (DSMC) results for heat transfer from beams of rectangular cross section to the substrate at free-molecular to near-continuum gas pressures. This simulation approach produces reasonably accurate gas-phase heat-transfer results for wide ranges of beam geometries and gas pressures. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

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

2008-11-01

199

Molecular mechanism of the hydration of Candida antarctica1 lipase B in gas phase: water adsorption isotherms and molecular2  

E-print Network

1 Molecular mechanism of the hydration of Candida antarctica1 lipase B in gas phase: water of Candida antarctica lipase B34 (CALB) and its dependence on the thermodynamic activity of water aw molecular modeling 58 deglycosylation59 60 hal-00647673,version1-2Dec2011 #12;3 INTRODUCTION61 62 Candida

Paris-Sud XI, Université de

200

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

201

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

PubMed Central

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

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

2013-01-01

202

Aminoethylation in model peptides reveals conditions for maximizing thiol specificity.  

PubMed

Control of pH in aminoethylation reactions is critical for maintaining high selectivity towards cysteine modification. Measurement of aminoethylation rate constants by liquid chromatography mass spectrometry demonstrates reaction selectivity of cysteine>amino-terminus>histidine. Lysine and methionine were not reactive at the conditions used. For thiol modification, the acid/base property of the gamma-thialysine residue measured by NMR results in a 1.15 decrease in pK(a) (relative to a lysine residue). NMR confirms ethylene imine is the reactive intermediate for alkylation of peptide nucleophiles with bromoethylamine. Conversion of bromoethylamine into ethylene imine prior to exposure to the target thiol, provides a reagent that promotes selectivity by allowing precise control of reaction pH. Reaction selectivity plots of relative aminoethylation rates for cysteine, histidine, and N-terminus imine demonstrate increasing alkaline conditions favors thiol modification. When applied to protein modification, the conversion of bromoethylamine into ethylene imine and buffering at alkaline pH will allow optimal cysteine residue aminoethylation. PMID:16229814

Hopkins, Christopher E; Hernandez, Gonzalo; Lee, Jonathan P; Tolan, Dean R

2005-11-15

203

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...

204

Estimation of global structural and transport properties of peptides through the modeling of their CZE mobility data.  

PubMed

Peptide electrophoretic mobility data are interpreted through a physicochemical CZE model, providing estimates of the equivalent hydrodynamic radius, hydration, effective and total charge numbers, actual ionizing pK, pH-near molecule and electrical permittivity of peptide domain, among other basic properties. In this study, they are used to estimate some peptide global structural properties proposed, providing thus a distinction among different peptides. Therefore, the solvent drag on the peptide is obtained through a characteristic friction power coefficient of the number of amino acid residues, defined from the global chain conformation in solution. As modeling of the effective electrophoretic mobility of peptides is carried out in terms of particle hydrodynamic size and shape coupled to hydration and effective charge, a packing dimension related to chain conformation within the peptide domain may be defined. In addition, the effective and total charge number fractions of peptides provide some clues on the interpretation of chain conformations within the framework of scaling laws. Furthermore, the model estimates transport properties, such as sedimentation, friction and diffusion coefficients. As the relative numbers of ionizing, polar and non-polar amino acid residues vary in peptides, their global structural properties defined here change appreciably. Needs for further research are also discussed. PMID:20506428

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

2010-08-01

205

Inhibition of new vessel growth in mouse model of laser-induced choroidal neovascularization by adiponectin peptide II  

PubMed Central

We have investigated the effect of adiponectin (APN) peptide II on new vessel growth in mouse model of choroidal neovascularization (CNV) or wet type age-related macular degeneration (AMD). Mice were injected intraperitoneally with APN peptide II, control peptide, or PBS on day 1–7 or day 5–14. APN, AdipoR1, PCNA, and VEGF localization was investigated using confocal microscopy, immunohistochemistry, and RT-PCR. APN peptide II decreased the relative area of FITC-dextran perfused vessels by 4-fold, PCNA expression by 3-fold, and the number of PCNA stained HUVEC and MAVEC cells by 38 and 46%, respectively. We concluded that APN peptide II inhibits CNV size on days 7 and 14 by inhibiting the proliferation of endothelial cells in vivo and in vitro. APN peptide II may have therapeutic potential to inhibit CNV or wet AMD. PMID:19422927

Lyzogubov, Valeriy V.; Tytarenko, Ruslana G.; Thotakura, Sushma; Viswanathan, Tito; Bora, Nalini S.; Bora, Puran S.

2012-01-01

206

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

PubMed

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed. PMID:11539835

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

1993-01-01

207

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

208

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

PubMed Central

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

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

1996-01-01

209

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

210

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, Tennessee; and § Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing, China #12 that the critical nucleus size for homogeneous nucleation process is 3 peptides. Here we set the minimal step size

Zhang, Yang

211

An all gas-phase iodine laser based on amine chemistry  

NASA Astrophysics Data System (ADS)

Laser action has been demonstrated for the 2P 1/2- 2P 3/2 transition of iodine atom pumped by energy transfer from NCl(a 1?) produced by a set of amine-based, all gas-phase chemical reactions. Continuous-wave laser output of 50 mW with 40% duty factor is obtained from a stable optical resonator consisting of two 99.99% reflective mirrors. The observed laser characteristics are reasonably explained by numerical model calculations.

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

2009-07-01

212

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

E-print Network

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

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

2008-01-29

213

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

SciTech Connect

Critical temperature T{sub c} for the nuclear liquid-gas phase transition is estimated from both the multifragmentation and fission data. In the first case, the critical temperature is obtained by analysis of the intermediate-mass-fragment yields in p(8.1 GeV) + Au collisions within the statistical model of multifragmentation. In the second case, the experimental fission probability for excited {sup 188}Os is compared with the calculated one with T{sub c} as a free parameter. It is concluded for both cases that the critical temperature is higher than 15 MeV.

Karnaukhov, V. A. [Joint Institute for Nuclear Research (Russian Federation); Oeschler, H. [Darmstadt University of Technology, Institut fuer Kernphysik (Germany); Budzanowski, A. [H. Niewodniczanski Institute of Nuclear Physics (Poland); Avdeyev, S. P. [Joint Institute for Nuclear Research (Russian Federation); Botvina, A. S. [Institute for Nuclear Research (Russian Federation); Cherepanov, E. A. [Joint Institute for Nuclear Research (Russian Federation); Karcz, W. [H. Niewodniczanski Institute of Nuclear Physics (Poland); Kirakosyan, V. V.; Rukoyatkin, P. A. [Joint Institute for Nuclear Research (Russian Federation); Skwirczynska, I. [H. Niewodniczanski Institute of Nuclear Physics (Poland); Norbeck, E. [University of Iowa (United States)

2008-12-15

214

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

PubMed

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

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

1995-01-01

215

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

216

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

E-print Network

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

Clemmer, David E.

217

Gas-phase silicon micromachining with xenon difluoride  

NASA Astrophysics Data System (ADS)

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 observed. Initial characteriation of wafer surface temperature during the etch indicates tens of degrees of self-heating, which is known to cause substantial decrease in etch rate.

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

1995-09-01

218

Mulitwatt all gas-phase iodine laser (AGIL)  

Microsoft Academic Search

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(a1Delta) 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

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

2003-01-01

219

The solar system/interstellar medium connection - Gas phase abundances  

NASA Technical Reports Server (NTRS)

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

Lutz, Barry L.

1987-01-01

220

The gas phase reactions of methylene with propionaldehyde  

E-print Network

carbonyls (30) was reported by Back . In this work acetaldehyde, propionaldehyde and formaldehyde were reacted in the gas phase with methylene. The main products found in the reaction with acetaldehyde were carbon monoxide, methane, ethane, ethylene... on the basis of oxygen effects on the 1, Z-epoxybutane yield. A singlet biradical like (I) is expected to close to 1, 2-epoxybutane rapidly, and a radical scavanger such as oxygen would not react with a singlet biradical such as ( I) rapidly enough to trap...

Fuqua, Peter Joseph

2012-06-07

221

Gas Phase Chemical Detection with an Integrated Chemical Analysis System  

SciTech Connect

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

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

1999-07-08

222

Gas-phase energetics of thorium fluorides and their ions.  

PubMed

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

Irikura, Karl K

2013-02-14

223

Neurotransmitters in the Gas Phase: La-Mb Studies  

NASA Astrophysics Data System (ADS)

LA-MB-FTMW spectroscopy combines laser ablation with Fourier transform microwave spectroscopy in supersonic jets overcoming the problems of thermal decomposition associated with conventional heating methods. We present here the results on LA-MB-FTMW studies of some neurotransmitters. Six conformers of dopamine, four of adrenaline, five of noradrenaline and three conformers of serotonin have been characterized in the gas phase. The rotational and nuclear quadrupole coupling constants extracted from the analysis of the rotational spectrum are directly compared with those predicted by ab initio methods to achieve the conclusive identification of different conformers and the experimental characterization of the intramolecular forces at play which control conformational preferences.

Cabezas, C.; Mata, S.; López, J. C.; Alonso, J. L.

2011-06-01

224

Minimum length of an idiotypic peptide and a model for its binding to a major histocompatibility complex class II molecule.  

PubMed Central

We have defined the minimum length of a synthetic peptide which can activate I-Ed-restricted BALB/c T cell clones specific for a mutated self-antigen: an idiotope on the syngeneic lambda 2315 immunoglobulin light chain. A peptide comprising residues 91-101 of the lambda 2315 sequence had full stimulatory potency. Surprisingly, a peptide analogue in which His97 was deleted was almost fully active. Truncated, deleted or substituted peptide analogues did not distinguish between seven T cell clones that use different alpha/beta T cell receptors. The 91-101 region in the lambda 2315 light chain does not form an amphipathic helix even though such a helix has been suggested to be important for T cell epitopes. Further, a motif proposed by Rothbard and Taylor as being common to T cell immunogenic peptides is not necessary for the lambda 2315 idiotypic peptide. Comparison with seven other I-Ed-restricted peptides revealed that the peptides are generally positively charged and have two basic amino acids clustered around the centre. On the basis of a model of the class II molecule peptide binding site, we suggest that these positively charged residues may interact with the negatively charged residues at positions 114(Glu) and 155(Asp) of the E beta d chain. Images PMID:2792076

Bogen, B; Lambris, J D

1989-01-01

225

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

226

Variations of the tautomeric preferences and ?-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM).  

PubMed

Quantum-chemical calculations were performed for all possible nine neutral tautomers of purine and their oxidized and reduced forms in water {PCM//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. PCM hydration influences geometries, ?-electron delocalization, and relative energies of purine tautomers in different ways. Generally, the harmonic oscillator model of electron delocalization (HOMED) indices increase when proceeding from the gas phase to aequeous solution for the neutral and redox forms of purine. Their changes for the neutral and oxidized tautomers are almost parallel to the relative energies showing that aromaticity plays an important role in the tautomeric preferences. Tautomeric stabilities and tautomeric preferences vary when proceeding from the gas phase to water indicating additionally that intra- and intermolecular interactions affect tautomeric equilibria. The tautomeric mixture of neutral purine in the gas phase consists mainly of the N9H tautomer, whereas two tautomers (N9H and N7H) dominate in water. For oxidized purine, N9H is favored in the gas phase, whereas N1H in water. A gain of one electron dramatically changes the relative stabilities of the CH and NH tautomers that C6H and C8H dominate in the tautomeric mixture in the gas phase, whereas N3H in water. These variations show exceptional sensitivity of the tautomeric purine system on environment in the electron-transfer reactions. PMID:23832652

Raczy?ska, Ewa D; Kami?ska, Beata

2013-09-01

227

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

E-print Network

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

Pablo Echenique; Gregory A. Chass

2008-11-08

228

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

PubMed Central

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

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

2013-01-01

229

Measurement and speciation of gas phase peroxides in the atmosphere  

SciTech Connect

An improved gas phase sampler and a recently developed nonenzymatic measurement method for H[sub 2]O[sub 2] and HOCH[sub 2]OOH(HMHP) are described. The gas phase sampler is equipped with a surfaceless intake to alleviate heterogeneous loss of H[sub 2]O[sub 2] in the sampling line. The nonenzymatic method makes use of the aqueous phase Fention reaction for H[sub 2]O[sub 2] measurement and is capable of speciation between H[sub 2]O[sub 2] and HMHP, using a dual channel technique. By adding a third channel employing the well-established method of p-hydroxyphenylacetic acid (POHPAA) and horseradish peroxidase for total peroxide measurement, it is possible to differentiate H[sub 2]O[sub 2], HMHP, and other organic peroxides, if present. The measurement technique was successfully deployed in a field study at George L. Smith III State Park, Georgia (82[degrees]20[prime]W, 32[degrees]30[prime]N). Preliminary data analysis indicates that the measured total peroxides range from 0.4 to [approximately]6 ppbv, depending on meteorological conditions, and that organic peroxides, mostly HMHP, constitute between 20 and 80% of the total peroxides. The work reported here represents the first continuous and real-time measurements for these peroxides in the atmosphere. 28 refs., 7 figs., 1 tab.

Lee, J.H.; Leahy, D.F.; Tang, I.N.; Newman, L. (Brookhaven National Lab., Upton, NY (United States))

1993-02-20

230

Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids  

NASA Astrophysics Data System (ADS)

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

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

2011-09-01

231

Closed-cage tungsten oxide clusters in the gas phase.  

PubMed

During the course of a study on the clustering of W-Se and W-S mixtures in the gas phase using laser desorption ionization (LDI) mass spectrometry, we observed several anionic W-O clusters. Three distinct species, W(6)O(19)(-), W(13)O(29)(-), and W(14)O(32)(-), stand out as intense peaks in the regular mass spectral pattern of tungsten oxide clusters suggesting unusual stabilities for them. Moreover, these clusters do not fragment in the postsource decay analysis. While trying to understand the precursor material, which produced these clusters, we found the presence of nanoscale forms of tungsten oxide. The structure and thermodynamic parameters of tungsten clusters have been explored using relativistic quantum chemical methods. Our computed results of atomization energy are consistent with the observed LDI mass spectra. The computational results suggest that the clusters observed have closed-cage structure. These distinct W(13) and W(14) clusters were observed for the first time in the gas phase. PMID:20377209

Singh, D M David Jeba; Pradeep, T; Thirumoorthy, Krishnan; Balasubramanian, Krishnan

2010-05-01

232

Gas phase oxidation downstream of a catalytic combustor  

NASA Technical Reports Server (NTRS)

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

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

1979-01-01

233

Gas phase contributions to topochemical hydride reduction reactions  

SciTech Connect

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

Kobayashi, Yoji [Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510 (Japan); CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012 (Japan); Li, Zhaofei [Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); Hirai, Kei [Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); Tassel, Cédric [Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510 (Japan); The Hakubi Center for Advanced Research, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8302 (Japan); Loyer, François [Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510 (Japan); Institut des Sciences Chimiques de Rennes, UMR 6226 Université de Rennes 1-CNRS, équipe CSM, Bât. 10B, Campus de Beaulieu, 263, Avenue du Général Leclerc, 35042 Rennes Cedex (France); Ichikawa, Noriya [CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012 (Japan); Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); Abe, Naoyuki [Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510 (Japan); Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan); Yamamoto, Takafumi [Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510 (Japan); Shimakawa, Yuichi [CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012 (Japan); Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); and others

2013-11-15

234

Position for determining gas-phase volatile organic compound concentrations in transuranic waste containers. Revision 2  

SciTech Connect

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

Connolly, M.J.; Liekhus, K.J. [Lockheed Martin Idaho Technologies Co., Idaho Falls, ID (United States). Idaho National Engineering and Environmental Lab.] [Lockheed Martin Idaho Technologies Co., Idaho Falls, ID (United States). Idaho National Engineering and Environmental Lab.; Djordjevic, S.M.; Loehr, C.A.; Spangler, L.R. [Benchmark Environmental Corp. (United States)] [Benchmark Environmental Corp. (United States)

1998-06-01

235

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

SciTech Connect

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

Connolly, M.J.; Liekhus, K.J. [Lockheed Idaho Technologies Co., Idaho Falls, ID (United States); Djordjevic, S.M.; Loehr, C.A.; Spangler, L.R. [Benchmark Environmental Corp., Albuquerque, NM (United States)

1995-08-01

236

Determinants of gas-phase disassembly behavior in homodimeric protein complexes with related yet divergent structures.  

PubMed

The overall structure of a protein-protein complex reflects an intricate arrangement of noncovalent interactions. Whereas intramolecular interactions confer secondary and tertiary structure to individual subunits, intermolecular interactions lead to quaternary structure--the ordered aggregation of separate polypeptide chains into multisubunit assemblies. The specific ensemble of noncovalent contacts dictates the stability of subunit folds, enforces protein-protein binding specificity, and determines multimer stability. Consequently, noncovalent architecture is likely to play a role in the gas-phase dissociation of these assemblies during tandem mass spectrometry (MS/MS). To further advance the applicability of MS/MS to analytical problems in structural biology, a better understanding of the interplay between the structures and fragmentation behaviors of noncovalent protein complexes is essential. The present work constitutes a systematic study of model protein homodimers (bacteriophage N15 Cro, bacteriophage ? Cro, and bacteriophage P22 Arc) with related but divergent structures, both in terms of subunit folds and protein-protein interfaces. Because each of these dimers has a well-characterized structure (solution and/or crystal structure), specific noncovalent features could be correlated with gas-phase disassembly patterns as studied by collision-induced dissociation, surface-induced dissociation, and ion mobility. Of the several respects in which the dimers differed in structure, the presence or absence of intermolecular electrostatic contacts exerted the most significant influence on the gas-phase dissociation behavior. This is attributed to the well-known enhancement of ionic interactions in the absence of bulk solvent. Because salt bridges are general contributors to both intermolecular and intramolecular stability in protein complexes, these observations are broadly applicable to aid in the interpretation or prediction of dissociation spectra for noncovalent protein assemblies. PMID:21486017

Dodds, Eric D; Blackwell, Anne E; Jones, Christopher M; Holso, Katie L; O'Brien, Dawne J; Cordes, Matthew H J; Wysocki, Vicki H

2011-05-15

237

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

PubMed

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

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

2012-01-01

238

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

Microsoft Academic Search

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

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

2005-01-01

239

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

240

STUDIES OF THE EFFECTS OF DOPAMINE NEURON STIMULATING PEPTIDES IN RODENT MODELS OF NORMAL AND DYSFUNCTIONAL DOPAMINERGIC SYSTEMS.  

E-print Network

??A theoretical post-translational processing model of the proprotein form of glial cell line-derived neurotrophic factor (GDNF) likely produces three biologically active peptides. The three prospective… (more)

Fuqua, Joshua Lee

2010-01-01

241

Energy and Entropy Effects in Dissociation of Peptide Radical Anions  

SciTech Connect

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

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

2012-04-15

242

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

PubMed

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

Nayar, Divya; Chakravarty, Charusita

2014-06-01

243

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

NASA Astrophysics Data System (ADS)

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

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

2011-01-01

244

Roles of ?-Turns in Protein Folding: From Peptide Models to Protein Engineering  

PubMed Central

Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein’s structure. PMID:18275088

Marcelino, Anna Marie C.; Gierasch, Lila M.

2010-01-01

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

Raman study of vibrational dynamics of aminopropylsilanetriol in gas phase  

NASA Astrophysics Data System (ADS)

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⋯Hsbnd O 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.

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

2014-01-01

247

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

248

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; Sudholter, Ernst J.R.; de Smet, Louis C.P.M.

2014-01-01

249

Regenerable Air Purification System for Gas-Phase Contaminant Control  

NASA Technical Reports Server (NTRS)

Tests of a pre-prototype regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an adsorbent column have been performed at NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. During the normal operation mode, contaminants are removed from the air on the column. Regeneration of the column is performed on-line. During regeneration, contaminants are displaced and destroyed inside the closed oxidation loop. In this presentation we discuss initial experimental results for the performance of RAPS in the removal and treatment of several important spacecraft contaminant species from air.

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

2000-01-01

250

Ab initio kinetics of gas phase decomposition reactions.  

PubMed

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

Sharia, Onise; Kuklja, Maija M

2010-12-01

251

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

252

A Bayesian Model Averaging Approach to the Quantification of Overlapping Peptides in an MALDI-TOF Mass Spectrum  

PubMed Central

In a high-resolution MALDI-TOF mass spectrum, a peptide produces multiple peaks, corresponding to the isotopic variants of the molecules. An overlap occurs when two peptides appear in the vicinity of the mass coordinate, resulting in the difficulty of quantifying the relative abundance and the exact masses of these peptides. To address the problem, two factors need to be considered: (1) the variability pertaining to the abundances of the isotopic variants (2) extra information content needed to supplement the information contained in data. We propose a Bayesian model for the incorporation of prior information. Such information exists, for example, for the distribution of the masses of peptides and the abundances of the isotopic variants. The model we develop allows for the correct estimation of the parameters of interest. The validity of the modeling approach is verified by a real-life case study from a controlled mass spectrometry experiment and by a simulation study. PMID:22091391

Zhu, Qi; Kasim, Adetayo; Valkenborg, Dirk; Burzykowski, Tomasz

2011-01-01

253

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

E-print Network

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

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

2007-07-09

254

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

255

Stabilization of a Cl(-)-Cl(-) anion pair in the gas phase: ab initio microsolvation study.  

PubMed

Despite the confirmation of Cl(-)-Cl(-) association in aqueous solution and crystalline state, there have been no reports about the existence of stable dichloride anion pair in the gas phase. In the current work we performed a systematic ab initio study of microsolvation of dichloride anion pair. The stepwise solvation mechanism observed for free gaseous [Cl2(H2O)n](2-) (n = 2-10) clusters was found to be quite interesting. The lowest structure for dichloride hexahydrate closely resembles cubic water octamer W8 in which two water molecules in the corners of the cube are substituted by two chloride anions. We have also shown that Cl(-)-Cl(-) pair may be completely stabilized by about 36 water molecules in the gas phase. Stabilization of the pair leads to the formation of cyclic H2O structures that bridge the Cl(-) ions. It has been predicted that the large clusters of [Cl2(H2O)36](2-) and [Cl2(H2O)40](2-) may exhibit properties analogous to bulk aqueous solutions, therefore they could become good molecular models for understanding complicated processes of solvation of Cl(-) in the bulk. PMID:24471443

Ivanov, Alexander S; Frenking, Gernot; Boldyrev, Alexander I

2014-09-01

256

Photoemission and Photoabsorption Spectroscopy of Glycyl-Glycine in the Gas Phase  

NASA Astrophysics Data System (ADS)

The high-resolution outer and inner valence band (VB) spectra, as well as core level X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectra at the carbon, nitrogen, and oxygen K-edges of glycyl-glycine in the gas phase have been measured, and the results interpreted by means of ab initio calculations. By comparison with our previous glycine spectra, the features characteristic of the peptide bond in the carbon, nitrogen, and oxygen XPS and NEXAFS spectra of glycyl-glycine have been identified and assigned. The K-edge NEXAFS spectra at all edges were found to be in reasonable agreement with published electron energy loss spectra, but showed more prominent structure due to the higher resolution. Effects on the nitrogen K-edge NEXAFS spectrum of glycyl-glycine due to intramolecular hydrogen bonding were observed. The N(NH2) 1s ? ?*CN resonance shifts to 0.6 eV lower energy, due to internal hydrogen bonding between the NH2 and NH groups.

Feyer, Vitaliy; Plekan, Oksana; Richter, Robert; Coreno, Marcello; Prince, Kevin C.; Carravetta, Vincenzo

2009-09-01

257

Photoemission and photoabsorption spectroscopy of glycyl-glycine in the gas phase.  

PubMed

The high-resolution outer and inner valence band (VB) spectra, as well as core level X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectra at the carbon, nitrogen, and oxygen K-edges of glycyl-glycine in the gas phase have been measured, and the results interpreted by means of ab initio calculations. By comparison with our previous glycine spectra, the features characteristic of the peptide bond in the carbon, nitrogen, and oxygen XPS and NEXAFS spectra of glycyl-glycine have been identified and assigned. The K-edge NEXAFS spectra at all edges were found to be in reasonable agreement with published electron energy loss spectra, but showed more prominent structure due to the higher resolution. Effects on the nitrogen K-edge NEXAFS spectrum of glycyl-glycine due to intramolecular hydrogen bonding were observed. The N(NH(2)) 1s --> pi*(CN) resonance shifts to 0.6 eV lower energy, due to internal hydrogen bonding between the NH(2) and NH groups. PMID:19757775

Feyer, Vitaliy; Plekan, Oksana; Richter, Robert; Coreno, Marcello; Prince, Kevin C; Carravetta, Vincenzo

2009-10-01

258

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.

259

Algorithm for peptide sequencing by tandem mass spectrometry based on better preprocessing and anti-symmetric computational model.  

PubMed

Peptide sequencing by tandem mass spectrometry is a very important, interesting, yet challenging problem in proteomics. This problem is extensively investigated by researchers recently, and the peptide sequencing results are becoming more and more accurate. However, many of these algorithms are using computational models based on some unverified assumptions. We believe that the investigation of the validity of these assumptions and related problems will lead to improvements in current algorithms. In this paper, we have first investigated peptide sequencing without preprocessing the spectrum, and we have shown that by introducing preprocessing on spectrum, peptide sequencing can be faster, easier and more accurate. We have then investigated one very important problem, the anti-symmetric problem in the peptide sequencing problem, and we have proved by experiments that model that simply ignore anti-symmetric of model that remove all anti-symmetric instances are too simple for peptide sequencing problem. We have proposed a new model for anti-symmetric problem in more realistic way. We have also proposed a novel algorithm which incorporate preprocessing and new model for anti-symmetric issue, and experiments show that this algorithm has better performance on datasets examined. PMID:17951809

Ning, Kang; Leong, Hon Wai

2007-01-01

260

Doping efficiencies of gas-phase and ion-implantation doped a-Si:H  

NASA Astrophysics Data System (ADS)

We compare the electronic properties of gas-phase and implantation doped a-Si:H films and analyze their properties within the framework of Street's auto-compensation model [1]. We find that this model can consistently explain the varying degrees of sensitivity with respect to doping for differently prepared a-Si:H materials. In agreement with sub-band-gap absorption data our analysis indicates that the density of native dangling bond defects is increased when the film thickness is decreased and when thin films are further subjected to ion bombardment. Considering the temperature dependence of conductivity, we find that the auto-compensation model can provide an explanation for the high-temperature kink in the conductivity of doped a-Si:H films but that it fails to account for the experimentally observed universality of the “Meyer-Neldel-rule” behaviour of the conductivity prefactor in differently prepared and doped a-Si:H films.

Mannsperger, H.; Kalbitzer, S.; Müller, G.

1986-12-01

261

Membrane interactions of a self-assembling model peptide that mimics the self-association, structure and toxicity of A?(1–40)  

Microsoft Academic Search

?-amyloid peptide (A?) is a primary protein component of senile plaques in Alzheimer's disease (AD) and plays an important, but not fully understood role in neurotoxicity. Model peptides with the demonstrated ability to mimic the structural and toxicity behavior of A? could provide a means to evaluate the contributions to toxicity that are common to self-associating peptides from many disease

Luiz C. Salay; Wei Qi; Ben Keshet; Lukas K. Tamm; Erik J. Fernandez

2009-01-01

262

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

PubMed Central

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

Andersen, N. H.; Tong, H.

1997-01-01

263

Mixed ligand Cu2+ complexes of a model therapeutic with Alzheimer's amyloid-? peptide and monoamine neurotransmitters.  

PubMed

8-Hydroxyquinolines (8HQ) have found widespread application in chemistry and biology due to their ability to complex a range of transition metal ions. The family of 2-substituted 8HQs has been proposed for use in the treatment of Alzheimer's disease (AD). Most notably, the therapeutic PBT2 (Prana Biotechnology Ltd.) has been shown to act as an efficient metal chaperone, disaggregate metal-enriched amyloid plaques comprised of the A? peptide, inhibit Cu/A? redox chemistry, and reverse the AD phenotype in transgenic animal models. Yet surprisingly little is known about the molecular interactions at play. In this study, we show that the homologous ligand 2-[(dimethylamino)methyl]-8-hydroxyquinoline (HL) forms a CuL complex with a conditional (apparent) dissociation constant of 0.33 nM at pH 6.9 and is capable of forming ternary Cu(2+) complexes with neurotransmitters including histamine (HA), glutamic acid (Glu), and glycine (Gly), with glutathione disulfide (GSSG), and with histidine (His) side chains of proteins and peptides including the A? peptide. Our findings suggest a molecular basis for the strong metal chaperone activity of PBT2, its ability to attenuate Cu(2+)/A? interactions, and its potential to promote neuroprotective and neuroregenerative effects. PMID:23537393

Kenche, Vijaya B; Zawisza, Izabela; Masters, Colin L; Bal, Wojciech; Barnham, Kevin J; Drew, Simon C

2013-04-15

264

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

Microsoft Academic Search

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

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

2001-01-01

265

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

266

QSAR modeling and design of cationic antimicrobial peptides based on structural properties of amino acids.  

PubMed

Drug resistance to existing antibiotics poses alarming threats to global public health, which inspires heightened interests in searching for new antibiotics, including antimicrobial peptides (AMPs). Accurate prediction of antibacterial activities of AMPs may expedite novel AMP design and reduce the costs and efforts involved in laboratory screening. In the present study, a novel quantitative prediction method of AMP was established by quantitative structure-activity relationship (QSAR) modeling based on the physicochemical properties of amino acids. The indices of these physicochemical properties were used to define AMP. The structural variables were optimized by stepwise regression (STR). Three series of AMPs from the QSAR model were constructed by multiple linear regressions (MLR). These QSAR models showed good performance in reliability and predictability. The normalized regression coefficients of the QSAR model and the contribution of amino acids at each position of AMP may determine the suitableness of a particular residue at any given position. QSAR models constructed by STR-MLR should prove to be useful tools in peptide design with respect to the calculation, explanation, good and reliable performance, and definition of physiochemical properties. PMID:22263858

Wang, Yuanqiang; Ding, Yuan; Wen, Haixia; Lin, Yong; Hu, Yong; Zhang, Ya; Xia, Qingyou; Lin, Zhihua

2012-05-01

267

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

268

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

Microsoft Academic Search

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

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

2004-01-01

269

A computational study of gas-phase and surface reactions in deposition and etching of GaAs and AlAs in the presence of HCl  

NASA Astrophysics Data System (ADS)

Gas-phase and surface reaction mechanisms underlying MOCVD of AlAs and GaAs in the presence of HCl are studied using quantum chemistry. Density functional theory and conventional transition state theory are used to determine kinetic constants of gas-phase reactions following the dissociation of Al(CH 3) 3 and Ga(CH 3) 3 and the subsequent reactions with HCl. The developed kinetic schemes are then explored through sensitivity analysis. Adsorption energies of the most abundant gas phase molecules as well as activation energies of key reactions on GaAs and AlAs (1 0 0) surfaces are predicted quantum chemistry computations. The surface is modeled as semiconductor clusters of increasing size. Comparisons of predictions to available experimental data show that a cluster need to reproduce the ?2(2×4) surface reconstruction in order to successfully predict the surface reactivity. Surface and gas phase kinetic schemes are developed on the basis of the calculations as well as published data. These reaction schemes are linked with a two-dimensional computational fluid dynamic model to simulate experimental growth rates measured in different reactors. The simulations suggest that the AlAs gas phase and surface chemistry differ from that of GaAs. In particular, the mechanism for desorption of CH 3 and Cl from an AlAs surface is different from that active for a GaAs surface.

Cavallotti, Carlo; Lengyel, Istvan; Nemirovskaya, Maria; Jensen, Klavs F.

2004-07-01

270

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

271

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

PubMed

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

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

2014-10-20

272

BIOINFORMATICS Peptide Sequence Tag-Based Blind Identification of Post-Translational Modifications with Point Process Model  

E-print Network

An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental spectra with theoretical spectra from peptides in a peptide database is very time consuming and may lead to high false positive rate. In this paper, we introduce a new approach that is both efficient and effective for blind PTM identification. Our work consists of the following phases. First, we develop a novel tree decomposition based algorithm that can efficiently generate peptide sequence tags (PSTs) from an extended spectrum graph. Sequence tags are selected from all maximum weighted antisymmetric paths in the graph and their reliabilities are evaluated with a score function. An efficient deterministic finite automaton (DFA) based model is then developed to search a peptide database for candidate peptides by using the generated sequence tags. Finally, a point process model ? an efficient blind search approach for PTM identification, is applied to report the correct peptide and PTMs if there are any. Our tests on 2657 experimental tandem mass spectra and 2620 experimental spectra with one artificially added PTM show that, in addition to high efficiency, our ab-initio sequence tag selection algorithm achieves better or comparable accuracy to other approaches. Database search results show that the sequence tags of lengths 3 and 4 filter out more than 98.3 % and 99.8 % peptides respectively when applied to a yeast peptide database. With the dramatically reduced search space, the point process model achieves significant improvement in accuracy as well. Availability: The software is available upon request. Contact: {chunmei,

Chunmei Liu; Bo Yan; Yinglei Song; Ying Xu; Liming Cai

273

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

274

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

E-print Network

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

Michael Bachmann; Wolfhard Janke

2007-10-24

275

Insights into large-scale cell-culture reactors: II. Gas-phase mixing and CO? stripping.  

PubMed

Most discussions about stirred tank bioreactors for cell cultures focus on liquid-phase motions and neglect the importance of the gas phase for mixing, power input and especially CO(2) stripping. Particularly in large production reactors, CO(2) removal from the culture is known to be a major problem. Here, we show that stripping is mainly affected by the change of the gas composition during the movement of the gas phase through the bioreactor from the sparger system towards the headspace. A mathematical model for CO(2)-stripping and O(2)-mass transfer is presented taking gas-residence times into account. The gas phase is not moving through the reactor in form of a plug flow as often assumed. The model is validated by measurement data. Further measurement results are presented that show how the gas is partly recirculated by the impellers, thus increasing the gas-residence time. The gas-residence times can be measured easily with stimulus-response techniques. The results offer further insights on the gas-residence time distributions in stirred tank reactors. PMID:21818861

Sieblist, Christian; Hägeholz, Oliver; Aehle, Mathias; Jenzsch, Marco; Pohlscheidt, Michael; Lübbert, Andreas

2011-12-01

276

De novo-derived cationic antimicrobial peptide activity in a murine model of Pseudomonas aeruginosa bacteraemia  

PubMed Central

Objectives We describe the antimicrobial activity against Pseudomonas aeruginosa of the de novo-derived antimicrobial peptide WLBU2 in an animal model of infection. Methods For this study, an intravenous (iv) model of P. aeruginosa infection was established. The minimum lethal murine dose of P. aeruginosa strain PA01 was determined to be 3 × 107 cfu when bacteria were administered iv. Increasing concentrations of WLBU2 were instilled either prior to or following PA01 septic exposure. Results For the mice given peptide post-bacterial infection, in the 1 mg/kg group, nine of nine animals died because of Pseudomonas sepsis; in the 3 mg/kg group, only one of nine succumbed to infection and in the 4 mg/kg group, all mice were protected (P < 0.0001). Similar results were obtained when WLBU2 was given 1 h prior to Pseudomonas infection. Conclusions Although the therapeutic window in this model is narrow, the results nonetheless provide encouraging evidence for WLBU2 as a potential prophylactic or treatment of bacterial infection. PMID:17623696

Deslouches, Berthony; Gonzalez, Ivan A.; DeAlmeida, Dilhari; Islam, Kazi; Steele, Chad; Montelaro, Ronald C.; Mietzner, Timothy A.

2007-01-01

277

Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation.  

PubMed

Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist. PMID:22260641

Heck, Alexander; Woiczikowski, P Benjamin; Kuba?, Tomáš; Giese, Bernd; Elstner, Marcus; Steinbrecher, Thomas B

2012-02-23

278

Determination of the location of positive charges in gas-phase polypeptide polycations by tandem mass spectrometry  

NASA Astrophysics Data System (ADS)

Location of protonated sites in electrospray-ionized gas-phase peptides and proteins was performed with tandem mass spectrometry using ion activation by both electron capture dissociation (ECD) and collisional activation dissociation (CAD). Charge-carrying sites were assigned based on the increment in the charge state of fragment ions compared to that of the previous fragment in the same series. The property of ECD to neutralize preferentially the least basic site was confirmed by the analysis of three thousand ECD mass spectra of doubly charged tryptic peptides. Multiply charged cations of bradykinin, neurotensin and melittin were studied in detail. For n+ precursors, ECD revealed the positions of (n - 1) most basic sites, while CAD could in principle locate alln charges. However, ECD introduced minimal proton mobilization and produced more conclusive data than CAD, for which N- and C-terminal data often disagreed. Consistent with the dominance of one charge conformer and its preservation in ECD, the average charge states of complementary fragments of n+ ions almost always added up to (n - 1)+, while the similar figure in CAD often deviated from n+, indicating extensive charge isomerization under collisional excitation. For bradykinin and neurotensin, the charge assignments were largely in agreement with the intrinsic gas-phase basicity of the respective amino acid residues. For melittin ions in higher charge states, ECD revealed the charging at both intrinsically basic as well as at less basic residues, which was attributed to charge sharing with other groups due to the presence of secondary and higher order structures in this larger polypeptide.

Kjeldsen, Frank; Savitski, Mikhail M.; Adams, Christopher M.; Zubarev, Roman A.

2006-06-01

279

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

280

Gas phase production and loss of isoprene epoxydiols.  

PubMed

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

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

2014-02-20

281

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

282

Logistic model of glucose-regulated C-peptide secretion: hysteresis pathway disruption in impaired fasting glycemia  

PubMed Central

The present analysis tests the hypothesis that quantifiable disruption of the glucose-stimulated insulin-secretion dose-response pathway mediates impaired fasting glycemia (IFG) and type 2 diabetes mellitus (DM). To this end, adults with normal and impaired fasting glycemia (NFG, n = 30), IFG (n = 32), and DM (n = 14) were given a mixed meal containing 75 g glucose. C-peptide and glucose were measured over 4 h, 13 times in NFG and IFG and 16 times in DM (age range 50–57 yr, body mass index 28–32 kg/m2). Wavelet-based deconvolution analysis was used to estimate time-varying C-peptide secretion rates. Logistic dose-response functions were constructed analytically of the sensitivity, potency, and efficacy (in the pharmacological sense of slope, one-half maximal stimulation, and maximal effect) of glucose's stimulation of prehepatic insulin (C-peptide) secretion. A hysteresis changepoint time, demarcating unequal glucose potencies for onset and recovery pathways, was estimated simultaneously. According to this methodology, NFG subjects exhibited distinct onset and recovery potencies of glucose in stimulating C-peptide secretion (6.5 and 8.5 mM), thereby defining in vivo hysteresis (potency shift ?2.0 mM). IFG patients manifested reduced glucose onset potency (8.6 mM), and diminished C-peptide hysteretic shift (?0.80 mM). DM patients had markedly decreased glucose potency (18.8 mM), reversal of C-peptide's hysteretic shift (+4.5 mM), and 30% lower C-peptide sensitivity to glucose stimulation. From these data, we conclude that a dynamic dose-response model of glucose-dependent control of C-peptide secretion can identify disruption of in vivo hysteresis in patients with IFG and DM. Pathway-defined analytic models of this kind may aid in the search for prediabetes biomarkers. PMID:22669243

Keenan, Daniel M.; Basu, Rita; Liu, Yan; Basu, Ananda; Bock, Gerlies

2012-01-01

283

Heterogeneous nucleation of a monomer gas on a growing gas-phase polymer  

E-print Network

Heterogeneous nucleation of a monomer gas on a growing gas-phase polymer Chaok Seok and David W for gas-phase polymerization. We have used a density functional approach to calculate the free energy and heterogeneous nucleation rate of liquid drops of monomer on oligomer chains of varying length. We show

Seok, Chaok

284

Reactions in HostGuest Complexes Molecular Mousetraps: Gas-Phase Studies of the  

E-print Network

Reactions in Host­Guest Complexes Molecular Mousetraps: Gas-Phase Studies of the Covalent Coupling of purposes.[1,2] These noncovalent complexes are easily transferred to the gas phase by electrospray. May The Arnold and Mabel Beckman Laboratories of Chemical Syn- thesis, Division of Chemistry

Stoltz, Brian M.

285

ccsd-00001067(version2):11Mar2004 Nuclear liquid-gas phase transition and  

E-print Network

ccsd-00001067(version2):11Mar2004 Nuclear liquid-gas phase transition and supernovae evolution J appearing at the onset of the first order nuclear liquid-gas phase transition can play an important role of matter near the proto-neutron star surface. The resulting increase of pressure may induce strong particle

Boyer, Edmond

286

Effects of the liquid-gas phase transition and cluster formation on the symmetry energy  

NASA Astrophysics Data System (ADS)

Various definitions of the symmetry energy are introduced for nuclei, dilute nuclear matter below saturation density and stellar matter, which is found in compact stars or core-collapse supernovae. The resulting differences are exemplified by calculations in a theoretical approach based on a generalized relativistic density functional for dense matter. It contains nucleonic clusters as explicit degrees of freedom with medium-dependent properties that are derived for light clusters from a quantum statistical approach. With such a model the dissolution of clusters at high densities can be described. The effects of the liquid-gas phase transition in nuclear matter and of cluster formation in stellar matter on the density dependence of the symmetry energy are studied for different temperatures. It is observed that correlations and the formation of inhomogeneous matter at low densities and temperatures causes an increase of the symmetry energy as compared to calculations assuming a uniform uncorrelated spatial distribution of constituent baryons and leptons.

Typel, S.; Wolter, H. H.; Röpke, G.; Blaschke, D.

2014-02-01

287

Process Conditions and Microstructures of Ceramic Coatings by Gas Phase Deposition Based on Plasma Spraying  

NASA Astrophysics Data System (ADS)

Plasma spraying at very low pressure (50-200 Pa) is significantly different from atmospheric plasma conditions (APS). By applying powder feedstock, it is possible to fragment the particles into very small clusters or even to evaporate the material. As a consequence, the deposition mechanisms and the resulting coating microstructures could be quite different compared to conventional APS liquid splat deposition. Thin and dense ceramic coatings as well as columnar-structured strain-tolerant coatings with low thermal conductivity can be achieved offering new possibilities for application in energy systems. To exploit the potential of such a gas phase deposition from plasma spray-based processes, the deposition mechanisms and their dependency on process conditions must be better understood. Thus, plasma conditions were investigated by optical emission spectroscopy. Coating experiments were performed, partially at extreme conditions. Based on the observed microstructures, a phenomenological model is developed to identify basic growth mechanisms.

Mauer, G.; Hospach, A.; Zotov, N.; Vaßen, R.

2013-03-01

288

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

E-print Network

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

Funk, Geoffrey Alexander

2013-02-22

289

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

SciTech Connect

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

Laskin, Julia; Yang, Zhibo

2011-12-01

290

ESEEM analysis of multi-histidine Cu(II)-coordination in model complexes, peptides, and amyloid-?.  

PubMed

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

Silva, K Ishara; Michael, Brian C; Geib, Steven J; Saxena, Sunil

2014-07-31

291

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

292

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

SciTech Connect

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

Hunter, D.

2009-03-16

293

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

PubMed Central

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

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

2014-01-01

294

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

295

The Gas-Phase Spectra of the 1-INDANYL Radical  

NASA Astrophysics Data System (ADS)

The gas-phase resonant two color two photon ionization (R2C2PI) spectrum of the 1-indanyl radical (m/z=117) has been identified in the region 20800 - 22600 cm^{-1} in a molecular beam. The radical was produced from the discharge of ˜1 % indene in Argon . Laser induced fluorescence (LIF) spectra were recorded in the same region revealing those features observed in R2C2PI. Other precursor molecules were investigated and it was found that the indane precursor resulted in the strongest signal. The fluorescence of the 1-indanyl radical origin band (21158 cm^{-1}) was dispersed in order to determine the ground state vibrational energies. The dispersed fluorescence (DF) spectrum is consistent with the previously observed condensed-phase emission spectrum of the 1-indanyl radical. The DF values were compared with those ground state energies determined by DFT. Franck-Condon factors computed based on the ab initio results showed good agreement with the observed spectrum. Based on the theoretical results we assigned the observed bands. The LIF spectrum contained other bands inconsistent with the 1-indanyl radical. These have been determined to be carried by 1-phenylpropargyl radical and another currently unknown radical determined by R2C2PI to have m/z=133. [1] T. Izumida, K. Inoue, S. Noda, and H. Yoshida, Bull. Chem. Soc. Jpn. 54, 2517 (1981). [2] N. J. Reilly, D. L. Kokkin, M. Nakajima, K. Nauta, S. H. Kable, and T. W. Schmidt, J. Am. Chem. Soc. 130, 3137 (2009).

Troy, Tyler P.; Nakajima, Masakazu; Chalyavi, Nahid; Clady, Raphaël G. C. R.; Nauta, Klaas; Kable, Scott H.; Schmidt, Timothy W.

2009-06-01

296

Trimethylsilyl derivatization of nucleic acid anions in the gas phase  

NASA Astrophysics Data System (ADS)

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

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

1997-03-01

297

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

298

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

299

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

300

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

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

301

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

302

Attaching molecular hydrogen to metal cations: perspectives from gas-phase infrared spectroscopy.  

PubMed

In this perspective article we describe recent infrared spectroscopic investigations of mass-selected M(+)-H(2) and M(+)-D(2) complexes in the gas-phase, with targets that include Li(+)-H(2), B(+)-H(2), Na(+)-H(2), Mg(+)-H(2), Al(+)-H(2), Cr(+)-D(2), Mn(+)-H(2), Zn(+)-D(2) and Ag(+)-H(2). Interactions between molecular hydrogen and metal cations play a key role in several contexts, including in the storage of molecular hydrogen in zeolites, metal-organic frameworks, and doped carbon nanostructures. Arguably, the clearest view of the interaction between dihydrogen and a metal cation can be obtained by probing M(+)-H(2) complexes in the gas phase, free from the complicating influences of solvents or substrates. Infrared spectra of the complexes in the H-H and D-D stretch regions are obtained by monitoring M(+) photofragments as the excitation wavelength is scanned. The spectra, which feature full rotational resolution, confirm that the M(+)-H(2) complexes share a common T-shaped equilibrium structure, consisting essentially of a perturbed H(2) molecule attached to the metal cation, but that the structural and vibrational parameters vary over a considerable range, depending on the size and electronic structure of the metal cation. Correlations are established between intermolecular bond lengths, dissociation energies, and frequency shifts of the H-H stretch vibrational mode. Ultimately, the M(+)-H(2) and M(+)-D(2) infrared spectra provide a comprehensive set of benchmarks for modelling and understanding the M(+)···H(2) interaction. PMID:23034736

Dryza, Viktoras; Poad, Berwyck L J; Bieske, Evan J

2012-11-21

303

Probing 'Spin-Forbidden' Oxygen Atom Transfer: Gas-Phase Reactions of Chromium-Porphyrin Complexes  

PubMed Central

Oxygen-atom transfer reactions of metalloporphyrin species play an important role in biochemical and synthetic oxidation reactions. An emerging theme in this chemistry is that spin-state changes can play important roles, and a ‘two-state’ reactivity model has been extensively applied especially in iron-porphyrin systems. Herein we explore the gas phase oxygen-atom transfer chemistry of meso-tetrakis(pentafluorophenyl)porphyrin (TPFPP) chromium complexes, as well as some other tetradentate macrocyclic ligands. Electrospray ionization in concert with Fourier transform ion cyclotron resonance (FT-ICR) spectrometry has been used to characterize and observe reactivity of the ionic species [(TPFPP)CrIII]+ (1) and [(TPFPP)CrVO]+ (2). These are an attractive system to examine the effects of spin state change on oxygen atom transfer because the d1 CrV species are doublets while the CrIII complexes have quartet ground states with high-lying doublet excited states. In the gas phase, [(TPFPP)CrIII]+ forms adducts with a variety of neutral donors but O-atom transfer is only observed for NO2. Pyridine N-oxide adducts of 1 do yield 2 upon collision induced dissociation (CID), but the ethylene oxide, DMSO, and TEMPO analogs do not. [(TPFPP)CrVO]+ is shown by its reactivity and by CID experiments to be a terminal metal-oxo with a single vacant coordination site. It also displays limited reaction chemistry, being deoxygenated only by the very potent reductant P(OMe)3. In general, [(TPFPP)CrVO]+ species are much less reactive than the Fe and Mn analogs. Thermochemical analysis of the reactions points towards the involvement of spin issues in the lower observed reactivity of the chromium complexes. PMID:20218631

Fornarini, Simonetta; Lanucara, Francesco; Warren, Jeffrey J.

2010-01-01

304

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

PubMed Central

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

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

2013-01-01

305

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

306

Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model  

PubMed Central

Background The binding of peptide fragments of extracellular peptides to class II MHC is a crucial event in the adaptive immune response. Each MHC allotype generally binds a distinct subset of peptides and the enormous number of possible peptide epitopes prevents their complete experimental characterization. Computational methods can utilize the limited experimental data to predict the binding affinities of peptides to class II MHC. Results We have developed the Regularized Thermodynamic Average, or RTA, method for predicting the affinities of peptides binding to class II MHC. RTA accounts for all possible peptide binding conformations using a thermodynamic average and includes a parameter constraint for regularization to improve accuracy on novel data. RTA was shown to achieve higher accuracy, as measured by AUC, than SMM-align on the same data for all 17 MHC allotypes examined. RTA also gave the highest accuracy on all but three allotypes when compared with results from 9 different prediction methods applied to the same data. In addition, the method correctly predicted the peptide binding register of 17 out of 18 peptide-MHC complexes. Finally, we found that suboptimal peptide binding registers, which are often ignored in other prediction methods, made significant contributions of at least 50% of the total binding energy for approximately 20% of the peptides. Conclusions The RTA method accurately predicts peptide binding affinities to class II MHC and accounts for multiple peptide binding registers while reducing overfitting through regularization. The method has potential applications in vaccine design and in understanding autoimmune disorders. A web server implementing the RTA prediction method is available at http://bordnerlab.org/RTA/. PMID:20089173

2010-01-01

307

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

PubMed Central

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

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

2014-01-01

308

Gas phase reaction products during tungsten atomic layer deposition using WF6 and Si2H6  

E-print Network

Gas phase reaction products during tungsten atomic layer deposition using WF6 and Si2H6 R. K; published 23 July 2004 The gas phase reaction products during tungsten W atomic layer deposition ALD using WF6 and Si2H6 were studied using quadrupole mass spectrometry. The gas phase reactions products were

George, Steven M.

309

A Nerve Growth Factor Peptide Retards Seizure Development and Inhibits Neuronal Sprouting in a Rat Model of Epilepsy  

Microsoft Academic Search

Kindling, an animal model of epilepsy wherein seizures are induced by subcortical electrical stimulation, results in the upregulation of neurotrophin mRNA and protein in the adult rat forebrain and causes mossy fiber sprouting in the hippocampus. Intraventricular infusion of a synthetic peptide mimic of a nerve growth factor domain that interferes with the binding of neurotrophins to their receptors resulted

Kashif Rashid; Catharina E. E. M. van der Zee; Gregory M. Ross; C. Andrew Chapman; Jolanta Stanisz; Richard J. Riopelle; Ronald J. Racine; Margaret Fahnestock

1995-01-01

310

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

SciTech Connect

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

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

2012-05-01

311

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

312

Amyloid peptides derived from CsgA and FapC modify the viscoelastic properties of biofilm model matrices.  

PubMed

The bacterial biofilm is a complex environment of cells, which secrete a matrix made of various components, mainly polysaccharides and proteins. An understanding of the precise role of these components in the stability and dynamics of biofilm architecture would be a great advantage for the improvement of anti-biofilm strategies. Here, artificial biofilm matrices made of polysaccharides and auto-assembled peptides were designed, and the influence of bacterial amyloid proteins on the mechanical properties of the biofilm matrix was studied. The model polysaccharides methylcellulose and alginate and peptides derived from the amyloid proteins curli and FapC found in biofilms of Enterobacteriaceae and Pseudomonas, respectively, were used. Rheological measurements showed that the amyloid peptides do not prevent the gelation of the polysaccharides but influence deformation of the matrices under shear stress and modify the gel elastic response. Hence the secretion of amyloids could be for the biofilm a way of adapting to environmental changes. PMID:24592895

Lembré, Pierre; Di Martino, Patrick; Vendrely, Charlotte

2014-01-01

313

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

PubMed Central

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

Sun, N; Funke, SA; Willbold, D

2012-01-01

314

Determination of Gas-Phase Dimethyl Sulfate and Monomethyl Hydrogen Sulfate.  

National Technical Information Service (NTIS)

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 ...

L. D. Hansen, V. F. White, D. J. Eatough

1986-01-01

315

Gas-Phase Geometry Optimization of Biological Molecules as a Reasonable Alternative to a Continuum Environment Description: Fact, Myth, or Fiction?  

NASA Astrophysics Data System (ADS)

Gas-phase optimization of single biological molecules and of small active-site biological models has become a standard approach in first principles computational enzymology. The important role played by the surrounding environment (solvent, enzyme, both) is normally only accounted for through higher-level single point energy calculations performed using a polarizable continuum model (PCM) and an appropriate dielectric constant with the gas-phase-optimized geometries. In this study we analyze this widely used approximation, by comparing gas-phase-optimized geometries with geometries optimized with different PCM approaches (and considering different dielectric constants) for a representative data set of 20 very important biological molecules-the 20 natural amino acids. A total of 323 chemical bonds and 469 angles present in standard amino acid residues were evaluated. The results show that the use of gas-phase-optimized geometries can in fact be quite a reasonable alternative to the use of the more computationally intensive continuum optimizations, providing a good description of bond lengths and angles for typical biological molecules, even for charged amino acids, such as Asp, Glu, Lys, and Arg. This approximation is particularly successful if the protonation state of the biological molecule could be reasonably described in vacuum, a requirement that was already necessary in first principles computational enzymology.

Sousa, Sérgio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria Joa˜O.

2009-09-01

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. 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.

2011-05-31

317

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

SciTech Connect

Two chemical mass balance receptor models are developed which can determine the source contributions to atmospheric pollutant concentrations using organic compounds as tracers. The first model uses particle-phase organic compounds to apportion the primary source contribution to atmospheric fine particulate organic carbon concentrations and fine particle mass concentrations. The second receptor model simultaneously uses both volatile gas-phase hydrocarbon and particle-phase organic compounds as tracers to determine source contributions to non-methane organic gases in the atmosphere. Both models are applied to data collected in California's San Joaquin Valley during two severe wintertime air pollution episodes. Source contributions to fine particle air quality are calculated for two urban sites, Fresno and Bakersfield, and one background site, Kern Wildlife Refuge. Primary particle emissions from hardwood combustion, softwood combustion, diesel engines, meat cooking, and gasoline-powered motor vehicles contribute on average 79% of the airborne fine particle organic compound mass at the urban sites during both episodes with smaller but still measurable contributions from fine particle road dust and natural gas combustion aerosol. Anthropogenic primary particle sources contribute less than 10% of the fine particle mass concentration at the background site. The combined gas-phase and particle-phase organic compound receptor model shows that gasoline-powered motor vehicle exhaust and gasoline vapors are the largest contributors to nonmethane organic gases concentrations followed by natural gas leakage. Smaller but statistically significant contributions to organic vapors from wood combustion, meat cooking, and diesel exhaust also are quantified.

Schauer, J.J.; Cass, G.R.

2000-05-01

318

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

PubMed Central

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

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

2004-01-01

319

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

PubMed

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

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

1997-01-01

320

Peptide sequence tag-based blind identification of post-translational modifications with point process model  

Microsoft Academic Search

An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental spectra with theoretical spectra from peptides in a peptide database is very time consuming and may lead to high false positive rate. In this paper, we introduce a new approach that is both

Chunmei Liu; Bo Yan; Yinglei Song; Ying Xu; Liming Cai

2006-01-01

321

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

PubMed

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

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

2008-04-01

322

The roles of individual oxidants in secondary organic aerosol formation from ? 3-carene: 1. gas-phase chemical mechanism  

NASA Astrophysics Data System (ADS)

Oxidation of certain gas-phase organic species results in secondary products of volatility that is sufficiently low that they partition between the gas and aerosol phases. The fraction that partitions to the aerosol phase is known as secondary organic aerosol (SOA). The present paper reviews the relevant chemistry and describes the development of a chemical mechanism that consists of the gas-phase reactions of ? 3-carene and its products, including the formation of individual organic oxidation products that are capable of forming SOA. The mechanism also incorporates ozone formation chemistry and other relevant inorganic reactions. The new mechanism differentiates specific oxidation products according to both molecular structure and routes of formation. The concentrations of oxidation products (termed cross-products) that are formed in pathways involving two or more oxidants (ozone, the oxygen atom, and the hydroxyl and nitrate radicals) are accurately accounted in this way. The mechanism is evaluated in a zero-dimensional model by simulating gas-phase concentrations of ? 3-carene, oxides of nitrogen, and ozone from ozonolysis, nitrate radical, and photooxidation chamber experiments in which ? 3-carene was oxidized. Simulation results indicate that the main characteristics of the chemistry are adequately described by the mechanism. Part 2 of this series of papers develops a gas-particle partitioning model and presents simulations of SOA formation in single oxidant (e.g., ozonolysis and nitrate radical) and photooxidation experiments. Part 2 examines in detail the role of individual oxidants in consumption of the parent organic, creation of cross-products, and formation of SOA.

Colville, Christopher J.; Griffin, Robert J.

323

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

Microsoft Academic Search

A detailed gas-phase photochemical chamber box model, incorporating the Master Chemical Mechanism (MCMv3.1) degradation scheme for the model anthropogenic aromatic compound 1,3,5-trimethylbenzene, has been used to simulate data measured during a series of aerosol chamber experiments in order to evaluate the mechanism under a variety of VOC\\/NOx conditions.The chamber model was used in the interpretation of comprehensive high (mass and

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

2010-01-01

324

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

PubMed

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

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

2012-09-18

325

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

NASA Astrophysics Data System (ADS)

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

Boies, Adam Meyer

326

Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model.  

PubMed

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

Tomar, Dheeraj S; Weber, Valéry; Pettitt, B Montgomery; Asthagiri, D

2014-04-17

327

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

PubMed

Natural and constructed wetlands have gained attention as potential tools for remediation of shallow sediments and groundwater contaminated with volatile organic compounds (VOCs). Wetland macrophytes are known to enhance rates of contaminant removal via volatilization, but the magnitude of different volatilization mechanisms, and the relationship between volatilization rates and contaminant physiochemical properties, remain poorly understood. Greenhouse mesocosm experiments using the volatile tracer sulfur hexafluoride were conducted to determine the relative magnitudes of gas-phase and transpiration-driven volatilization mechanisms. A numerical model for vegetation-mediated volatilization was developed, calibrated with tracer measurements, and used to predict plant-mediated volatilization of common VOCs as well as quantify the contribution of different volatilization pathways. Model simulations agree with conclusions from previous work that transpiration is the main driver for volatilization of VOCs, but also demonstrate that vapor-phase transport in wetland plants is significant, and can represent up to 50% of the total flux for compounds with greater volatility like vinyl chloride. PMID:22509995

Reid, Matthew C; Jaffé, Peter R

2012-05-15

328

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

329

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

NASA Astrophysics Data System (ADS)

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

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

1987-08-01

330

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

NASA Astrophysics Data System (ADS)

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

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

1987-09-01

331

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

PubMed Central

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

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

2010-01-01

332

In situ mass spectroscopy and thermogravimetric studies of GaAs MOCVD gas phase and surface reactions  

NASA Astrophysics Data System (ADS)

Two special MOCVD reactors systems designed for in situ monitoring of gas phase and surface reactions are presented. The gas phase decomposition mechanisms of Ga(CH 3) 3, Ga(C 2H 5) 3 and As(CH 3) 3 in H 2, He and D 2 are investigated by molecular beam sampled mass spectroscopy. The data show that the initial thermal pyrolysis reaction of Ga(CH 3) 3 and As(CH 3) 3 is a unimolecular reaction leading to the loss of methyl groups. This is supported by the observations of similar decomposition temperatures in H 2 and He, an increased C 2H 6 formation in He, and the production of CH 3D in D 2 carrier gas. The decomposition of Ga(C 2H 5) 3 proceeds either via the loss of ethyl radicals or ?-elimination of ethene, and the latter mechanism dominates above 650 K. This model is supported by variation in the product distribution of C 2H 4, C 2H 5·, C 2H 6 and C 4H 10 with pyrolysis temperature. A new thermogravimetric MOCVD system is used to measure surface reaction rates of Ga(CH 3) 3 and As(CH 3) 3 at low pressures, where mass transfer effects are absent. Data for varying total pressures and constant partial pressures of Ga(CH 3) 3 and As(CH 3) 3 indicate that the growth rate at reduced pressures is influenced by gas phase reactions. At low pressures surface reactions appear to dominate and at high temperatures the growth rate goes to zero and etching takes place.

Lee, Peter W.; Omstead, Thomas R.; McKenna, Donald R.; Jensen, Klavs F.

1987-11-01

333

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

334

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

335

Interaction of small gas phase molecules with alumina supported rhodium nanoparticles: an in situ spectroscopic study  

NASA Astrophysics Data System (ADS)

Supported nanoparticulate Rh systems are studied as a model system for the important three way catalysts as used in the combustion engines of cars. Small Rh nanoparticles with a small particle size distribution can be easily synthesized and their morphology is studied using x-ray absorption fine structure (XAFS) spectroscopy. The interaction of the supported rhodium nanoparticles on ?-Al2O3 with small gas phase molecules like H2, O2, CO, NO, H2S and SO2 is investigated, in situ and time resolved, using a combination of techniques, i.e. XAFS, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and mass spectrometry. The surface species formed upon exposure of the metal particles to the adsorbing molecules, and their sometimes disruptive interaction with the metal particles, are identified as a function of temperature and time. Dynamic equilibria are observed which change the oxidation state and the nuclearity of the supported rhodium particles under operational conditions. Rather than merely adsorb on a catalyst particle, these gases have a substantial role in defining the nature of the particle.

Evans, J.; Tromp, M.

2008-05-01

336

Electronic excitation of gas-phase furan molecules by electron impact  

NASA Astrophysics Data System (ADS)

Experiments and ab initio calculations of the differential and integral cross sections for the electronic excitation from the ground state 1A1 to the 3B2 and 3A1 states of gas-phase furan molecules by low-energy electron impact were performed. Experimental differential cross sections were measured at incident electron energies between 5 and 15 eV and for scattering angles from 10? to 130?. The calculated cross sections were obtained using the Schwinger multichannel method implemented with pseudopotentials. The influence of channel-coupling and polarization effects is investigated through the comparison between three different models of scattering calculations, each one considering a distinct channel-coupling scheme. The comparison of experimental and calculated cross sections for electronically inelastic electron scattering by C4H4O molecules is found to be mostly reasonable. The existing discrepancies in this combined theoretical and experimental study help to illustrate difficulties in readily establishing reliable electronic excitation cross sections of polyatomic molecules by low-energy electrons.

da Costa, Romarly F.; Bettega, Márcio H. F.; Lima, Marco A. P.; Lopes, Maria C. A.; Hargreaves, Leigh R.; Serna, Gabriela; Khakoo, Murtadha A.

2012-06-01

337

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

338

OH yields in the gas-phase reactions of ozone with alkenes  

SciTech Connect

Hydroxyl radical yields are reported for the gas-phase ozonolyses of a range of alkenes. 1,3,5-Trimethylbenzene was employed as an OH tracer, and the diminution in its concentration was used to calculate OH yields by both a simple analytical kinetic expression and a numerically integrated model. The following OH yields were obtained, relative to alkene consumed: ethene (0.14), propene (0.32), 2-methylpropene (0.60), 2,3-dimethyl-2-butene (0.89), isoprene (0.44), {beta}-pinene (0.24), and {alpha}-pinene (0.83). A structure activity relationship (SAR) is presented for the estimation of OH yields based on structural moieties and reaction branching ratios. Reaction stoichiometries ({Delta}[alkene]/{Delta}[ozone]) are also reported, along with primary carbonyl yields measured in the presence and absence of excess SO{sub 2}, both under OH-free conditions. Reaction stoichiometries are shown to be correlated with alkene OH yields, and the mechanistic implications of this observation are discussed. The fractional increase in primary carbonyl yield in the presence of excess SO{sub 2} is shown to be inversely related to the OH yield and is interpreted as a measure of the fraction of the vibrationally excited Criegee intermediate that is stabilized in air at a pressure of 1 atm.

Rickard, A.R.; Johnson, D.; McGill, C.D.; Marston, G.

1999-09-23

339

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

340

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

NASA Astrophysics Data System (ADS)

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

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

2012-09-01

341

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

342

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

PubMed

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

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

2002-01-01

343

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

NASA Astrophysics Data System (ADS)

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

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

2010-08-01

344

Sequence dependence of kinetics and morphology of collagen model peptide self-assembly into higher order structures  

PubMed Central

The process of self-assembly of the triple-helical peptide (Pro-Hyp-Gly)10 into higher order structure resembles the nucleation-growth mechanism of collagen fibril formation in many features, but the irregular morphology of the self-assembled peptide contrasts with the ordered fibers and networks formed by collagen in vivo. The amino acid sequence in the central region of the (Pro-Hyp-Gly)10 peptide was varied and found to affect the kinetics of self-assembly and nature of the higher order structure formed. Single amino acid changes in the central triplet produced irregular higher order structures similar to (Pro-Hyp-Gly)10, but the rate of self-association was markedly delayed by a single change in one Pro to Ala or Leu. The introduction of a Hyp-rich hydrophobic sequence from type IV collagen resulted in a more regular suprastructure of extended fibers that sometimes showed supercoiling and branching features similar to those seen for type IV collagen in the basement membrane network. Several peptides, where central Pro-Hyp sequences were replaced by charged residues or a nine-residue hydrophobic region from type III collagen, lost the ability to self-associate under standard conditions. The inability to self-assemble likely results from loss of imino acids, and lack of an appropriate distribution of hydrophobic/electrostatic residues. The effect of replacement of a single Gly residue was also examined, as a model for collagen diseases such as osteogenesis imperfecta and Alport syndrome. Unexpectedly, the Gly to Ala replacement interfered with self-assembly of (Pro-Hyp-Gly)10, while the peptide with a Gly to Ser substitution self-associated to form a fibrillar structure. PMID:18441232

Kar, Karunakar; Wang, Yuh-Hwa; Brodsky, Barbara

2008-01-01

345

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

346

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

347

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

348

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

349

Comparing gas-phase and grain-catalyzed H2 formation  

E-print Network

Because H2 formation on dust grain surfaces completely dominates gas-phase H2 formation in local molecular clouds, it is often assumed that gas-phase formation is never important. In fact, it is the dominant mechanism in a number of cases. In this paper, I briefly summarize the chemistry of gas-phase H2 formation, and show that it dominates for dust-to-gas ratios less than a critical value D_cr. I also show that D_cr is simple to calculate for any given astrophysical situation, and illustrate this with a number of examples, ranging from H2 formation in warm atomic gas in the Milky Way to the formation of protogalaxies at high redshift.

Simon C. O. Glover

2002-10-22

350

Measurement of gas-phase ionic mercury(II) species in ambient air  

SciTech Connect

One of the important questions in the biogeochemical cycling of mercury is the speciation of mercury in the atmosphere. Although a large fraction of Hg in ambient air is Hg(O), a small fraction is believed to be gas-phase Hg(II). This fraction is highly water-soluble and thus is important to explaining the high concentration of Hg in precipitation. We have developed a novel technique for measuring gas-phase Hg(II), using a high-flow refluxing mist chamber to trap the water-soluble Hg(II) in an aerosol mist. Measured concentrations of gas-phase Hg(II) in ambient air are generally in the range 0.05-0.1 ng/m{sup 3}, or 2-4% of the total gaseous Hg. In this talk, representative data under different atmospheric and geographic conditions will be presented, along with a summary of some of the experimental difficulties and unanswered questions.

Stratton, W.J. [Earlharn College, Richmond, IN (United States); Lindberg, S.E. [Oak Ridge National Lab., TN (United States)

1995-12-31

351

Intermolecular Modeling Methods in Drug Design\\/Modeling the Mechanism of Peptide Cleavage by Thermolysin  

Microsoft Academic Search

As an outgrowth of our small molecule modeling effort, we have begun to develop a large molecule modeling system. This new effort centers around a VAX 11\\/780 coupled to an Evans and Sutherland Color Multi-Picture system. The software currently available is A. Jones' FRODO program for display and manipulation, M. Connolly's SURFACE program, A. Hagler's VFF energy calculation program, and

Graham M. Smith; David G. Hangauer; Joseph D. Andose; Bruce L. Bush; Eugene M. Fluder; Peter Gund; Eugene F. McIntyre

1984-01-01

352

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

SciTech Connect

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

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

1985-01-01

353

The nuclear liquid-gas phase transition at large $N_c$ in the Van der Waals approximation  

E-print Network

We examine the nuclear liquid-gas phase transition at large number of colors ($N_c$) within the framework of the Van Der Waals (VdW) model. We argue that the VdW equation is appropriate at describing inter-nucleon forces, and discuss how each parameter scales with $N_c$. We demonstrate that $N_c=3$ (our world) is not large with respect to the other dimensionless scale relevant to baryonic matter, the number of neighbors in a dense system $N_N$. Consequently, we show that the liquid-gas phase transition looks dramatically different at $N_c \\to \\infty$ with respect of our world: The critical point temperature becomes of the order of $\\lqcd$ rather than below it. The critical point density becomes of the order of the baryonic density, rather than an order of magnitude below it. These are precisely the characteristics usually associated with the "Quarkyonic phase". We therefore conjecture that quarkyonic matter is simply the large $N_c$ limit of the nuclear liquid, and the interplay between $N_c$ and $N_N$ is the reason why the nuclear liquid in our world is so different from quarkyonic matter. We conclude by suggesting ways our conjecture can be tested in future lattice measurements.

Giorgio Torrieri; Igor Mishustin

2010-06-12

354

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

355

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

356

Deprotonated N-(2,4-Dinitrophenyl)amino Acids Undergo Cyclization in Solution and the Gas Phase  

PubMed Central

The collisionally activated mass spectral fragmentations of N-(2,4-dinitrophenyl)alanine and phenylalanine [M – H]- may be gas-phase analogs of the base-catalyzed cyclization of N-(2,4-dinitrophenyl)amino acids in aqueous dioxane. This latter reaction is one source of the 2-substituted 5-nitro-1H-benzimidazole-3-oxides, which are antibacterial agents. The fragmentation of both compounds, established by tandem mass spectrometric experiments and supported by molecular modeling using DFT methods, indicate that the [M - H]- ions dissociate via sequential eliminations of CO2 and H2O to produce deprotonated benzimidazole-N-oxide derivatives. The gas-phase cyclization reactions are analogous to the base-catalyzed cyclization in solution, except that in the latter case, the reactant must be a dianion for the reaction to occur on a reasonable time scale. The cyclization of N-(2-nitrophenyl)phenylalanine, which has one less nitro group, requires a stronger base for the cyclization than the compound with a second nitro group at the 4-position. Following losses of CO2 and H2O are expulsions of both neutral molecules and free radicals, the latter being examples of violations of the even-electron ion rule. PMID:21966244

George, M.; Ramesh, V.; Srinivas, R.; Giblin, Daryl; Gross, Michael L.

2011-01-01

357

Gas phase investigations of sulfonium salts by electrospray ft-icr/ms  

NASA Astrophysics Data System (ADS)

Twelve sulfonium salts were studied by electrospray Fourier transform ion cyclotron resonance mass spectrometry. Collisionally activated dissociation, CAD, reactions, using neutral argon as the collision gas, were performed to investigate dissociation pathways in the gas phase and to study the stabilizing/destabilizing effects of electron donating/withdrawing substituents on the sulfonium ions. Ion-molecule reactions were attempted to identify SN2 reaction mechanisms, but to date we have detected exclusively SN1-type reactions in the gas phase. Literature reports on the mass spectrometry of sulfonium cations are reviewed.

Katritzky, Alan R.; Shipkova, Petia A.; Watson, Clifford H.; Eyler, John R.; Kevill, Dennis N.

1997-11-01

358

Density functional molecular computations on protonated serotonin in the gas phase and various solvent media  

NASA Astrophysics Data System (ADS)

5-Hydroxytryptamine (serotonin) was geometry optimized at the B3YP/6-31G(d) level of theory to determine the energetically most favourable conformations of the aromatic hydroxyl group and the protonated ethylamine side chain. The hydroxyl group was found to be most stable at anti for all conformations, and the two lowest energy gas phase conformers found were: ?2= g+, ?3= g- and ?2= g-, ?3= g+. The protonated amino group was found equally stable at g+, g- and anti. The transition structures linking each gas phase minimum were also computed. Minima found were subjected to solvation calculations in chloroform, DMSO, ethanol and water, which shifted their relative stabilities.

Pisterzi, Luca F.; Almeida, David R. P.; Chass, Gregory A.; Torday, Ladislaus L.; Papp, Julius Gy; Varro, Andras; Csizmadia, Imre G.

2002-11-01

359

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

360

Thermodynamic analysis of the gas phase composition over uranium-plutonium carbonitride irradiated with fast neutrons  

Microsoft Academic Search

A thermodynamic analysis of the gas phase composition over uranium-plutonium carbonitride U0.8Pu0.2(C0.5N0.5)0.995 irradiated with fast neutrons was carried out with respect to temperature and burnout. In the temperature range of 900–2500\\u000a K, accumulation of fission products in fuel resulted in the formation of a multicomponent gas phase containing the following\\u000a basic elements and compounds: volatile (Cs, Sr, Ba, Se, Te,

G. S. Bulatov; K. N. Gedgovd; D. Yu. Lyubimov

2009-01-01

361

Hydrodynamic and gas phase axial dispersion in an air-molten salt two-phase system (molten salt oxidation reactor)  

Microsoft Academic Search

The effects of the gas velocity (0.05–0.22m\\/s) and temperature (870–970°C) on the gas holdup and the gas phase axial dispersion coefficient have been studied in a molten salt oxidation reactor (0.076m i.d.×0.653m H., air-molten sodium carbonate salt two-phase system). The gas phase holdup and the amount of the axial gas phase dispersion coefficient were experimentally evaluated by means of the

Yong-Jun Cho; Hee-Chul Yang; Hee-Chul Eun; Jae-Hyung Yoo; Joon-Hyung Kim

2005-01-01

362

Ab initio and Monte Carlo calculations for a nucleophilic addition reaction in the gas phase and in aqueous solution  

Microsoft Academic Search

Energy profiles for the nucleophilic addition of hydroxide ion to formaldehyde in the gas phase and in aqueous solution have been determined with quantum and statistical mechanical methods. Ab initio calculations at the 6-31+G* level were utilized to study the gas-phase potential energy surface. In the gas phase, the conversion of reactants to the tetrahedral intermediate is exothermic by 35

Jeffry D. Madura; William L. Jorgensen

1986-01-01

363

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

364

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

PubMed

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

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

2009-01-01

365

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

PubMed

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

Venugopalan, Paloth; Kishore, Raghuvansh

2013-07-22

366

Structural basis for the enhanced stability of protein model compounds and peptide backbone unit in ammonium ionic liquids.  

PubMed

Protein folding/unfolding is a fascinating study in the presence of cosolvents, which protect/disrupt the native structure of protein, respectively. The structure and stability of proteins and their functional groups may be modulated by the addition of cosolvents. Ionic liquids (ILs) are finding a vast array of applications as novel cosolvents for a wide variety of biochemical processes that include protein folding. Here, the systematic and quantitative apparent transfer free energies (?G'(tr)) of protein model compounds from water to ILs through solubility measurements as a function of IL concentration at 25 °C have been exploited to quantify and interpret biomolecular interactions between model compounds of glycine peptides (GPs) with ammonium based ILs. The investigated aqueous systems consist of zwitterionic glycine peptides: glycine (Gly), diglycine (Gly(2)), triglycine (Gly(3)), tetraglycine (Gly(4)), and cyclic glycylglycine (c(GG)) in the presence of six ILs such as diethylammonium acetate (DEAA), diethylammonium hydrogen sulfate (DEAS), triethylammonium acetate (TEAA), triethylammonium hydrogen sulfate (TEAS), triethylammonium dihydrogen phosphate (TEAP), and trimethylammonium acetate (TMAA). We have observed positive values of ?G'(tr) for GPs from water to ILs, indicating that interactions between ILs and GPs are unfavorable, which leads to stabilization of the structure of model protein compounds. Moreover, our experimental data ?G'(tr) is used to obtain transfer free energies (?g'(tr)) of the peptide backbone unit (or glycyl unit) (-CH(2)C?ONH-), which is the most numerous group in globular proteins, from water to IL solutions. To obtain the mechanism events of the ILs' role in enhancing the stability of the model compounds, we have further obtained m-values for GPs from solubility limits. These results explicitly elucidate that all alkyl ammonium ILs act as stabilizers for model compounds through the exclusion of ILs from model compounds of proteins and also reflect the effect of alkyl chain on the stability of protein model compounds. PMID:22963600

Vasantha, T; Attri, Pankaj; Venkatesu, Pannuru; Devi, R S Rama

2012-10-01

367

Vertical Sleeve Gastrectomy Is Effective in Two Genetic Mouse Models of Glucagon-Like Peptide 1 Receptor Deficiency  

PubMed Central

Glucagon-like peptide 1 (GLP-1) is a peptide hormone that is released from the gut in response to nutrient ingestion and that has a range of metabolic effects, including enhancing insulin secretion and decreasing food intake. Postprandial GLP-1 secretion is greatly enhanced in rats and humans after some bariatric procedures, including vertical sleeve gastrectomy (VSG), and has been widely hypothesized to contribute to reduced intake, weight loss, and the improvements in glucose homeostasis after VSG. We tested this hypothesis using two separate models of GLP-1 receptor deficiency. We found that VSG-operated GLP-1 receptor–deficient mice responded similarly to wild-type controls in terms of body weight and body fat loss, improved glucose tolerance, food intake reduction, and altered food selection. These data demonstrate that GLP-1 receptor activity is not necessary for the metabolic improvements induced by VSG surgery. PMID:23434938

Wilson-Perez, Hilary E.; Chambers, Adam P.; Ryan, Karen K.; Li, Bailing; Sandoval, Darleen A.; Stoffers, Doris; Drucker, Daniel J.; Perez-Tilve, Diego; Seeley, Randy J.

2013-01-01

368

Gas phase measurements of hydrogen peroxide in Greenland and their meaning for the interpretation of H2O2 records in ice cores  

Microsoft Academic Search

The gas phase concentration of hydrogen peroxide at Summit, Central Greenland, has been measured continuously during June\\/July 1990 using a coil scrubber technique combined with liquid phase fluorometry. The concentrations ranged between 0.3 ppbv and 3.5 ppbv, which is considerably higher than expected from model calculations and can be explained by low deposition rates. The record shows pronounced diurnal variations

A. Sigg; T. Staffelbach; A. Neftel

1992-01-01

369

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

370

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

371

Site-specific protonation directs low-energy dissociation pathways of dinucleotides in the gas phase  

NASA Astrophysics Data System (ADS)

Fourier transform ion cyclotron resonance mass spectroscopy has been used to examine the low-energy collision-induced dissociation (CID) pathways of protonated dinucleotides. Collisional activation using continuous off-resonance excitation permits observation of energetically favorable dissociation pathways. Dissociation products were examined under multiple collision conditions over a range of average center-of-mass collision energies from 0 to 8.1 eV. Semiempirical calculations were performed using AM1 and PM3 methods to obtain gas-phase model structures of the protonated dinucleotides and their CID fragments. These calculations indicate that the proton is localized exclusively on one of the nucleic acid bases, with additional stabilization of some systems resulting from hydrogen bonding interactions between the bases. Protonated molecular ions dissociate to yield several characteristic products. The major fragmentation pathways are directed by the site of protonation leading to elimination of a protonated base, generally the 3'-terminus base. Exceptions are observed only in systems having thymine as the 3'-terminus base, where the major product is the protonated 5'-terminus base. These observations agree with the known relative proton affinities of the nucleic acid bases, and the existence of stable tautomeric structures of adenine, cytosine, and guanine which make these bases better leaving groups when protonated. In addition, application of statistical RRKM calculations to model the unimolecular dissociation dynamics of the reaction leading to the protonated 3'-terminus base provides an estimate of 1.9 eV for the activation energy associated with this major fragmentation pathway. In some systems, moderate yields of other fragment ions are also observed. Only minor yields of sequence ions are observed with these quasi-molecular ions. Reaction mechanisms accounting for the observed products are proposed.

Rodgers, M. T.; Campbell, Sherrie; Marzluff, Elaine M.; Beauchamp, J. L.

1995-09-01

372

Large amplitude vibrations of Urea in gas phase  

NASA Astrophysics Data System (ADS)

Large amplitude motions of isolated Urea are analyzed using CCSD(T) calculations. Urea shows two conformers of C s and C 2 symmetries that interconvert through the NH 2 torsion and the NH 2 inversion motions. Anharmonic frequencies are computed using second order perturbation theory and an ab initio force field. The potential energy surface shows 16 minima. Nine stationary points are determined. Five reduced Hamiltonians are used for the vibrational energy determination, concluding that at least a variational treatment based on a 4D model is required for the FIR spectrum simulation. The inversion barrier produces a large splitting of the vibrational ground state.

Inostroza, N.; Senent, M. L.

2012-02-01

373

Conformational ordering of biomolecules in the gas phase: nitrogen collision cross sections measured on a prototype high resolution drift tube ion mobility-mass spectrometer.  

PubMed

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

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

2014-02-18

374

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

PubMed Central

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

2014-01-01

375

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

EPA Science Inventory

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

376

Chemical reaction of metal-fullerene in gas phase ^  

E-print Network

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

Maruyama, Shigeo

377

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

E-print Network

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

Maruyama, Shigeo

378

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

E-print Network

,5,6]; obtaining high-resolution gas-phase spectra of C60 and C70 would allow astronomers to search for fullerenes60 and C70, were discovered by Kroto et al. [1] in 1985 during experiments meant to simulate. This hypothesis seemed to be supported by the first detection of extraterrestrial C60 and C70 by Cami et al. [2

McCall, Benjamin J.

379

Comparison of infrared absorption intensities of benzene in the liquid and gas phases  

Microsoft Academic Search

This paper presents a comparison of the absolute infrared absorption intensities in the liquid and gas phases for the four infrared active fundamentals of benzene. In Herzberg’s notation these are ?12 (?3070 cm?1), and ?4 (?675 cm?1). Published data are used, including the recently published spectra of liquid benzene that have been accepted by the International Union of Pure and

John E. Bertie; C. Dale Keefe

1994-01-01

380

Gas-phase boundary layer ignition on a catalytic flat plate with heat loss  

Microsoft Academic Search

The gas-phase ignition of a premixed boundary layer flow by a nonisothermal plate with very large catalytic efficiency is studied. The catalytic upper side of the plate is in contact with the premixed gas while the lower side is held at constant temperature. The catalytic reaction is assumed to be ignited and diffusion controlled. The temperature on this side changes

C. Trevino; N. Peters

1985-01-01

381

Intense Mechanoluminescence and Gas Phase Reactions from the Sonication of an Organic Slurry  

E-print Network

reported ML from sonication of slurries of piezoelectric organic crystals in long chain alkanes,5 and the NIntense Mechanoluminescence and Gas Phase Reactions from the Sonication of an Organic Slurry Nathan of mechanical stress to a crystal.1 This light is the result of a dielectric breakdown of the intervening gas

Suslick, Kenneth S.

382

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

383

Air purification in chemical and biological warfare environments using gas-phase corona reactor technology  

Microsoft Academic Search

Chemical and biological warfare materials create difficulties when designing or retrofitting high value targets such as buildings to withstand terrorist attack. The gas-phase corona reactor (GPCR) is a synergistic combination of plasma (or ionized gas) and catalyst technologies to produce an air purification system. The GPCR has demonstrated both chemical agent decomposition and biological material deactivation creating a universal air

Joseph G. Birmingham; Gautam Pillay

1997-01-01

384

The partial gas?phase hydrogenation of benzene to cyclohexene on supported and coated ruthenium catalysts  

Microsoft Academic Search

The conversion of benzene to useful products such as cyclohexene is of industrial interest because of the expected surplus of benzene due to its substitution in gasoline by other non-polluting components in the next years. Therefore, the partial gas-phase hydrogenation of benzene to cyclohexene at atmospheric pressure was performed in order to develop catalysts as an alternative to those used

Enrico Dietzsch; Peter Claus; Dieter Hönicke

2000-01-01

385

Moving Horizon Estimation and Control for an Industrial Gas Phase Polymerization Reactor  

Microsoft Academic Search

Moving horizon estimation (MHE) has been ap- plied to an industrial gas phase polymerization reactor to improve estimates of current states and parameters. MHE is compared to Implicit Dynamic Feedback (IDFTM)1. With MHE, there is improved estimation of unmodeled disturbances in the UNIPOLTMpolyethylene plant. The UNIPOLTMtechnology is licensed by Univation, a joint venture between ExxonMobil and Dow. The polymerization reactor

John D. Hedengren; Kenneth V. Allsford; Jasmeer Ramlal

2007-01-01

386

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...

387

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/...

388

Structural properties of iron disilicide nanocrystals from the gas phase investigated by advanced electron microscopy  

E-print Network

) and iron pentacarbonyl (Fe(CO)5) in a hot wall reactor. The as-prepared material typically consistsStructural properties of iron disilicide nanocrystals from the gas phase investigated by advanced, planar defects, Stripe-STEM, Cc corrected EFTEM Beta-phase iron disilicide (-FeSi2) is a promising

Dunin-Borkowski, Rafal E.

389

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...

390

Spatial distribution of the gas phase in an axisymmetric submerged impact jet  

Microsoft Academic Search

Experimental data on the spatial distribution of the gas phase in an axisymmetric impact jet are obtained by the particle\\u000a image velocimetry\\/laser-induced fluorescence (PIV\\/LIF) method. It is shown that the distribution of bubbles in the flow is determined by the dynamics of vortex structures.

A. P. Belousov

2009-01-01

391

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...

392

Influence of gas-phase reactions on catalytic reforming of isooctane  

Microsoft Academic Search

The significance of gas-phase reactions in catalytic partial oxidation (CPOX) of isooctane at short contact times and high temperatures is studied experimentally and numerically to gain further understanding of hydrogen production by CPOX of logistic fuels for on-board applications. Special attention is given to the formation of coke precursors. CPOX of isooctane over a rhodium coated monolith with a molar

Torsten Kaltschmitt; Lubow Maier; Marco Hartmann; Christian Hauck; Olaf Deutschmann

2011-01-01

393

Changing the shape of molecular ions: photoisomerization action spectroscopy in the gas phase.  

PubMed

A new approach for studying the photoisomerization of molecular ions in the gas phase is described. Packets of molecular ions are injected into a drift tube filled with helium buffer gas, where they are irradiated with tunable laser light. Photoisomerization changes the ions' cross section for collisions with helium atoms so that they arrive at the ion detector slightly earlier or later than the parent ions. By monitoring the photo-isomer peak as a function of laser wavelength one can record an action spectrum that is related to the ions' absorption spectrum modulated by the photoisomerization probability. The approach is demonstrated using the polymethine dye HITC (1,3,3,1',3',3'-hexamethylindotricarbocyanine). The data show that both trans and cis forms of HITC(+) exist in the gas phase with trans?cis photoisomerization predominating over the 550-710 nm range and cis?trans photoisomerization occurring over the 735-770 nm range. The gas-phase photoisomerization action spectrum is comparable to the absorption spectra of trans HITC and cis HTIC in the condensed phase, but with the absorption peaks shifted to shorter wavelength. The gas-phase photoisomerization action spectrum of the (HITC)2(2+) dication dimer is also reported. (HITC)2(2+) cations photoisomerize over the 550-770 nm range to form more compact structures. PMID:23674245

Adamson, B D; Coughlan, N J A; Continetti, R E; Bieske, E J

2013-06-28

394

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

SciTech Connect

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

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

1983-09-01

395

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

E-print Network

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

Mench, Matthew M.

396

Nonexistent electron affinity of OCS and the stabilization of carbonyl sulfide anions by gas phase hydration  

E-print Network

Nonexistent electron affinity of OCS and the stabilization of carbonyl sulfide anions by gas phase are supported by the results of an extensive theoretical investigation of the adiabatic electron affinity EA are the cases in which the corresponding neutral molecule has no electron affinity, yet the anion can

Sanov, Andrei

397

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...

398

Amino Acids and Sugars in the Gas Phase: Microwave Data for Astrochemistry  

Microsoft Academic Search

Microwave spectroscopy, considered the most definitive gas phase structural probe, can distinguish between different conformational structures since they have unique spectroscopic constants and give separate rotational spectra. However it has been limited to molecular specimens having an appreciable vapor pressure. In general, molecules of biological importance have low vapor pressures and tend to undergo degradation upon heating. The combination of

S. Mata; C. Cabezas; M. Varela; I. Peña; C. Perez; S. Blanco; M. E. Sanz; J. C. Lopez; J. L. Alonso

2011-01-01

399

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

EPA Science Inventory

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

400

Quantum control of I2 in the gas phase and in condensed phase solid Kr matrix  

E-print Network

into account using both exact quantum dynamics and nearly classical theory. For the condensed phase, since control is indeed possible in con- densed phases. There are two paradigms for quantum control: a dynamicQuantum control of I2 in the gas phase and in condensed phase solid Kr matrix Christopher J

Apkarian, V. Ara

401

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...

402

Quantification of Gas-Phase H-Atom Number Density by Tungsten Phosphate Glass  

Microsoft Academic Search

It is shown that H-atom densities in the gas phase can be evaluated by simply measuring the change in optical transmittance of tungsten phosphate glass plates. Tungst