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


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

Rožman, Marko



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



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.



Gas-Phase Dissociation Pathways of Multiply Charged Peptide Clusters  

PubMed Central

Numerous studies of cluster formation and dissociation have been conducted to determine properties of matter in the transition from the condensed phase to the gas phase using materials as diverse as atomic nuclei, noble gasses, metal clusters, and amino acids. Here, electrospray ionization is used to extend the study of cluster dissociation to peptides including leucine enkephalin with 7–19 monomer units and 2–5 protons, and somatostatin with 5 monomer units and 4 protons under conditions where its intramolecular disulfide bond is either oxidized or reduced. Evaporation of neutral monomers and charge separation by cluster fission are the competing dissociation pathways of both peptides. The dominant fission product for all leucine enkephalin clusters studied is a proton-bound dimer, presumably due to the high gas-phase stability of this species. The branching ratio of the fission and evaporation processes for leucine enkephalin clusters appears to be determined by the value of z2/n for the cluster where z is the charge and n the number of monomer units in the cluster. Clusters with low and high values of z2/n dissociate primarily by evaporation and cluster fission respectively, with a sharp transition between dissociation primarily by evaporation and primarily by fission measured at a z2/n value of ~0.5. The dependence of the dissociation pathway of a cluster on z2/n is similar to the dissociation of atomic nuclei and multiply charged metal clusters indicating that leucine enkephalin peptide clusters exist in a state that is more disordered, and possibly fluid, rather than highly structured in the dissociative transition state. The branching ratio, but not the dissociation pathway of [somatostatin5 + 4H]4+ is altered by the reduction of its internal disulfide bond indicating that monomer conformational flexibility plays a role in peptide cluster dissociation. PMID:14652186

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



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

E-print Network

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

Clemmer, David E.


Gas Phase Dissociation Behavior of Acyl-Arginine Peptides  

PubMed Central

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

McGee, William M.; McLuckey, Scott A.



International Journal of Mass Spectrometry 228 (2003) 851864 Biomimetic approaches to gas phase peptide chemistry  

E-print Network

peptide chemistry: combining selective binding motifs with reactive carbene precursors to form molecular with peptides in the gas phase are presented. In the present work, 18-crown-6 ether (18C6) is utilized to bind peptide bonds, are synthesized and tested experimentally. A third class of reagent designed to covalently

Stoltz, Brian M.


Controlled Formation of Peptide Bonds in the Gas Phase  

PubMed Central

Photoexcitation (using 157 nm vacuum ultraviolet radiation) of proton-bound peptide complexes leads to water elimination and the formation of longer amino acid chains. Thus, it appears that proton-bound dimers are long-lived intermediates along the pathway to peptide formation. Product specificity can be controlled by selection of specific complexes and the incorporation of blocking groups at the N- or C-termini. The product peptide sequences are confirmed using collision induced dissociation. PMID:21910477

Lee, Sunyoung; Valentine, Stephen J.; Reilly, James P.; Clemmer, David E.



Controlled formation of peptide bonds in the gas phase.  


Photoexcitation (using 157 nm vacuum ultraviolet radiation) of proton-bound peptide complexes leads to water elimination and the formation of longer amino acid chains. Thus, it appears that proton-bound dimers are long-lived intermediates along the pathway to peptide formation. Product specificity can be controlled by selection of specific complexes and the incorporation of blocking groups at the N- or C-termini. The product peptide sequences are confirmed using collision-induced dissociation. PMID:21910477

Lee, Sunyoung; Valentine, Stephen J; Reilly, James P; Clemmer, David E



Peptide Secondary Structures in the Gas Phase: Consensus Motif of N-Linked Glycoproteins  

E-print Network

Peptide Secondary Structures in the Gas Phase: Consensus Motif of N-Linked Glycoproteins Emilio J-linked glycoproteins, has been addressed by determining the intrinsic secondary structures of the capped oligopeptide-Linked glycoproteins found in eukaryotes are created by similar enzyme complexes, oligosac- charyltransferases (OSTs

Davis, Ben G.


Gas-phase separations of complex tryptic peptide mixtures.  


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

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



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




E-print Network

), the elementary steps included in the models of the oxidation of cyclic alkanes are close to those proposed to describe the oxidation of acyclic alkanes. Consequently, it has been possible to obtain the model proposedMODELING OF THE GAS-PHASE OXIDATION OF CYCLOHEXANE Frédéric BUDA, Barbara HEYBERGER, René FOURNET

Boyer, Edmond


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


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

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



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.



Multiscale Aspects of Modeling Gas-Phase Nanoparticle Synthesis  

PubMed Central

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

Buesser, B.; Gröhn, A.J.



Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.  


The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion. PMID:20973555

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



Statistical and mechanistic approaches to understanding the gas-phase fragmentation behavior of methionine sulfoxide containing peptides.  


Recently, we carried out a statistical analysis of a 'tryptic' peptide tandem mass spectrometry database in order to identify sequence-dependent patterns for the gas-phase fragmentation behavior of protonated peptide ions, and to improve the models for peptide fragmentation currently incorporated into peptide sequencing and database search algorithms [Kapp, E. A., Schutz, F., Reid, G. E., Eddes, J. S., Moritz, R. L., O'Hair, R. A. J., Speed, T. P. and Simpson, R. J. Anal. Chem. 2003, 75, 6251-6264.]. Here, we have reexamined this database in order to determine the effect of a common post-translational or process induced modification, methionine oxidation, on the appearance and relative abundances of the product ions formed by low energy collision induced dissociation of peptide ions containing this modification. The results from this study indicate that the structurally diagnostic neutral loss of methane sulfenic acid (CH3SOH, 64Da) from the side chain of methionine sulfoxide residues is the dominant fragmentation process for methionine sulfoxide containing peptide ions under conditions of low proton mobility, i.e., when ionizing proton(s) are sequestered at strongly basic amino acids such as arginine, lysine or histidine. The product ion abundances resulting from this neutral loss were found to be approximately 2-fold greater than those resulting from the cleavage C-terminal to aspartic acid, which has previously been shown to be enhanced under the same conditions. In close agreement with these statistical trends, experimental and theoretical studies, employing synthetic "tryptic" peptides and model methionine sulfoxide containing peptide ions, have determined that the mechanism for enhanced methionine sulfoxide side chain cleavage proceeds primarily via a 'charge remote' process. However, the mechanism for dissociation of the side chain for these ions was observed to change as a function of proton mobility. Finally, the transition state barrier for the charge remote side chain cleavage mechanism is predicted to be energetically more favorable than that for charge remote cleavage C-terminal to aspartic acid. PMID:15359728

Reid, Gavin E; Roberts, Kade D; Kapp, Eugene A; Simpson, Richard I



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.



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.



Probing Peptide Cation-Radicals by Near-UV Photodissociation in the Gas Phase. Structure Elucidation of Histidine Radical Chromophores Formed by Electron Transfer Reduction.  


Electron transfer reduction of gas-phase ions generated from histidine-containing peptides forms stable cation-radicals that absorb light at 355 nm, as studied for AAHAR, AAHAK, DSHAK, FHEK, HHGYK, and HHSHR. Laser photodissociation of mass-selected cation-radicals chiefly resulted in loss of H atoms, contrasting dissociations induced by slow collisional heating. The 355 nm absorption was due to new chromophores created by electron transfer and radical rearrangements in the cation-radicals. The chromophores were identified by time-dependent density functional theory calculations as 2H,3H-imidazoline and 2H-dihydrophenol radicals, formed by hydrogen atom transfer to the histidine and tyrosine side chain groups, respectively. These radicals undergo facile C-H bond dissociations upon photon absorption. In contrast, dissociations of histidine peptide cation-radicals containing the 1H,3H-imidazoline ring prefer loss of 4-methylimidazole via a multistep reaction pathway. The isomeric cation-radicals can be distinguished by a combination of collision-induced dissociation and near-UV photodissociation. The TD-DFT excitation energies in model imidazoline radicals were benchmarked on EOM-CCSD energies, and a satisfactory agreement was found for the M06-2X and ?B97XD functionals. The combination of electron transfer, photodissociation, collisional activation, and theory is presented as a powerful tool for studying structures and electronic properties of peptide cation-radicals in the gas phase. PMID:25688483

Nguyen, Huong T H; Shaffer, Christopher J; Ture?ek, František



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


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

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



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

NASA Astrophysics Data System (ADS)

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

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



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

SciTech Connect

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

Malandra, J.



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

NASA Astrophysics Data System (ADS)

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

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




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...


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.



Unusual ECD fragmentation attributed to gas-phase helix formation in a conformationally dynamic peptide.  


The helix-forming character of a model decapeptide, L4PL4K, is determined in the absence of solvent using ion mobility mass spectrometry, electron capture dissociation and molecular mechanics simulations. Unusual ECD fragmentation patterns dominated by b ions are attributed to helix formation upon electron capture and as a signature of conformational dynamics. PMID:24217599

Kalapothakis, Jason M D; Berezovskaya, Yana; Zampronio, Cleidiane G; Faull, Peter A; Barran, Perdita E; Cooper, Helen J



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

E-print Network

A reaction class approach for modeling gas phase reaction rates Thanh N. Truong,* Wendell T. Duncan the growing number of known elementary reaction rate constants, the current kinetic data- base is far from of polyatomic gas-phase reactions. It is now possible to calculate rate con- stants for reactions of moderate

Truong, Thanh N.


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

NASA Astrophysics Data System (ADS)

In this study, we demonstrated the formation of gas-phase peptide perthiyl (RSS•) and thiyl (RS•) radical ions besides sulfinyl radical (RSO•) ions from atmospheric pressure (AP) ion/radical reactions of peptides containing inter-chain disulfide bonds. The identity of perthiyl radical was verified from characteristic 65 Da (•SSH) loss in collision-induced dissociation (CID). This signature loss was further used to assess the purity of peptide perthiyl radical ions formed from AP ion/radical reactions. Ion/molecule reactions combined with CID were carried out to confirm the formation of thiyl radical. Transmission mode ion/molecule reactions in collision cell (q2) were developed as a fast means to estimate the population of peptide thiyl radical ions. The reactivity of peptide thiyl, perthiyl, and sulfinyl radical ions was evaluated based on ion/molecule reactions toward organic disulfides, allyl iodide, organic thiol, and oxygen, which followed in order of thiyl (RS•) > perthiyl (RSS•) > sulfinyl (RSO•). The gas-phase reactivity of these three types of sulfur-based radicals is consistent with literature reports from solution studies.

Tan, Lei; Xia, Yu



Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests  

PubMed Central

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421




Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification  

E-print Network

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification Aaron A Bayesian networks: modeling sequential data ­ Tandem mass spectrometry (MS/MS) and peptide fragmentation Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification ­ Hypothesis

Valtorta, Marco


The role of gas-phase reactions in modeling of the forced-flow chemical vapor infiltration process  

Microsoft Academic Search

An analytical model is presented, which includes the effects of both gas-phase and surface reactions, and the pressure changes due to the chemical reactions in the forced-flow chemical vapor infiltration (FCVI) process. For the FCVI process controlled by the gas-phase reactions, improvements of the process by using the forced-flow are limited. However, for the FCVI process controlled by the surface

Ching Yi Tsai; J. N. Reddy; Seshu B. Desu; Chien C. Chiu



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.



Electron Transfer Reduction of the Diazirine Ring in Gas-Phase Peptide Ions. On the Peculiar Loss of [NH4O] from Photoleucine  

NASA Astrophysics Data System (ADS)

Electron transfer to gas-phase peptide ions with diazirine-containing amino acid residue photoleucine (L*) triggers diazirine ring reduction followed by cascades of residue-specific radical reactions. Upon electron transfer, substantial fractions of (GL*GGR +2H)+? cation-radicals undergo elimination of [NH4O] radicals and N2H2 molecules from the side chain. The side-chain dissociations are particularly prominent on collisional activation of long-lived (GL*GGR +2H)+? cation-radicals formed by electron transfer dissociation of noncovalent peptide-18-crown-6-ether ion complexes. The ion dissociation products were characterized by multistage tandem mass spectrometry (MSn) and ion mobility measurements. The elimination of [NH4O] was elucidated with the help of 2H, 15 N, and 18O-labeled peptide ions and found to specifically involve the amide oxygen of the N-terminal residue. The structures, energies, and electronic states of the peptide radical species were elucidated by a combination of near-UV photodissociation experiments and electron structure calculations combining ab initio and density functional theory methods. Electron transfer reaching the ground electronic states of charge reduced (GL*GGR +2H)+? cation-radicals was found to reduce the diazirine ring. In contrast, backbone N - C? bond dissociations that represent a 60%-75% majority of all dissociations because of electron transfer are predicted to occur from excited electronic states.

Marek, Aleš; Shaffer, Christopher J.; Pepin, Robert; Slováková, Kristina; Laszlo, Kenneth J.; Bush, Matthew F.; Ture?ek, František



Electron Transfer Reduction of the Diazirine Ring in Gas-Phase Peptide Ions. On the Peculiar Loss of [NH4O] from Photoleucine.  


Electron transfer to gas-phase peptide ions with diazirine-containing amino acid residue photoleucine (L*) triggers diazirine ring reduction followed by cascades of residue-specific radical reactions. Upon electron transfer, substantial fractions of (GL*GGR +2H)(+[Symbol: see text]) cation-radicals undergo elimination of [NH4O] radicals and N2H2 molecules from the side chain. The side-chain dissociations are particularly prominent on collisional activation of long-lived (GL*GGR +2H)(+[Symbol: see text]) cation-radicals formed by electron transfer dissociation of noncovalent peptide-18-crown-6-ether ion complexes. The ion dissociation products were characterized by multistage tandem mass spectrometry (MS(n)) and ion mobility measurements. The elimination of [NH4O] was elucidated with the help of (2)H, (15)?N, and (18)O-labeled peptide ions and found to specifically involve the amide oxygen of the N-terminal residue. The structures, energies, and electronic states of the peptide radical species were elucidated by a combination of near-UV photodissociation experiments and electron structure calculations combining ab initio and density functional theory methods. Electron transfer reaching the ground electronic states of charge reduced (GL*GGR +2H)(+[Symbol: see text]) cation-radicals was found to reduce the diazirine ring. In contrast, backbone N?-?C? bond dissociations that represent a 60%-75% majority of all dissociations because of electron transfer are predicted to occur from excited electronic states. PMID:25515220

Marek, Aleš; Shaffer, Christopher J; Pepin, Robert; Slováková, Kristina; Laszlo, Kenneth J; Bush, Matthew F; Ture?ek, František



Dynamical Modeling of the Gas Phase in Fluidized Bed Combustion-Accounting for Fluctuations  

NASA Astrophysics Data System (ADS)

A model for gas phase mixing in fluidized bed boiler furnaces is presented. The model takes its basis in a description of the dynamics of the dense bottom bed which strongly govern the gas mixing up through the furnace. Thus, a time-resolved approach is used to link the modeling to the physics of the underlying processes determining the gas mixing. As output, the model gives the fluctuating flux of gas species, in contrast to the classical modeling approach which is limited to time-averaged gas fluxes. Such a dynamical approach allows assumption of the volatile combustion system as transport-controlled which avoids complete consumption of either oxygen or combustible gases in each modeled cell. Thus, the time-resolved analysis employed enables application of a realistic criterion for the mixing such as that reactants can coincide in both space and time in order to react. While fitting of kinetics is strongly dependent on the system and operational conditions, the present model integrates key system variables such as the bottom bed height and the characteristic pressure-drop constant over the primary air distributor, allowing application of transport-controlled (i.e. infinitely fast kinetics) volatile combustion.

Pallarès, D.; Johnsson, F.


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

E-print Network

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

Guang-Hua Zhang; Wei-Zhou Jiang



Negatively-charged helices in the gas phase.  


A polyalanine-based peptide which forms a stable, negatively-charged ?-helix in the gas phase is reported. Addition of an N-terminal acidic residue forms a stabilizing hydrogen bond network and an electrostatic interaction with the helical dipole. Formation of this secondary structure was demonstrated using ion mobility-mass spectrometry and molecular modelling techniques. PMID:24901462

Johnson, Andrew R; Dilger, Jonathan M; Glover, Matthew S; Clemmer, David E; Carlson, Erin E



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

E-print Network

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

Goddard III, William A.


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

E-print Network

report what is largely a qualitative description of the general features observed. We focus on metal stabilities of different conformations for different metal ions are discussed in terms of simple qualitative. A number of research groups have investigated the fragmentation of metalated peptides,4 oligonucleotides,5

Clemmer, David E.


An Electrostatic Charge Partitioning Model for the Dissociation of Protein Complexes in the Gas Phase  

NASA Astrophysics Data System (ADS)

Electrosprayed multi-protein complexes can be dissociated by collisional activation in the gas phase. Typically, these processes follow a mechanism whereby a single subunit gets ejected with a disproportionately high amount of charge relative to its mass. This asymmetric behavior suggests that the departing subunit undergoes some degree of unfolding prior to being separated from the residual complex. These structural changes occur concomitantly with charge (proton) transfer towards the subunit that is being unraveled. Charge accumulation takes place up to the point where the subunit loses physical contact with the residual complex. This work develops a simple electrostatic model for studying the relationship between conformational changes and charge enrichment during collisional activation. Folded subunits are described as spheres that carry continuum surface charge. The unfolded chain is envisioned as random coil bead string. Simulations are guided by the principle that the system will adopt the charge configuration with the lowest potential energy for any backbone conformation. A finite-difference gradient algorithm is used to determine the charge on each subunit throughout the dissociation process. Both dimeric and tetrameric protein complexes are investigated. The model reproduces the occurrence of asymmetric charge partitioning for dissociation events that are preceded by subunit unfolding. Quantitative comparisons of experimental MS/MS data with model predictions yield estimates of the structural changes that occur during collisional activation. Our findings suggest that subunit separation can occur over a wide range of scission point structures that correspond to different degrees of unfolding.

Sciuto, Stephen V.; Liu, Jiangjiang; Konermann, Lars



From solution to the gas phase: stepwise dehydration and kinetic trapping of substance P reveals the origin of peptide conformations.  


Past experimental results and molecular dynamics simulations provide evidence that, under some conditions, electrospray ionization (ESI) of biomolecules produces ions that retain elements of solution phase structures. However, there is a dearth of information regarding the question raised by Breuker and McLafferty, "for how long, under what conditions, and to what extent, can solution structure be retained without solvent?" (Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 18145). Here, we use cryogenic ion mobility-mass spectrometry to experimentally probe the structural evolution of the undecapeptide substance P (SP) during the final stages of ESI. The results reveal that anhydrous SP conformers originate from evaporation of cluster ions, specifically, [SP + 2H](2+) (H2O)n (n = 0 to ?50) and [SP + 3H](3+) (H2O)n (n = 0 to ?30), and that major structural changes do not occur during the evaporative process. In the case of [SP + 3H](3+), the results demonstrate that a compact dehydrated conformer population can be kinetically trapped on the time scale of several milliseconds, even when an extended gas phase conformation is energetically favorable. PMID:24313458

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



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

Microsoft Academic Search

The RegCM-CHEM4 is a new online climate-chemistry model based on the International Centre for Theoretical Physics (ICTP) regional climate model (RegCM4). Tropospheric gas-phase chemistry is integrated into the climate model using the condensed version of the Carbon Bond Mechanism (CBM-Z; Zaveri and Peters, 1999) with a fast solver based on radical balances. We evaluate the model over Continental Europe for

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




EPA Science Inventory

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


A detailed chemical kinetic model for gas phase combustion of TNT  

Microsoft Academic Search

A detailed chemical kinetic mechanism for gas phase combustion of 2,4,6-tri-nitrotoluene (TNT) has been developed to explore problems of explosive performance and of soot formation during the destruction of munitions. Thermodynamic properties of intermediate and radical species are estimated by group additivity. Reactions for the decomposition and oxidation of TNT and its intermediate products are assembled, based on information from

William J. Pitz; Charles K. Westbrook



Analysis of nonlinear model of gas dynamics in a vertical reactor for gas phase epitaxy  

NASA Astrophysics Data System (ADS)

In this paper, we consider a vertical reactor for gas phase epitaxy. Based on the recently obtained results of Pankratov and Bulaeva [2013, Univ. J. Mater. Sci.1, 180-200], we analyzed the dynamics of gas transport in the reactor with account nonlinearity of dynamics and rotation of keeper of substrate with the substrate. Based on the analysis, we formulated recommendation to optimize regime of rotation to increase homogeneity of properties of epitaxial layer.

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



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



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.



SHORT COMMUNICATION Gas-Phase Separations of Protease Digests  

E-print Network

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

Clemmer, David E.


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.



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

ions.24 Of the ion-molecule probes employed for structural determination, none have been as successful as hydrogen/deuterium (H/D) exchange. This isotope-labeling technique is based upon the exchange of labile hydrogens (i.e. amine, amide, and ?OH... on non-polar, aliphatic amino acids and peptides.39,43,44,45,46 In these systems, the most likely site for protonation is the N- terminal amine, with possible charge site solvation by amide carbonyl groups.47 Although understanding of gas-phase H...

Marini, Joseph Thomas



An Effective Continuum Model for the Liquid-to-Gas Phase Change in a Porous Medium Driven by Solute Diffusion: II. Constant Liquid Withdrawal Rates  

SciTech Connect

This report describes the development of an effective continuum model to describe the nucleation and subsequent growth of a gas phase from a supersaturated, slightly compressible binary liquid in a porous medium, driven by solute diffusion.This report also focuses on the processes resulting from the withdrawal of the liquid at a constant rate. As before, the model addresses two stages before the onset of bulk gas flow, nucleation and gas phase growth. Because of negligible gradients due to gravity or viscous forces, the critical gas saturation, is only a function of the nucleation fraction.

Tsimpanogiannis, Ioannis N.; Yortsos, Yanis C.



Gas Phase Nanoparticle Synthesis  

NASA Astrophysics Data System (ADS)

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

Granqvist, Claes; Kish, Laszlo; Marlow, William


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

SciTech Connect

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

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



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




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

SciTech Connect

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

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




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...


Gas phase and aerosol model simulations in the greater Athens area  

NASA Astrophysics Data System (ADS)

This study analyzes air quality data provided by numerical simulations for the Greater Athens Area (GAA) using the latest release of the emission inventory (industry, traffic, off road activities, airport, railway, harbor). The three-dimensional photochemical Urban Airshed Model (UAM-V) was coupled with the meteorological Mesoscale Model (MM5). All the simulated days favored high concentration levels of air pollutants. The concentrations of the air pollutants produced by the simulations were compared with routine measurements from the operating stations of the existing air pollution monitor network in Athens. The comparison revealed good agreement for the stations sited in the center of Athens while the observed discrepancies in a few suburban stations could be explained by the fact that few sectors (e.g. biogenic) are not included in the Athens emission inventory. Moreover, the importance of the VOCs reactivity on photochemical modeling, especially on ozone productivity, was investigated after constructing various speciation profiles of the VOCs emissions in agreement with the different land uses (urban, semi-urban). These profiles were derived from a large number of VOC species (about 200) contained in detailed emission inventories. Furthermore, the role of biogenic emissions was examined by incorporating the rural environments. Finally, a modeling contribution to the aerosols’ concentration levels in the Greater Athens Area is attempted using the three dimensional Regional Modeling System for Aerosols and Deposition (REMSAD). The aerosol distribution/deposition and toxic chemistry is examined, making use of the emissions of particulate matter included in the emission inventory such as PM, NH3 and toxics (Hg, Pb, Zn, As, Cu). Further simulations are performed by considering changes in the PM speciation. Finally, the correlation between the gaseous pollutants and the aerosol species is performed in order to provide important conclusions in areas or time-periods lacking PM measurements.

Bossioli, E.; Tombrou, M.; Dandou, A.



Modeling-gas phase reactions in indoor environments using computational fluid dynamics  

NASA Astrophysics Data System (ADS)

This CFD modeling study examines the concentrations of two gaseous compounds that react in an indoor setting to produce a hypothetical product. The reactants are ozone and either d-limonene or ?-terpinene (which reacts with ozone about 40 times faster than d-limonene). In addition to two different terpenes, the scenarios include two air exchange rates (0.5 and 2.0 h-1). The terpene is introduced as a floor source with an emission pattern similar to a floor-care product. These four scenarios have been set in a fairly large two-dimensional room (13.6×40.6 m) with a supply at the top of the left wall and an exhaust at the bottom of the right wall. The room has been deliberately scaled so that the Reynolds numbers for key flow regimes match those of a room in which the calculated flow field has been validated against measured data. It has been further assumed that ozone interacts with room surfaces while the terpenes do not. The results show that for all four scenarios, under steady-state conditions, there are large concentration gradients within the room for both reactants and product. To some extent this is due to imperfect mixing. However, it also reflects that reactions occur at different rates across the room (because of varying reactant concentrations) and that the time available for reactions to occur varies with the room location (because the "age of the air" varies from point to point). Locally, within the room, the concentrations calculated by the CFD method differ significantly from those calculated by a one-compartment mass-balance model assuming perfect mixing.

Sørensen, Dan Nørtoft; Weschler, Charles J.


A density functional theory (DFT) study on gas-phase proton transfer reactions of derivatized and underivatized peptide ions generated by matrix-assisted laser desorption ionization  

Microsoft Academic Search

In this study, classic molecular dynamics (MD) simulations followed by density functional theory (DFT) calculations are employed\\u000a to calculate the proton transfer reaction enthalpy shifts for native and derivatized peptide ions in the MALDI plume. First,\\u000a absolute protonation and deprotonation enthalpies are calculated for native peptides (RPPGF and AFLDASR), the corresponding\\u000a hexyl esters and three common matrices ?-cyano-4-hydroxycinnamic acid (4HCCA),

Francesco L. Brancia; Mauro Stener; Alessandra Magistrato



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.



Observation of an unusually facile fragmentation pathway of gas-phase peptide ions: a study on the gas-phase fragmentation mechanism and energetics of tryptic peptides modified with 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC) and their 18-crown-6 complexes.  


Various peptide modifications have been explored recently to facilitate the acquisition of sequence information. N-terminal sulfonation is an interesting modification because it allows unambiguous de novo sequencing of peptides, especially in conjunction with MALDI-PSD-TOF analysis; such modified peptide ions undergo fragmentation at energies lower than those required conventionally for unmodified peptide ions. In this study, we systematically investigated the fragmentation mechanisms of N-terminal sulfonated peptide ions prepared using two different N-terminal sulfonation reagents: 4-sulfophenyl isothiocyanate (SPITC) and 4-chlorosulfophenyl isocyanate (SPC). Collision-induced dissociation (CID) of the SPC-modified peptide ions produced a set of y-series ions that were more evenly distributed relative to those observed for the SPITC-modified peptides; y(n-1) ion peaks were consistently and significantly larger than the signals of the other y-ions. We experimentally investigated the differences between the dissociation energies of the SPITC- and SPC-modified peptide ions by comparing the MS/MS spectra of the complexes formed between the crown ether 18-crown-6 (CE) and the modified peptides. Upon CID, the complexes formed between 18-crown-6 ether and the protonated amino groups of C-terminal lysine residues underwent either peptide backbone fragmentation or complex dissociation. Although the crown ether complexes of the unmodified ([M + CE + 2H]2+) and SPC-modified ([M* + CE + 2H]2+) peptides underwent predominantly noncovalent complex dissociation upon CID, the low-energy dissociations of the crown ether complexes of the SPITC-modified peptides ([M' + CE + 2H]2+) unexpectedly resulted in peptide backbone fragmentations, along with a degree of complex dissociation. We performed quantum mechanical calculations to address the energetics of fragmentations observed for the modified peptides. PMID:17200996

Shin, Joong-Won; Lee, Yong Ho; Hwang, Sungu; Lee, Sang-Won



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

PubMed Central

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

Sitkiewicz, Ewa; Ol?dzki, Jacek; Pozna?ski, Jaros?aw; Dadlez, Micha?



Di-tyrosine cross-link decreases the collisional cross-section of a? peptide dimers and trimers in the gas phase: an ion mobility study.  


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

Sitkiewicz, Ewa; Ol?dzki, Jacek; Pozna?ski, Jaros?aw; Dadlez, Micha?



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


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

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



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

NASA Astrophysics Data System (ADS)

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

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



Fragmentation of peptide negative molecular ions induced by resonance electron capture  

Microsoft Academic Search

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

Yury V. Vasil'Ev; Benjamin J. Figard; Jeff Morré; Max L. Deinzer



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.



Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits  

NASA Astrophysics Data System (ADS)

It is demonstrated that many-body force field models based solely on pairwise Coulomb screening cannot simultaneously reproduce both gas-phase and condensed-phase polarizability limits. Several many-body force field model forms are tested and compared with basis set-corrected ab initio results for a series of bifurcated water chains. Models are parameterized to reproduce the ab initio polarizability of an isolated water molecule, and pairwise damping functions are set to reproduce the polarizability of a water dimer as a function of dimer separation. When these models are applied to extended water chains, the polarization is over-predicted, and this over-polarization increased as a function of the overlap of molecular orbitals as the chains are compressed. This suggests that polarizable models based solely on pairwise Coulomb screening have some limitations, and that coupling with non-classical many-body effects, in particular exchange terms, may be important.

Giese, Timothy J.; York, Darrin M.



Structural determination and gas-phase synthesis of monomeric, unsolvated IZnCH3 (X?(1)A(1)): a model organozinc halide.  


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



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


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

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




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...



EPA Science Inventory

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


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

EPA Science Inventory

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


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)



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

PubMed Central

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

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



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

NASA Astrophysics Data System (ADS)

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

Bhaskaran, Renjith; Sarma, Manabendra



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

PubMed Central

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

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



Gas Phase Reactivity of Carboxylates with N-Hydroxysuccinimide Esters  

NASA Astrophysics Data System (ADS)

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

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




EPA Science Inventory

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


Bistability in Interstellar Gas-Phase Chemistry  

E-print Network

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

Gai I. Boger; Amiel Sternberg



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.



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

PubMed Central

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

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



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



In Silico Models for Designing and Discovering Novel Anticancer Peptides  

NASA Astrophysics Data System (ADS)

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

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



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



Gas-Phase Reactivity of Carboxylic Acid Functional Groups with Carbodiimides  

PubMed Central

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

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



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



Gas-phase photolysis of tungsten hexachloride  

NASA Astrophysics Data System (ADS)

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

Kullmer, R.



An Effective Continuum Model for the Liquid-to-Gas Phase Change in a Porous Medium Driven by Solute Diffusion: I. Constant Pressure Decline Rates  

SciTech Connect

This report, focuses on the isothermal gas phase growth from a supersaturated, slightly compressible, binary liquid in a porous medium. This is driven by mass transfer, the extent of which is controlled by the application of either a constant-rate decline of the system pressure or the withdrawal of the liquid at a constant rate. This report deals with the first process. Pressure depletion due to constant-rate liquid withdrawal is analyzed in a companion report .

Tsimpanogiannis, Ioannis N.; Yortsos, Yanis C.



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.



5, 51675182, 2005 Gas-phase reaction  

E-print Network

the reactions of NaCl in sea salt particles 5168 #12;ACPD 5, 5167­5182, 2005 Gas-phase reaction of atomicACPD 5, 5167­5182, 2005 Gas-phase reaction of atomic chlorine with aldehydes D. Rodr´iguez et al and Physics Discussions Kinetic study of the gas-phase reaction of atomic chlorine with a series of aldehydes

Paris-Sud XI, Université de


Structure and chemistry of the heteronuclear oxo-cluster [VPO4]•+: a model system for the gas-phase oxidation of small hydrocarbons.  


The heteronuclear oxo-cluster [VPO4](•+) is generated via electrospray ionization and investigated with respect to both its electronic structure as well as its gas-phase reactivity toward small hydrocarbons, thus permitting a comparison to the well-known vanadium-oxide cation [V2O4](•+). As described in previous studies, the latter oxide exhibits no or just minor reactivity toward small hydrocarbons, such as CH4, C2H6, C3H8, n-C4H10, and C2H4, while substitution of one vanadium by a phosphorus atom yields the reactive [VPO4](•+) ion; the latter brings about oxidative dehydrogenation (ODH) of saturated hydrocarbons, e.g., propane and butane as well as oxygen-atom transfer (OAT) to unsaturated hydrocarbons, e.g. ethene, at thermal conditions. Further, the gas-phase structure of [VPO4](•+) is determined by IR photodissociation spectroscopy and compared to that of [V2O4](•+). DFT calculations help to elucidate the reaction mechanism. The results underline the crucial role of phosphorus in terms of C-H bond activation of hydrocarbons by mixed VPO clusters. PMID:23432112

Dietl, Nicolas; Wende, Torsten; Chen, Kai; Jiang, Ling; Schlangen, Maria; Zhang, Xinhao; Asmis, Knut R; Schwarz, Helmut



Optimal grade transitions in a gas phase polyethylene reactor  

Microsoft Academic Search

This paper reports that using gas-phase technology many grades of polyethylene can be produced in a single reactor. For a series of three polyethylene products, model-based dynamic optimization is used to determine optimal grade changeover policies. Optimal manipulated variable profiles are determined for hydrogen and butene feed rates, reactor temperature setpoint, gas bleed flow, catalyst feed rate, and bed level

K. B. McAuley; J. F. MacGregor



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.


Gas-phase pulsed power switches  

Microsoft Academic Search

A review of plasma science that is related to gas-phase pulsed power switching is presented. Switch plasmas include uniform glow-type plasmas and constricted arc-type plasmas, and the science involves understanding transport processes in hydrogen, helium, metal vapor, and other plasmas, and electrode processes including limitations related to cathode emission and sheaths. Gas-phase pulsed power switches include spark gaps, vacuum, metal

Martin A. Gundersen



Photodissociation pathways of gas-phase photoactive yellow protein chromophores  

NASA Astrophysics Data System (ADS)

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

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



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

NASA Astrophysics Data System (ADS)

Various thermal (radiative, conductive, and convective) initiation experiments are performed to demonstrate the importance of the gas phase role in combustion modeling of energetic materials (EM). A previously published condensed phase model that includes a predicted critical irradiance above which ignition is not possible is compared to experimental laser ignition results for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 2,4,6-trinitrotoluene (TNT). Experimental results conflict with the predicted critical irradiance concept. The failure of the model is believed to result from a misconception about the role of the gas phase in the ignition process of energetic materials. The model assumes that ignition occurs at the surface and that evolution of gases inhibits ignition. High speed video of laser ignition, oven cook-off and hot wire ignition experiments captures the ignition of HMX and TNT in the gas phase. A laser ignition gap test is performed to further evaluate the effect of gas phase laser absorption and gas phase disruption on the ignition process. Results indicate that gas phase absorption of the laser energy is probably not the primary factor governing the gas phase ignition observations. It is discovered that a critical gap between an HMX pellet and a salt window of 6mm±0.4mm exists below which ignition by CO2 laser is not possible at the tested irradiances of 29W /cm2 and 38W/cm2 for HMX ignition. These observations demonstrate that a significant disruption of the gas phase, in certain scenarios, will inhibit ignition, independent of any condensed phase processes. These results underscore the importance of gas phase processes and illustrate that conditions can exist where simple condensed phase models are inadequate to accurately predict the behavior of energetic materials.

Ali, A. N.; Son, S. F.; Asay, B. W.; Sander, R. K.



A structural model for desmosine cross-linked peptides.  

PubMed Central

Desmosine-enriched peptides were isolated from a thermolysin digest of bovine ligamentum nuchae elastin and a partial sequence was determined. A 'two-cross-link' model is proposed in which a second cross-link, perhaps lysinonorleucine, joins two peptide chains approx. 35 amino acid residues removed from the desmosine. Implied in this model is a certain asymmetry or directionality which places restrictions on the 'sense' of the peptide chains (either always parallel or anti-parallel) in order to align the cross-linking sites. Imposing such restrictions raises the possibility of specific alignment of elastin precursor molecules by microfibrillar proteins and/or aligning peptides on the precursor molecules themselves. PMID:697739

Mecham, R P; Foster, J A



PeptideBuilder: A simple Python library to generate model peptides  

PubMed Central

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

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



PeptideBuilder: A simple Python library to generate model peptides.  


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

Tien, Matthew Z; Sydykova, Dariya K; Meyer, Austin G; Wilke, Claus O



Effects of ammonium sulfate aerosols on the gas-phase reactions of the hydroxyl radical with organic compounds  

Microsoft Academic Search

Air quality modeling is of seminal importance to the assessment of air pollution control strategies. Traditionally, these models include four basic components: meteorology data, emissions data, transport mechanisms, and chemistry. The gas-phase chemistry portions have been based on kinetic and product laboratory studies in relatively pristine gas-phase environments. However, given the abundance of particles in the atmosphere, it is possible

Sewon Oh; Jean M. Andino



Gas-Phase Photoionization Of A Protein  

NASA Astrophysics Data System (ADS)

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

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



Gas-phase electron diffraction studies of unstable molecules   

E-print Network

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

Noble-Eddy, Robert



Streptavidin-peptide interaction as a model system for molecular recognition  

E-print Network

Streptavidin-peptide interaction as a model system for molecular recognition K.S. Laml, M. Lebl2, S.S.A. Introduction Peptide library sereening has been proven to be a valuable tool in identifying peptide ligands for various macromolecular targets [I]. Our peptide library method (Selectide Technology) is based on the "one

Lam, Kit S.


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

NASA Astrophysics Data System (ADS)

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

Hoffmann, Marcin; Szarecka, Agnieszka; Rychlewski, Jacek


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


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

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



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.



Infrared spectroscopic and modeling studies of H{sub 2}/CH{sub 4} microwave plasma gas phase from low to high pressure and power  

SciTech Connect

InfraRed Tunable Diode Laser Absorption Spectroscopy technique has been implemented in a H{sub 2}/CH{sub 4} Micro-Wave (MW frequency f?=?2.45 GHz) plasma reactor dedicated to diamond deposition under high pressure and high power conditions. Parametric studies such as a function of MW power, pressure, and admixtures of methane have been carried out on a wide range of experimental conditions: the pressure up to 270 mbar and the MW power up to 4?kW. These conditions allow high purity Chemical Vapor Deposition diamond deposition at high growth rates. Line integrated absorption measurements have been performed in order to monitor hydrocarbon species, i.e., CH{sub 3}, CH{sub 4}, C{sub 2}H{sub 2}, C{sub 2}H{sub 4}, and C{sub 2}H{sub 6}. The densities of the stable detected species were found to vary in the range of 10{sup 12}–10{sup 17} molecules cm{sup ?3}, while the methyl radical CH{sub 3} (precursor of diamond growth under these conditions) measured into the plasma bulk was found up to 10{sup 14} molecules cm{sup ?3}. The experimental densities have been compared to those provided by 1D-radial thermochemical model for low power and low pressure conditions (up to 100 mbar/2?kW). These densities have been axially integrated. Experimental measurements under high pressure and power conditions confirm a strong increase of the degree of dissociation of the precursor, CH{sub 4}, associated to an increase of the C{sub 2}H{sub 2} density, the most abundant reaction product in the plasma.

Rond, C., E-mail:; Lombardi, G.; Gicquel, A. [LSPM CNRS UPR 3407 Université Paris 13, 99 Avenue J.-B. Clément, 93430 Villetaneuse (France); Hamann, S.; Röpcke, J. [INP Greifswald, Felix-Hausdorff-Str. 2, 17489 Greifswald (Germany); Wartel, M. [GREMI UMR 7344, CNRS/Université d'Orléans, site de Bourges, rue G. Berger, 18000 Bourges (France)



Prediction of peptide bonding affinity: kernel methods for nonlinear modeling  

E-print Network

This paper presents regression models obtained from a process of blind prediction of peptide binding affinity from provided descriptors for several distinct datasets as part of the 2006 Comparative Evaluation of Prediction Algorithms (COEPRA) contest. This paper finds that kernel partial least squares, a nonlinear partial least squares (PLS) algorithm, outperforms PLS, and that the incorporation of transferable atom equivalent features improves predictive capability.

Bergeron, Charles; Sundling, C Matthew; Krein, Michael; Katt, Bill; Sukumar, Nagamani; Breneman, Curt M; Bennett, Kristin P



Gas Phase Study of C+ Reactions of Interstellar Relevance  

NASA Astrophysics Data System (ADS)

The current uncertainty in many reaction rate constants causes difficulties in providing satisfactory models of interstellar chemistry. Here we present new measurements of the rate constants and product branching ratios for the gas phase reactions of C+ with NH3, CH4, O2, H2O, and C2H2, using the flowing afterglow-selected ion flow tube (FASIFT) technique. Results were obtained using two instruments that were separately calibrated and optimized; in addition, low ionization energies were used to ensure formation of ground-state C+, the purities of the neutral reactants were verified, and mass discrimination was minimized.

Martinez, Oscar, Jr.; Betts, Nicholas B.; Villano, Stephanie M.; Eyet, Nicole; Snow, Theodore P.; Bierbaum, Veronica M.



Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer  

PubMed Central

The hydrogen bonds and electrostatic interactions that form between the protonated side chain of a basic residue and the negatively charged phosphate of a phosphopeptide can play crucial roles in governing their dissociation pathways under low-energy collision-induced dissociation (CID). Understanding how phosphoramidate (i.e. phosphohistidine, phospholysine and phosphoarginine), rather than phosphomonoester-containing peptides behave during CID is paramount in investigation of these problematic species by tandem mass spectrometry. To this end, a synthetic peptide containing either phosphohistidine (pHis) or phospholysine (pLys) was analyzed by ESI-MS using a Paul-type ion trap (AmaZon, Bruker) and by traveling wave ion mobility-mass spectrometry (Synapt G2-Si, Waters). Analysis of the products of low-energy CID demonstrated formation of a doubly ‘phosphorylated’ product ion arising from intermolecular gas-phase phosphate transfer within a phosphopeptide dimer. The results are explained by the formation of a homodimeric phosphohistidine (pHis) peptide non-covalent complex (NCX), likely stabilized by the electrostatic interaction between the pHis phosphate group and the protonated C-terminal lysine residue of the peptide. To the best of our knowledge this is the first report of intermolecular gas-phase phosphate transfer from one phosphopeptide to another, leading to a doubly phosphorylated peptide product ion.

Gonzalez-Sanchez, Maria-Belen; Lanucara, Francesco; Hardman, Gemma E.; Eyers, Claire E.



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.



Photoinduced gas-phase electron transfer reactions.  


The electron transfer quenching process, when a reactive excited state is singlet or triplet, for gas-phase systems (benzophenone and anthraquinone with amines and pyridine as well as carbazole with halomethanes) was systematically investigated using time-resolved fluorescence. Bimolecular rate constants were obtained. Variable-temperature measurements were performed for eight donor-acceptor pairs. It was found that under solvent-free conditions various quenchers differing in photochemical reactivity led to change in quenching rates by almost three orders of magnitude. Positive and negative temperature dependences for the electron transfer rate constants were observed. The data were analyzed in terms of the Marcus-Jortner theory. PMID:15615042

Zalesskaya, G A; Sambor, E G; Bely, N N



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

NASA Astrophysics Data System (ADS)

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

Balucani, Nadia; Ceccarelli, Cecilia; Taquet, Vianney



Infrared Spectroscopy of Gas Phase Metal Clusters  

NASA Astrophysics Data System (ADS)

The combination of its various performance characteristics make the free electron laser FELIX ideally suited to resonantly pump large amounts of vibrational energy into isolated gas-phase species. This energy can then subsequently trigger reactions, it can lead to the emission of photons (fluorescence), to the release of fragments (dissociation) or to the ejection of electrons (ionization). By monitoring these IR laser induced processes as a function of excitation wavelength, IR spectroscopic information, can be obtained. In one experiment, FELIX is used to excite strongly bound gas-phase clusters to levels that are high enough to enable the thermal emission of an electron. When the (mass selected) ion yield is monitored as a function of wavelength, IR spectra of the clusters can be obtained. This IR laser induced ionization has been found to work very efficiently for clusters that are strongly bound and that have comparatively low ionization potentials. The spectra of various metal-carbide, -oxide and -nitride clusters have been measured and the analysis of these spectra as a function of size of the cluster yields information on the cluster structure and on its evolution from small systems to the bulk limit.

van Heijnsbergen, Deniz; Meijer, Gerard; Duncan, Michael; von Helden, Gert



Electron scattering from gas-phase glycine molecules.  


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

Tashiro, Motomichi



Gas-phase chemistry of molecular containers.  


The remarkable technical advances in mass spectrometry during the last decades, including soft ionisation techniques, the coupling of electrospray ionisation to flow reactors, and the broad scope of tandem mass spectrometric experiments applicable to mass-selected ions allow investigating the chemistry of molecular capsules in solution as well as in the absence of any environment. With these methods, mass spectrometry is capable of answering many questions starting from providing analytical characterisation data (elemental composition, stoichiometry, etc.) to structural aspects (connectivities, positions of building blocks in supramolecular complexes) and to the examination of solution and gas-phase reactivity including reactions inside molecular containers. The present article reviews this work with a focus rather on the chemical questions that can be answered than on the technical specialities of (tandem) mass spectrometry. PMID:24956973

Qi, Zhenhui; Heinrich, Thomas; Moorthy, Suresh; Schalley, Christoph A



Biophysical studies of anhydrous peptide structure  

E-print Network

peptide folding motifs in the absence of solvent, suggesting that in vacuo studies may potentially discern the role of solvation in protein structure. Ion mobility-mass spectrometry (IMMS) combines a gas-phase ion separation based on collision cross...

McLean, Janel Renee



Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model  

E-print Network

Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model Marc new potent, non-toxic compounds to treat bacterial infections. Antimicrobial peptides (AMPs inspire the design of new peptide leads with enhanced activity. Here, we describe an artificial neural

Pompeu Fabra, Universitat


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


A missing sink for gas-phase glyoxal in Mexico City: Formation of secondary organic aerosol  

Microsoft Academic Search

(1) The sources of secondary organic aerosol (SOA) are highly uncertain. Direct measurements of gas-phase glyoxal in Mexico City are compared to experimentally constrained model predictions. Observed glyoxal concentrations are found significantly below those predicted. Additional glyoxal sources are likely and would increase these differences; an additional glyoxal sink must be operative. The model-measurement differences are fully resolved by a

Rainer Volkamer; Federico San Martini; Luisa T. Molina; Dara Salcedo; Jose L. Jimenez; Mario J. Molina



Pressure Dependence of Gas-Phase Reaction Rates  

ERIC Educational Resources Information Center

It is presented that only simple concepts, mainly taken from activated-complex or transition-state theory, are required to explain and analytically describe the influence of pressure on gas-phase reaction kinetics. The simplest kind of elementary gas-phase reaction is a unimolecular decomposition reaction.

De Persis, Stephanie; Dollet, Alain; Teyssandier, Francis



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



Instabilities in Lean Gas-Phase Combustion  

NASA Astrophysics Data System (ADS)

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

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



Reactivity of ambident anions in the gas phase  

NASA Astrophysics Data System (ADS)

Ambident anions are negative ions in which several reactive centra are coupled via resonance. When these ions react, there is a competition possible between the reaction channels via each of these reactive centra. A systematic study on the reactivity of several ambident anions in a Fourier transform ion cyclotron resonance mass spectrometer is described in the thesis. Via probe reactions it is shown that a gas-phase ion/molecule reaction between an ambident anion and an unsaturated polyfluorocarbon compound enables a distinction between the competing reaction channels mentioned. The obtained product distributions can be interpreted using simple perturbation theory. In chapter one of the thesis several models and concepts (such as hard and soft acids and bases, HSAB, perturbation theory and the Allopolarisierungs-Prinzip) are described which have been used previously to explain the reactivity of ambident ions in solution.

Freriks, Ivo. L.



Optical properties of anthocyanins in the gas phase  

NASA Astrophysics Data System (ADS)

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

Ge, Xiaochuan; Calzolari, Arrigo; Baroni, Stefano



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)



Chemistry inside molecular containers in the gas phase  

NASA Astrophysics Data System (ADS)

Inner-phase chemical reactions of guest molecules encapsulated in a macromolecular cavity give fundamental insight into the relative stabilization of transition states by the surrounding walls of the host, thereby modelling the situation of substrates in enzymatic binding pockets. Although in solution several examples of inner-phase reactions are known, the use of cucurbiturils as macrocyclic hosts and bicyclic azoalkanes as guests has now enabled a systematic mass spectrometric investigation of inner-phase reactions in the gas phase, where typically the supply of thermal energy results in dissociation of the supramolecular host-guest assembly. The results reveal a sensitive interplay in which attractive and repulsive van der Waals interactions between the differently sized hosts and guests need to be balanced with a constrictive binding to allow thermally activated chemical reactions to compete with dissociation. The results are important for the understanding of supramolecular reactivity and have implications for catalysis.

Lee, Tung-Chun; Kalenius, Elina; Lazar, Alexandra I.; Assaf, Khaleel I.; Kuhnert, Nikolai; Grün, Christian H.; Jänis, Janne; Scherman, Oren A.; Nau, Werner M.



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



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



Modeling of mixed-mode chromatography of peptides.  


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

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



Gas-phase nitronium ion affinities.  

PubMed Central

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

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



Atmospheric Consequences of the Hydration in Gas Phase of Aldehydes and Ketones  

Microsoft Academic Search

Aldehydes and ketones are known oxidation products of biogenic and anthropogenic VOCs and have been observed by field studies to be present in aerosol and cloud particles. While the gas-phase chemistry of these compounds is fairly well understood, their modeled concentration and role in SOA formation remains controversial. In aqueous solution aldehydes and ketones hydrate to form alcohols. We explore

V. Vaida; J. L. Axson; M. K. Maron



Gas phase precursors to anthropogenic secondary organic aerosol: Using the Master Chemical Mechanism to probe detailed  

E-print Network

hydrocarbons Chemical ionisation reaction time-of-flight mass spectrometry a b s t r a c t A detailed gas-phase photochemical chamber box model, incorporating the Master Chemical Mechanism (MCMv3.1) degradation scheme during a series of aerosol chamber experiments in order to evaluate the mechanism under a variety of VOC


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

Microsoft Academic Search

We present a model study demonstrating that surface partitioning of volatile surfactants enhances their uptake by submicron liquid droplets. In submicron-sized droplets, surface partitioning of a surface-active volatile species may significantly decrease its equilibrium partial pressure, thus increasing the total flux of the surfactant from gas phase to aqueous phase. Such uptake of volatile organic species into aqueous aerosols can

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



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

PubMed Central

Antimicrobial resistance is a persistent problem in the public health sphere. However, recent attempts to find effective substitutes to combat infections have been directed at identifying natural antimicrobial peptides in order to circumvent resistance to commercial antibiotics. This study describes the development of synthetic peptides with antimicrobial activity, created in silico by site-directed mutation modeling using wild-type peptides as scaffolds for these mutations. Fragments of antimicrobial peptides were used for modeling with molecular modeling computational tools. To analyze these peptides, a decision tree model, which indicated the action range of peptides on the types of microorganisms on which they can exercise biological activity, was created. The decision tree model was processed using physicochemistry properties from known antimicrobial peptides available at the Antimicrobial Peptide Database (APD). The two most promising peptides were synthesized, and antimicrobial assays showed inhibitory activity against Gram-positive and Gram-negative bacteria. Colossomin C and colossomin D were the most inhibitory peptides at 5 ?g/ml against Staphylococcus aureus and Escherichia coli. The methods described in this work and the results obtained are useful for the identification and development of new compounds with antimicrobial activity through the use of computational tools. PMID:23455341

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



Peptide immunotherapy in models of allergic airways disease   

E-print Network

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

MacKenzie, Karen Joan



Equilibrium structures from gas-phase electron-diffraction data   

E-print Network

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

McCaffrey, Philip D



Multimaterial nanostructures Mimicking Electrodeposition in the Gas Phase  

E-print Network

in the Gas Phase [Ã?] Prof. H. O. Jacobs, J. J. Cole,[+] E.-C. Lin,[+] Dr. C. R. Barry Electrical Engineering for Selected-Area Fabrication of Multimaterial Nanostructures Jesse J. Cole, En-Chiang Lin, Chad R. Barry, and Heiko O. Jacobs* An in situ gas-phase process that produces charged streams of Au, Si, TiO2, ZnO, and Ge

Jacobs, Heiko O.


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



Gas phase reaction of sulfur trioxide with water vapor  

Microsoft Academic Search

Sulfur trioxide (SO3) has long been known to react with water to produce sulfuric acid (H2S04). It has been commonly assumed that the gas phase reaction in the Earth`s atmosphere between SO3 and water vapor to produce sulfuric acid vapor is an important step in the production of sulfuric acid aerosol particles. The kinetics of the gas phase reaction of

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



Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model  

Microsoft Academic Search

A hidden Markov model of signal peptides has been devel- oped. It contains submodels for the N-terminal part, the hy- drophobic region, and the region around the cleavage site. For known signal peptides, the model can be used to assign objec- tive boundaries between these three regions. Applied to our data, the length distributions for the three regions are signifi-

Henrik Nielsen; Anders Krogh



Comparison of different gas-phase mechanisms and aerosol modules for simulating particulate matter formation.  


The effects of two gas-phase chemical kinetic mechanisms, Regional Atmospheric Chemistry Mechanism version 2 (RACM2) and Carbon-Bond 05 (CB05), and two secondary organic aerosol (SOA) modules, the Secondary Organic Aerosoi Model (SORGAM) and AER/EPRI/Caltech model (AEC), on fine (aerodynamic diameter < or =2.5 microm) particulate matter (PM2.5) formation is studied. The major sources of uncertainty in the chemistry of SOA formation are investigated. The use of all major SOA precursors and the treatment of SOA oligomerization are found to be the most important factors for SOA formation, leading to 66% and 60% more SOA, respectively. The explicit representation of high-NO, and low-NOx gas-phase chemical regimes is also important with increases in SOA of 30-120% depending on the approach used to implement the distinct SOA yields within the gas-phase chemical kinetic mechanism; further work is needed to develop gas-phase mechanisms that are fully compatible with SOA formation algorithms. The treatment of isoprene SOA as hydrophobic or hydrophilic leads to a significant difference, with more SOA being formed in the latter case. The activity coefficients may also be a major source of uncertainty, as they may differ significantly between atmospheric particles, which contain a myriad of SOA, primary organic aerosol (POA), and inorganic aerosol species, and particles formed in a smog chamber from a single precursor under dry conditions. Significant interactions exist between the uncertainties of the gas-phase chemistry and those of the SOA module. PMID:22168105

Kim, Youngseob; Couvidat, Florian; Sartelet, Karine; Seigneur, Christian



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



Structural and functional characterization of mycobactericidal ubiquitin-derived peptides in model and bacterial membranes  

PubMed Central

The mycobactericidal properties of macrophages include the delivery of bacteria to a hydrolytic lysosome enriched in bactericidal Ubiquitin-derived peptides (Ub-peptides). To better understand interactions of ubiquitin-derived peptides with mycobacteria, we further characterized the structure and function of the bactericidal Ub-peptide Ub2. We found that Ub2 adopts a ?-sheet conformation in the context of sodium dodecyl sulfate (SDS) micelles and phospholipid (POPC:POPG, 1:1) vesicles that was dependent upon the primary sequence of the peptide. Point mutations in Ub2 that reduced the net charge of the peptide decreased Ub2 bactericidal activity. We investigated Ub-peptide function in the context of model membranes and intact bacteria. Differential scanning calorimetry analysis demonstrated that Ub2 inserts into and perturbs model phospholipid vesicles. In addition, we demonstrate that Ub2 disrupts the integrity of the mycobacterial membrane, equilibrates the transmembrane potential and localizes within both the mycobacterial membrane and cytoplasm of treated bacteria. Finally, we identified additional bactericidal Ub-peptides and characterized their activity and structure. This study provides new insight into the mycobactericidal mechanisms of Ub-peptides. PMID:23173767

Foss, Marie H.; Powers, Katelyn M.; Purdy, Georgiana E.



C-peptide promotes lesion development in a mouse model of arteriosclerosis  

PubMed Central

Abstract Patients with insulin resistance and early type 2 diabetes exhibit an increased propensity to develop a diffuse and extensive pattern of arteriosclerosis. Typically, these patients show elevated serum levels of the proinsulin cleavage product C-peptide and immunohistochemical data from our group revealed C-peptide deposition in early lesions of these individuals. Moreover, in vitro studies suggest that C-peptide could promote atherogenesis. This study examined whether C-peptide promotes vascular inflammation and lesion development in a mouse model of arteriosclerosis. ApoE-deficient mice on a high fat diet were treated with C-peptide or control injections for 12 weeks and the effect on lesion size and plaque composition was analysed. C-peptide treatment significantly increased C-peptide blood levels by 4.8-fold without having an effect on glucose or insulin levels, nor on the lipid profile. In these mice, C-peptide deposition in atherosclerotic plaques was significantly increased compared with controls. Moreover, lesions of C-peptide–treated mice contained significantly more macrophages (1.6 ± 0.3% versus 0.7 ± 0.2% positive area; P < 0.01) and more vascular smooth muscle cells (4.8 ± 0.6% versus 2.4 ± 0.3% positive area; P < 0.01). Finally, lipid deposition measured by Oil-red-O staining in the aortic arch was significantly higher in the C-peptide group compared with controls. Our results demonstrate that elevated C-peptide levels promote inflammatory cell infiltration and lesion development in ApoE-deficient mice without having metabolic effects. These data obtained in a mouse model of arteriosclerosis support the hypothesis that C-peptide may have an active role in atherogenesis in patients with diabetes and insulin resistance. PMID:21707916

Vasic, Dusica; Marx, Nikolaus; Sukhova, Galina; Bach, Helga; Durst, Renate; Grüb, Miriam; Hausauer, Angelina; Hombach, Vinzenz; Rottbauer, Wolfgang; Walcher, Daniel



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

Microsoft Academic Search

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

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



Estimation of gas phase mixing in packed beds  

SciTech Connect

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

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



Engine exhaust particulate and gas phase contributions to vascular toxicity.  


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




SciTech Connect

In this chapter we review the spectroscopic data for actinide molecules and the reaction dynamics for atomic and molecular actinides that have been examined in the gas phase or in inert cryogenic matrices. The motivation for this type of investigation is that physical properties and reactions can be studied in the absence of external perturbations (gas phase) or under minimally perturbing conditions (cryogenic matrices). This information can be compared directly with the results from high-level theoretical models. The interplay between experiment and theory is critically important for advancing our understanding of actinide chemistry. For example, elucidation of the role of the 5f electrons in bonding and reactivity can only be achieved through the application of experimentally verified theoretical models. Theoretical calculations for the actinides are challenging due the large numbers of electrons that must be treated explicitly and the presence of strong relativistic effects. This topic has been reviewed in depth in Chapter 17 of this series. One of the goals of the experimental work described in this chapter has been to provide benchmark data that can be used to evaluate both empirical and ab initio theoretical models. While gas-phase data are the most suitable for comparison with theoretical calculations, there are technical difficulties entailed in generating workable densities of gas-phase actinide molecules that have limited the range of species that have been characterized. Many of the compounds of interest are refractory, and problems associated with the use of high temperature vapors have complicated measurements of spectra, ionization energies, and reactions. One approach that has proved to be especially valuable in overcoming this difficulty has been the use of pulsed laser ablation to generate plumes of vapor from refractory actinide-containing materials. The vapor is entrained in an inert gas, which can be used to cool the actinide species to room temperature or below. For many spectroscopic measurements, low temperatures have been achieved by co-condensing the actinide vapor in rare gas or inert molecule host matrices. Spectra recorded in matrices are usually considered to be minimally perturbed. Trapping the products from gas-phase reactions that occur when trace quantities of reactants are added to the inert host gas has resulted in the discovery of many new actinide species. Selected aspects of the matrix isolation data were discussed in chapter 17. In the present chapter we review the spectroscopic matrix data in terms of its relationship to gas-phase measurements, and update the description of the new reaction products found in matrices to reflect the developments that have occurred during the past two years. Spectra recorded in matrix environments are usually considered to be minimally perturbed, and this expectation is borne out for many closed shell actinide molecules. However, there is growing evidence that significant perturbations can occur for open shell molecules, resulting in geometric distortions and/or electronic state reordering. Studies of actinide reactions in the gas phase provide an opportunity to probe the relationship between electronic structure and reactivity. Much of this work has focused on the reactions of ionic species, as these may be selected and controlled using various forms of mass spectrometry. As an example of the type of insight derived from reaction studies, it has been established that the reaction barriers for An+ ions are determined by the promotion energies required to achieve the 5fn6d7s configuration. Gas-phase reaction studies also provide fundamental thermodynamic properties such as bond dissociation and ionization energies. In recent years, an increased number of gas-phase ion chemistry studies of bare (atomic) and ligated (molecular) actinide ions have appeared, in which relevant contributions to fundamental actinide chemistry have been made. These studies were initiated in the 1970's and carried out in an uninterrupted way over the course of the past three d

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



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.



Numerical analysis of an impinging jet reactor for the CVD and gas-phase nucleation of titania  

NASA Astrophysics Data System (ADS)

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.



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

SciTech Connect

Hydrazine is an important rocket fuel, used as both a monopropellant and a bipropellant. This paper presents theoretical results to complement the extensive experimental studies of the gas phase and Ir catalyzed decompositions involved in the monopropellant applications of hydrazine. Gas phase electronic structure theory calculations that include electron correlation predict that numerous molecular and free radical reactions occur within the same energy range as the basic free radical pathways: NN bond breaking around 65 kcal/mol and NH bond breaking around 81 kcal/mol. The data suggest that a revision to existing kinetics modeling is desirable, based on the energetics and the new elementary steps reported herein. A supported Ir-6 octahedron model for the Shell 405 Iridium catalyst used in thrusters was developed. Self-Consistent Field and electron correlation calculations (with core potentials and associated basis sets) find a rich chemistry for hydrazine on this catalyst model. The model catalyst provides dramatically lower NN and NH bond cleavage energies and an even smaller barrier to breaking the NH bond by NH2 abstractions. Thus, the low temperature decomposition over the catalyst is interpreted in terms of consecutive NH2 abstractions to produce ammonia and nitrogen. The higher temperature channel, which has hydrogen and nitrogen products, may be due to a mixture of two mechanisms. These two mechanisms are successive NH cleavages with surface H + H recombinations, and the same type of assisted H-2 eliminations found to occur in the gas phase part of this study.

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



Mechanical Stability of Helical ?-Peptides and a Comparison of Explicit and Implicit Solvent Models  

PubMed Central

Synthetic ?-peptide oligomers have been shown to form stable folded structures analogous to those encountered in naturally occurring proteins. Literature studies have speculated that the conformational stability of ?-peptides is greater than that of ?-peptides. Direct measurements of that stability, however, are not available. Molecular simulations are used in this work to quantify the mechanical stability of four helical ?-peptides. This is achieved by subjecting the molecules to tension. The potential of mean force associated with the resulting unfolding process is determined using both an implicit and an explicit solvent model. It is found that all four molecules exhibit a highly stable helical structure. It is also found that the energetic contributions to the potential of mean force do not change appreciably when the molecules are stretched in explicit water. In contrast, the entropic contributions decrease significantly. As the peptides unfold, a loss of intramolecular energy is compensated by the formation of additional water-peptide hydrogen bonds. These entropic effects lead in some cases to a loss of stability upon cooling the peptides, a phenomenon akin to the cold denaturing of some proteins. While the location of the free energy minimum and the structural helicity of the peptides are comparable in the implicit-solvent and explicit-water cases, it is found that, in general, the helical structure of the molecules is more stable in the implicit solvent model than in explicit water. PMID:18621835

Miller, Clark A.; Gellman, Samuel H.; Abbott, Nicholas L.; de Pablo, Juan J.



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

E-print Network

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

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



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


This article constitutes the fourth part of a general review of the gas-phase protonation thermochemistry of polyfunctional molecules (Part 1: Theory and methods, Mass Spectrom Rev 2007, 26:775-835, Part 2: Saturated basic sites, Mass Spectrom Rev 2012, 31:353-390, Part 3: Amino acids, Mass Spectrom Rev 2012, 31:391-435). This fourth part is devoted to carbonyl containing polyfunctional molecules. After a short reminder of the methods of determination of gas-phase basicity and the underlying physicochemical concepts, specific examples are examined under two major chapters. In the first one, aliphatic and unsaturated (conjugated and cyclic) ketones, diketones, ketoalcohols, and ketoethers are considered. A second chapter describes the protonation energetic of gaseous acids and derivatives including diacids, diesters, diamides, anhydrides, imides, ureas, carbamates, amino acid derivatives, and peptides. Experimental data were re-evaluated according to the presently adopted basicity scale. Structural and energetic information given by G3 and G4 quantum chemistry computations on typical systems are presented. © 2014 Wiley Periodicals, Inc. Mass Spec Rev. PMID:24399766

Bouchoux, Guy



Two-dimensional gas-phase separations coupled to mass spectrometry for analysis of complex mixtures.  


Ion mobility spectrometry (IMS) has been explored for decades, and its versatility in separation and identification of gas-phase ions is well established. Recently, field asymmetric waveform IMS (FAIMS) has been gaining acceptance in similar applications. Coupled to mass spectrometry (MS), both IMS and FAIMS have shown the potential for broad utility in proteomics and other biological analyses. A major attraction of these separations is extremely high speed, exceeding that of condensed-phase alternatives by orders of magnitude. However, modest separation peak capacities have limited the utility of FAIMS and IMS for analyses of complex mixtures. We report 2-D gas-phase separations that join FAIMS to IMS, in conjunction with high-resolution and accuracy time-of-flight (TOF) MS. Implementation of FAIMS/IMS and IMS/MS interfaces using electrodynamic ion funnels greatly improves sensitivity. Evaluation of FAIMS/IMS/TOF performance for a protein mixture tryptic digest reveals high orthogonality between FAIMS and IMS dimensions and, hence, the benefit of FAIMS filtering prior to IMS/MS. The effective peak capacities in analyses of tryptic peptides are approximately 500 for FAIMS/IMS separations and approximately 10(6) for 3-D FAIMS/IMS/MS, providing a potential platform for ultrahigh-throughput analyses of complex mixtures. PMID:16194103

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



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

NASA Astrophysics Data System (ADS)

Preformed ion emission is the main assumption in one of the prevailing theories for peptide and protein ion formation in matrix-assisted laser desorption ionization (MALDI). Since salts are in preformed ion forms in the matrix-analyte mixture, they are ideal systems to study the characteristics of preformed ion emission. In this work, a reliable method to measure the ion yield (IY) in MALDI was developed and used for a solid salt benzyltriphenylphosphonium chloride and two room-temperature ionic liquids 1-butyl-3-methylimidazolium hexafluorophosphate and trihexyltetradecylphosphonium bis(2,4,4-trimethylpentyl)phosphinate. IY for the matrix (?-cyano-4-hydroxycinnamic acid, CHCA) was also measured. Taking 1 pmol salts in 25 nmol CHCA as examples, IYs for three salts were similar, (4-8) × 10-4, and those for CHCA were (0.8-1.2) × 10-7. Even though IYs for the salts and CHCA remained virtually constant at low analyte concentration, they decreased as the salt concentrations increased. Two models, Model 1 and Model 2, were proposed to explain low IYs for the salts and the concentration dependences. Both models are based on the fact that the ion-pair formation equilibrium is highly shifted toward the neutral ion pair. In Model 1, the gas-phase analyte cations were proposed to originate from the same cations in the solid that were dielectrically screened from counter anions by matrix neutrals. In Model 2, preformed ions were assumed to be released from the solid sample in the form of neutral ion pairs and the anions in the ion pairs were assumed to be eliminated via reactions with matrix-derived cations.

Moon, Jeong Hee; Shin, Young Sik; Bae, Yong Jin; Kim, Myung Soo



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

NASA Astrophysics Data System (ADS)

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

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



Atmospheric Consequences of the Hydration in Gas Phase of Aldehydes and Ketones  

NASA Astrophysics Data System (ADS)

Aldehydes and ketones are known oxidation products of biogenic and anthropogenic VOCs and have been observed by field studies to be present in aerosol and cloud particles. While the gas-phase chemistry of these compounds is fairly well understood, their modeled concentration and role in SOA formation remains controversial. In aqueous solution aldehydes and ketones hydrate to form alcohols. We explore the hydration of these compounds in the gas phase and examine the water and photon mediated processes of these hydrates. The formation of hydrates can contribute to aerosol growth and formation by partitioning into clouds and aerosols because of their lower vapor pressure and tendency to form intermolecular hydrogen bonds. Hydration of aldehydes and ketones has important consequences to the atmospheric photochemistry of these organic compounds. The experimental approaches employ Fourier transform spectroscopy (FTS) and cavity ringdown spectroscopy (CRDS) to observe the formation of diols and hydrates by these molecules as a function of relative humidity.

Vaida, V.; Axson, J. L.; Maron, M. K.



CHEMKIN2. General Gas-Phase Chemical Kinetics  

SciTech Connect

CHEMKIN is a high-level tool for chemists to use to describe arbitrary gas-phase chemical reaction mechanisms and systems of governing equations. It remains, however, for the user to select and implement a solution method; this is not provided. It consists of two major components: the Interpreter and the Gas-phase Subroutine Library. The Interpreter reads a symbolic description of an arbitrary, user-specified chemical reaction mechanism. A data file is generated which forms a link to the Gas-phase Subroutine Library, a collection of about 200 modular subroutines which may be called to return thermodynamic properties, chemical production rates, derivatives of thermodynamic properties, derivatives of chemical production rates, or sensitivity parameters. Both single and double precision versions of CHEMKIN are included. Also provided is a set of FORTRAN subroutines for evaluating gas-phase transport properties such as thermal conductivities, viscosities, and diffusion coefficients. These properties are an important part of any computational simulation of a chemically reacting flow. The transport properties subroutines are designed to be used in conjunction with the CHEMKIN Subroutine Library. The transport properties depend on the state of the gas and on certain molecular parameters. The parameters considered are the Lennard-Jones potential well depth and collision diameter, the dipole moment, the polarizability, and the rotational relaxation collision number.

Rupley, F.M. [Sandia National Labs., Livermore, CA (United States)



Sustained Perchlorate Degradation in an Autotrophic, Gas-Phase,  

E-print Network

, The Pennsylvania State University, University Park, Pennsylvania16802 An autotrophic packed-bed biofilm reactorSustained Perchlorate Degradation in an Autotrophic, Gas-Phase, Packed-Bed Bioreactor J O E L P . M feed concentration of 50 mg/L to build up biofilm on the reactor packing. The reactor feed


Ion-Molecule Reactions in Gas Phase Radiation Chemistry.  

ERIC Educational Resources Information Center

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

Willis, Clive



First measurements of gas phase sulphuric acid in the stratosphere  

Microsoft Academic Search

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

F. Arnold; R. Fabian



DSMC Convergence for Microscale Gas-Phase Heat Conduction  

Microsoft Academic Search

The convergence of Bird's Direct Simulation Monte Carlo (DSMC) method is investigated for gas-phase heat conduction at typical microscale conditions. A hard-sphere gas is confined between two fully accommodating walls of unequal temperature. Simulations are performed for small system and local Knudsen numbers, so continuum flow exists outside the Knudsen layers. The ratio of the DSMC thermal conductivity to the

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



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.



Gas-phase silicon micromachining with xenon difluoride  

Microsoft Academic Search

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

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



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

NASA Astrophysics Data System (ADS)

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

Bapat, Parimal V.


Gas-Phase Combustion Synthesis of Nonoxide Nanoparticles in Microgravity  

NASA Technical Reports Server (NTRS)

Gas-phase combustion synthesis is a promising process for creating nanoparticles for the growing nanostructure materials industry. The challenges that must be addressed are controlling particle size, preventing hard agglomerates, maintaining purity, and, if nonoxides are synthesized, protecting the particles from oxidation and/or hydrolysis during post-processing. Sodium-halide Flame Encapsulation (SFE) is a unique methodology for producing nonoxide nanoparticles that addresses these challenges. This flame synthesis process incorporates sodium and metal-halide chemistry, resulting in nanoparticles that are encapsulated in salt during the early stages of their growth in the flame. Salt encapsulation has been shown to allow control of particle size and morphology, while serving as an effective protective coating for preserving the purity of the core particles. Metals and compounds that have been produced using this technology include Al, W, Ti, TiB2, AlN, and composites of W-Ti and Al-AlN. Oxygen content in SFE synthesized nano- AlN has been measured by neutron activation analysis to be as low as 0.54wt.%, as compared to over 5wt.% for unprotected AlN of comparable size. The overall objective of this work is to study the SFE process and nano-encapsulation so that they can be used to produce novel and superior materials. SFE experiments in microgravity allow the study of flame and particle dynamics without the influence of buoyancy forces. Spherical sodium-halide flames are produced in microgravity by ejecting the halide from a spherical porous burner into a quiescent atmosphere of sodium vapor and argon. Experiments are performed in the 2.2 sec Drop Tower at the NASA-Glenn Research Center. Numerical models of the flame and particle dynamics were developed and are compared with the experimental results.

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



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


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



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

PubMed Central

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

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



Gas Phase Theoretical Kinetics for Astrochemistry  

NASA Astrophysics Data System (ADS)

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

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




SciTech Connect

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

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



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


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 under the terms of the BSD open source license. PMID:24688855

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



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 under the terms of the BSD open source license. PMID:24688855

Hamelryck, Thomas; Jensen, Jan H.



Membrane Active Peptides Peptaibols: models for ion channels  

E-print Network

Peptaibols are membrane-active polypeptides iso- lated from fungal sources. They are characterized. Peptaibols exhibit antibiotic activity against bacteria and fungi. Their amphi- pathic nature allows them of the same SFs. Introduction The peptaibols are a family of antibiotic peptides isolated from soil fungi

Wallace, Bonnie Ann


Comparison of two gas-phase chemical kinetic mechanisms of ozone formation over Europe  

Microsoft Academic Search

Two recent gas-phase chemical kinetic mechanisms for tropospheric ozone formation, one based on the lumped-structure approach\\u000a (CB05) and the other based on the lumped-molecule approach (RACM2), are compared for simulations of ozone over Europe. The\\u000a host air quality model is POLAIR3D of the Polyphemus modeling platform. A one-month period (15 July to 15 August 2001) is\\u000a simulated. Model performance is

Youngseob Kim; Karine Sartelet; Christian Seigneur



On Utilizing Optimal and Information Theoretic Syntactic Modeling for Peptide Classification  

NASA Astrophysics Data System (ADS)

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

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


Gas-phase reactivity of ruthenium carbonyl cluster anions.  


Partially-ligated anionic ruthenium carbonyl clusters react with alkenes, arenes, and alkanes in the gas phase; the products undergo extensive C-H activation and lose dihydrogen and carbon monoxide under collision-induced dissociation conditions. Triethylsilane and phenylsilane are also reactive towards the unsaturated clusters, and oxygen was shown to rapidly break down the cluster core by oxidative cleavage of the metal-metal bonds. These qualitative gas-phase reactivity studies were conducted using an easily-installed and inexpensive modification of a commercial electrospray ionization mass spectrometer. Interpretation of the large amounts of data generated in these studies is made relatively straightforward by employing energy-dependent electrospray ionization mass spectrometry (EDESI-MS). PMID:19185511

Henderson, Matthew A; Kwok, Samantha; McIndoe, J Scott



Gas phase fractionation method using porous ceramic membrane  


Flaw-free porous ceramic membranes fabricated from metal sols and coated onto a porous support are advantageously used in gas phase fractionation methods. Mean pore diameters of less than 40 .ANG., preferably 5-20 .ANG. and most preferably about 15 .ANG., are permeable at lower pressures than existing membranes. Condensation of gases in small pores and non-Knudsen membrane transport mechanisms are employed to facilitate and increase membrane permeability and permselectivity.

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



Gas-phase reactivity of ruthenium carbonyl cluster anions  

Microsoft Academic Search

Partially-ligated anionic ruthenium carbonyl clusters react with alkenes, arenes, and alkanes in the gas phase; the products\\u000a undergo extensive C-H activation and lose dihydrogen and carbon monoxide under collision-induced dissociation conditions.\\u000a Triethylsilane and phenylsilane are also reactive towards the unsaturated clusters, and oxygen was shown to rapidly break\\u000a down the cluster core by oxidative cleavage of the metal-metal bonds. These

Matthew A. Henderson; Samantha Kwok; J. Scott McIndoe



Gas-phase photolysis of phorate, a phosphorothioate insecticide  

Microsoft Academic Search

Novel methods are described for determining atmospheric photolysis rates for the moderately volatile pesticide, phorate. The gas-phase sunlight photolysis of this substance was determined in three test systems which include: (1) 3-L borosilicate flasks exposed to sunlight and laboratory solar simulation, (2) 100-L Tedlar sunlight exposed air sample bags, and (3) 12,800-L Tedlar sunlight exposed chamber studies using a photochemically

Vincent R. Hebert; Jason D. Geddes; Joy Mendosa; Glenn C. Miller




Microsoft Academic Search

Total and sectional gas-phase holdups are measured in a wide (0.305 m internal diameter) and long (3.7 m) glass bubble column al ambient conditions as a function of superficial gas velocity. Sectional gas holdup values vary along the length of the column and decrease as the height above the gas distributor plate increases in the transitional and turbulent flow regimes.




The nucleoside uridine isolated in the gas phase.  


Herein we present the first experimental observation of the isolated nucleoside uridine, placed in the gas phase by laser ablation and characterized by Fourier transform (FT) microwave techniques. Free from the bulk effects of their native environments, anti/C2'-endo-g+ conformation has been revealed as the most stable form of uridine. Intramolecular hydrogen bonds involving uracil and ribose moieties have been found to play an important role in the stabilization of the nucleoside. PMID:25683559

Peña, Isabel; Cabezas, Carlos; Alonso, José L



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



[Solid-phase synthesis of peptides modelling the transmembrane segment of bacteriorhodopsin].  


Peptides modelling transmembrane segments C, D, E and G of bacteriorhodopsin were obtained by solid phase method using the conventional Boc strategy. Protected peptides were assembled on PAM polystyrene support. Side chain protecting groups were: Tos for Arg, Bzl for Thr and Ser, cHx for Asp and Glu, Bzl(Cl2) for Tyr, For for Trp, Z(Cl) for Lys. Syntheses were performed on a modernized Beckman 990 synthesizer in the automatic mode. Double couplings by a preformed hydroxybenzotriazole ester were used for all residues. Qualitative and quantitative ninhydrine tests were used to monitor coupling efficiency. Removal of protecting groups and peptide cleavage were achieved by hydrogen fluoride, containing p-cresol and p-thiocresol as scavengers. Preparative reverse phase HPLC was used for purification. Peptide structure and homogeneity were confirmed by amino acid analysis, 1H-NMR and analytical HPLC. PMID:8484815

Chikin, L D; Moshnikova, A B; Grebennikova, Zh O; Kozhich, A T; Ivanov, V T



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.



Gas phase basicities of polyfunctional molecules. Part 3: Amino acids.  


The present article is the third part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules (first part: Mass Spectrom. Rev., 2007, 26:775-835, second part: Mass Spectrom. Rev., 2011, in press). This review is devoted to the 20 proteinogenic amino acids and is divided in two parts. In the first one, the experimental data obtained during the last 30 years using the equilibrium, thermokinetic and kinetic methods are presented. A general re-assignment of the values originating from these various experiments has been done on the basis of the commonly accepted Hunter & Lias 1998 gas-phase basicity scale in order to provide an homogeneous set of data. In the second part, theoretical investigations on gaseous neutral and protonated amino acids are reviewed. Conformational landscapes of both types of species were examined in order to provide theoretical protonation thermochemistry based on the truly identified most stable conformers. Proton affinities computed at the presently highest levels of theory (i.e. composite methods such as Gn procedures) are presented. Estimates of thermochemical parameters calculated using a Boltzmann distribution of conformers at 298K are also included. Finally, comparison between experiment and theory is discussed and a set of evaluated proton affinities, gas-phase basicities and protonation entropies is proposed. PMID:22611554

Bouchoux, Guy



Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes  

NASA Technical Reports Server (NTRS)

Lipid vesicles became the precursors to protocells by acquiring the capabilities needed to survive and reproduce. These include transport of ions, nutrients and waste products across cell walls and capture of energy and its conversion into a chemically usable form. In modem organisms these functions are carried out by membrane-bound proteins (about 30% of the genome codes for this kind of proteins). A number of properties of alpha-helical peptides suggest that their associations are excellent candidates for protobiological precursors of proteins. In particular, some simple a-helical peptides can aggregate spontaneously and form functional channels. This process can be described conceptually by a three-step thermodynamic cycle: 1 - folding of helices at the water-membrane interface, 2 - helix insertion into the lipid bilayer and 3 - specific interactions of these helices that result in functional tertiary structures. Although a crucial step, helix insertion has not been adequately studied because of the insolubility and aggregation of hydrophobic peptides. In this work, we use computer simulation methods (Molecular Dynamics) to characterize the energetics of helix insertion and we discuss its importance in an evolutionary context. Specifically, helices could self-assemble only if their interactions were sufficiently strong to compensate the unfavorable Free Energy of insertion of individual helices into membranes, providing a selection mechanism for protobiological evolution.

Rodriquez-Gomez, D.; Darve, E.; Pohorille, A.



H/D Exchange Levels of Shape-Resolved Cytochrome c Conformers in the Gas Phase  

E-print Network

H/D Exchange Levels of Shape-Resolved Cytochrome c Conformers in the Gas Phase Stephen J. Valentine) in the gas phase are examined by simultaneous ion-mobility and hydrogen-deuterium exchange measurements with the idea that compact structures protect some hydrogens in the gas phase. Many sites that rapidly exchange

Clemmer, David E.


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

EPA Science Inventory

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


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.



Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics  

PubMed Central

A synthetic approach to model the analytical complexity of biological proteolytic digests has been developed. Combinatorial peptide libraries ranging in length between nine and twelve amino acids that represent typical tryptic digests were designed, synthesized and analyzed. Individual libraries and mixtures thereof were studied by replicate liquid chromatography-ion trap mass spectrometry and compared to a tryptic digest of Deinococcus radiodurans. Similar to complex proteome analysis, replicate study of individual libraries identified additional unique peptides. Fewer novel sequences were revealed with each additional analysis in a manner similar to that observed for biological data. Our results demonstrate a bimodal distribution of peptides sorting to either very low or very high levels of detection. Upon mixing of libraries at equal abundance, a length-dependent bias in favor of longer sequence identification was observed. Peptide identification as a function of site-specific amino acid content was characterized with certain amino acids proving to be of considerable importance. This report demonstrates that peptide libraries of defined character can serve as a reference for instrument characterization. Furthermore, they are uniquely suited to delineate the physical properties that influence identification of peptides which provides a foundation for optimizing the study of samples with less defined heterogeneity. PMID:20669997

Bohrer, Brian C.; Li, Yong Fuga; Reilly, James P.; Clemmer, David E.; DiMarchi, Richard D.; Radivojac, Predrag; Tang, Haixu; Arnold, Randy J.



NMR chemical shift study of the interaction of selected peptides with liposomal and micellar models of apoptotic cells.  


The interaction between two peptides previously selected by phage display to target apoptotic cells and phospholipidic models of these cells (liposomes or micelles made of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and/or 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS, phosphatidylserine analog) was studied by the simple analysis of the changes induced on the proton NMR chemical shifts of the peptides. Our approach which does not need healthy and/or apoptotic cells for assessing the affinity of different peptides is fast and efficient and requires small amounts of peptide to determine the association constant, the interacting protons, and the number of interaction sites. The micellar model gave more reliable results than the liposomal one. The preferential interaction of the peptide with DPPS was evidenced by the change of the chemical shifts of specific amino acids of the peptides. Our micellar model is thus well suited to mimic apoptotic cells. PMID:25287364

Van Koninckxloo, Aurore; Henoumont, Céline; Laurent, Sophie; Muller, Robert N; Vander Elst, Luce



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

SciTech Connect

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

Duncan, M.A.



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



The unusually high proton affinity of Aza-18-crown-6 ether: Implications for the molecular recognition of lysine in peptides by lariat crown ethers  

Microsoft Academic Search

Recent studies have shown that 18-crown-6 ether (18C6) will selectively form adducts in the gas phase with small, lysine containing\\u000a peptides. The present study extends this work by investigating the ability of aza-18-crown-6 ether (A18C6) and L1 (a simple\\u000a lariat crown ether derivative of A18C6) to form similar noncovalent adducts with the side chain of lysine in model peptides\\u000a in

Ryan R. Julian; Jesse L. Beauchamp



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

NASA Astrophysics Data System (ADS)

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

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



Revision of the thermodynamics of the proton in gas phase.  


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



Coupling a stochastic soot population balance to gas-phase chemistry using operator splitting  

SciTech Connect

The feasibility of coupling a stochastic soot algorithm to a deterministic gas-phase chemistry solver is investigated for homogeneous combusting systems. A second-order splitting technique was used to decouple the particle population and gas phase in order to solve. A numerical convergence study is presented that demonstrates convergence with splitting step size and particle count for a batch reactor and a perfectly stirred reactor. Simulation results are presented alongside experimental data for a plug flow reactor (PFR) and are compared to a method of moments simulation of a perfectly stirred reactor. Coupling of the soot and chemistry solvers is shown to converge for both systems; however, numerical instabilities present significant challenges in the PSR case. Comparison with the experimental data for a PFR showed good agreement of the soot mass and reasonable agreement of the particle size distribution. Two different soot particle models were used to simulate the PFR: a spherical particle model and a surface-volume model that takes some account of particle shape. The results for the two models are compared. Additionally, the stochastic soot solver is used to track the evolution of the C/H ratio of individual soot particles in the PFR for the first time. (author)

Celnik, Matthew; Patterson, Robert; Kraft, Markus [Department of Chemical Engineering, University of Cambridge, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); Wagner, Wolfgang [Weierstrass Institute for Applied Analysis and Stochastics, Mohrenstrasse 39, D-10117 Berlin (Germany)



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


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



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.



Gas-phase chemiluminescent reactions of ozone with monoterpenes  

NASA Astrophysics Data System (ADS)

Chemiluminescent reactions of ozone with monoterpenes such as linallol, geraniol, d-limonene and ?-pinene have been studied in the gas phase at low pressures. Methylglyoxal phosphorescence has been observed in the first two reactions. Emissions from HCHO( 1A 2) and glyoxal ( 3A u) are observed in the reaction of ozone with d-limonene and formation of excited glyoxal is found to be first order in ozone. The reaction of ozone with ?-pinene gives rise to emission from a ?-dicarbonyl compound and this is found to be first order in ozone. The mechanisms for the formation of excited species are proposed.

Arora, P. K.; Chatha, J. P. S.; Vohra, K. G.



The shape of ibuprofen in the gas phase.  


Ibuprofen's pain-relieving properties arise from its ability to physically block the active site of an enzyme, thus making its structural and conformational properties highly interesting. We here present a conformer-selective high-resolution broadband rotational spectroscopy study of gas-phase ibuprofen. The interpretation of the spectroscopic results is supported by quantum-chemical calculations. We identify four low-energy conformers that differ in the structural arrangement of the isobutyl moiety with respect to the remainder of the molecule. While the isobutyl group shows high structural flexibility - resulting in distinct low-energy conformers - the propanoic acid group favors a stable arrangement. PMID:25582126

Betz, Thomas; Zinn, Sabrina; Schnell, Melanie



Comparison of cyclic delta-opioid peptides with non-peptide delta-agonist spiroindanyloxymorphone (SIOM) using the message-address concept: a molecular modeling study.  


Based upon the message-address concept, this molecular modeling study used the delta-selective agonist spiroindanyloxymorphone (SIOM) as a molecular template for a conformational search and analysis of delta-selective opioid peptides. It was assumed that the tyramine moiety plays the same role for delta-opioid receptor recognition in both peptide and non-peptide ligands. Using 20 reported low-energy conformations of Tyr-cyclo[D-Cys-D-Pen]-OH (JOM-13) for comparison, the geometrical relationship of the two aromatic rings present in SIOM was used for the identification of potential active conformations of JOM-13, from which two delta-receptor-binding models (I and II) were constructed. Models I and II differ from each other in the arrangement of the peptide backbones. To evaluate the two models, a conformational search of two other known delta-selective ligands, [D-Pen2,D-Pen5]enkephalin (DPDPE) and [D-Pen2,L-Pen5]enkephalin (DPLPE) was performed, using the geometrical relationship of the two aromatic rings defined in the two receptor-binding models as a molecular template. Among the conformations generated from the molecular simulation, low-energy conformers of DPDPE and DPLPE conforming to models I and II were identified. Unlike model I, conformers of DPDPE and DPLPE that fit model II contain a cis amide bond in the Gly3 residue. PMID:8877704

Gao, P



Support Vector Machine Classification of Probability Models and Peptide Features for Improved Peptide Identification from Shotgun Proteomics  

SciTech Connect

Proteomics is a rapidly advancing field offering a new perspective to biological systems. Mass spectrometry (MS) is a popular experimental approach because it allows global protein characterization of a sample in a high-throughput manner. The identification of a protein is based on the spectral signature of fragments of the constituent proteins, i.e., peptides. This peptide identification is typically performed with a computational database search algorithm; however, these database search algorithms return a large number of false positive identifications. We present a new scoring algorithm that uses a SVM to integrate database scoring metrics with peptide physiochemical properties, resulting in an improved ability to separate true from false peptide identification from MS. The Peptide Identification Classifier SVM (PICS) score using only five variables is significantly more accurate than the single best database metric, quantified as the area under a Receive Operating Characteristic curve of ~0.94 versus ~0.90.

Webb-Robertson, Bobbie-Jo M.; Oehmen, Chris S.; Cannon, William R.



Incorporating the molecular gas phase in galaxy-size numerical simulations: first applications in dwarf galaxies  

E-print Network

We present models of the evolution of the gaseous and stellar content of galaxies incorporating the formation of H_2 out of HI gas as part of such a model. We do so by formulating a subgrid model for gas clouds that uses well-known cloud scaling relations and solves for the HI-H_2 balance set by the H_2 formation on dust grains and its FUV-induced photodissociation by the temporally and spatially varying interstellar radiation field. This allows the seamless tracking of the evolution of the H_2 gas phase, its precursor Cold Neutral Medium (CNM) HI gas, simultaneously with the star formation. Our most important findings are: a) a significant dependence of the HI-H_2 transition and the resultant H_2 gas mass on the ambient metallicity and the H_2 formation rate, b) the important influence of the characteristic star formation timescale (regulating the ambient FUV radiation field) on the equilibrium H_2 gas mass and c) the possibility of a diffuse H_2 gas phase. Finally, we implement and briefly explore a novel approach of using the ambient H_2 gas mass fraction as a criterion for the onset of star formation. (abridged)

F. I. Pelupessy; P. P. Papadopoulos; P. P. van der Werf



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)



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

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. The EPA required the DOE to ensure that each waste container has no layer of confinement that contains flammable mixtures of gases or mixtures of gases that could become flammable when mixed with air. The EPA also required that sampling of the headspace of waste containers outside inner layers of confinement be representative of the entire void space of the container. The EPA stated that all layers of confinement in a container would have to be sampled until DOE can demonstrate to the EPA that sampling of all layers is unnecessary. A test program was conducted to demonstrate that the gas phase VOC concentration in the void space of each layer of confinement in vented drums can be estimated from measured drum headspace using a theoretical transport model and that sampling of each layer of confinement is unnecessary. This report summarizes the studies performed in the INEL test program and extends them for the purpose of developing a methodology for determining gas phase VOC concentrations in both vented and unvented TRU waste containers. The methodology specifies conditions under which waste drum headspace gases can be said to be representative of drum gases as a whole and describes a method for predicting drum concentrations in situations where the headspace concentration is not representative.

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)



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)



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

NASA Astrophysics Data System (ADS)

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

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



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

PubMed Central

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

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



Gas-phase Dissociation of homo-DNA Oligonucleotides  

NASA Astrophysics Data System (ADS)

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

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



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.



Gas-phase fragmentation analysis of nitro-fatty acids.  


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 HNO(2). 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 (13)C and (15)N 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. PMID:21953257

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



Combinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics  

E-print Network

chromatography-ion trap mass spectrometry and compared to a tryptic digest of Deinococcus radiodurans. Similar and dynamic range.1-3 Current analytical platforms, such as the liquid chromatography- mass spectrometry (LCCombinatorial Libraries of Synthetic Peptides as a Model for Shotgun Proteomics Brian C. Bohrer

Radivojac, Predrag


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

E-print Network

Biomimetic membranes of lipid-peptide model systems prepared on solid support Chenghao Li, Doru. Introduction Compared to isotropic bulk solutions, biomimetic membranes deposited on solid surfaces offer deposited on top of them. Biomimetic interfaces and bio-functional surfaces are therefore an active field

Boyer, Edmond


The peptide-catalyzed stereospecific synthesis of tetroses: A possible model for prebiotic molecular evolution  

PubMed Central

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

Weber, Arthur L.; Pizzarello, Sandra



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



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

SciTech Connect

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

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



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.



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

NASA Technical Reports Server (NTRS)

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.

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



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



Transport and Metabolism of Opioid Peptides across BeWo Cells, An In Vitro Model of the Placental Barrier  

E-print Network

of the transport and metabolism of opioid peptides across the in vitro model of the placental barrier. Opioid peptides, both naturally occurring and their synthetic analogs, are of interest to be developed as potent analgesics and were included in this study...

Ampasavate, Chadarat; Chandorkar, Gurudatt A.; Velde, David Vande; Stobaugh, John F.; Audus, Kenneth L.



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


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

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



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


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

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



Aqueous and Gas Phase Sorption Properties of Mercury in Burned Soils  

NASA Astrophysics Data System (ADS)

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

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



Peptide identification  


Peptides are identified from a list of candidates using collision-induced dissociation tandem mass spectrometry data. A probabilistic model for the occurrence of spectral peaks corresponding to frequently observed partial peptide fragment ions is applied. As part of the identification procedure, a probability score is produced that indicates the likelihood of any given candidate being the correct match. The statistical significance of the score is known without necessarily having reference to the actual identity of the peptide. In one form of the invention, a genetic algorithm is applied to candidate peptides using an objective function that takes into account the number of shifted peaks appearing in the candidate spectrum relative to the test spectrum.

Jarman, Kristin H [Richland, WA; Cannon, William R [Richland, WA; Jarman, Kenneth D [Richland, WA; Heredia-Langner, Alejandro [Richland, WA



Conformational Study of Taurine in the Gas Phase  

NASA Astrophysics Data System (ADS)

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

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



Gas-phase synthesis of magnetic metal/polymer nanocomposites  

NASA Astrophysics Data System (ADS)

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.

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



Silicon Nanowire-Based Devices for Gas-Phase Sensing  

PubMed Central

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

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



Synthesis and Gas Phase Thermochemistry of Germanium-Containing Compounds  

SciTech Connect

The driving force behind much of the work in this dissertation was to gain further understanding of the unique olefin to carbene isomerization observed in the thermolysis of 1,1-dimethyl-2-methylenesilacyclobutane by finding new examples of it in other silicon and germanium compounds. This lead to the examination of a novel phenylmethylenesilacyclobut-2-ene, which did not undergo olefin to carbene rearrangement. A synthetic route to methylenegermacyclobutanes was developed, but the methylenegermacyclobutane system exhibited kinetic instability, making the study of the system difficult. In any case the germanium system decomposed through a complex mechanism which may not include olefin to carbene isomerization. However, this work lead to the study of the gas phase thermochemistry of a series of dialkylgermylene precursors in order to better understand the mechanism of the thermal decomposition of dialkylgermylenes. The resulting dialkylgermylenes were found to undergo a reversible intramolecular {beta} C-H insertion mechanism.

Nathan Robert Classen



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)



Gas-Phase Production of Titanium Nitride and Carbide Powders  

NASA Astrophysics Data System (ADS)

The Bureau of Mines investigated a procedure to produce fine-sized titanium nitride, carbide, and carbonitride powders. These powders, because of their high hardness and abrasion resistance, can be substituted for tungsten carbide in some cutting tool applications. Titanium nitride and carbide powders can be cemented together with nickel. The investigated approach produces titanium nitride by reducing titanium tetrachloride with magnesium or sodium vapor in a nitrogen atmosphere at temperatures between 750 and 1,050°C (1,382 and 1,922°F). Titanium carbide and titanium carbonitride can be formed by adding methane to the nitrogen atmosphere. Titanium tetrachloride reduction efficiencies as high as 98% are achieved. X-ray diffraction analyses showed that the powders contain no major impurities. Because the reactions occur in the gas phase, powders finer than 1 ?m are produced.

Harbuck, Donna D.; Davidson, Charles F.; Shirts, Monte B.



Tautomeric properties and gas-phase structure of acetylacetone.  


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

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



Surfactants from the gas phase may promote cloud droplet formation.  


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



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



Thermochemical determinations and gas-phase transacetalization reactions studied by tandem mass spectrometry  

Microsoft Academic Search

By using the kinetic method, the proton affinity, gas-phase basicity and gas-phase acidity of urea are determined to be 873.5 ± 5.0, 841.6 ± 5.0, and 1513.8 ± 12.0 kJ\\/mol, respectively. Both the gas-phase basicity and acidity of urea are predominantly controlled by resonance stabilization effects in the corresponding protonated and deprotonated amide moieties. ^ The kinetic method is also

Feng Wang



Mechanisms of antimicrobial peptide action: studies of indolicidin assembly at model membrane interfaces by in situ atomic force microscopy.  


We report here on an in situ atomic force microscopy study of the interaction of indolicidin, a tryptophan-rich antimicrobial peptide, with phase-segregated zwitterionic DOPC/DSPC supported planar bilayers. By varying the peptide concentration and bilayer composition through the inclusion of anionic lipids (DOPG or DSPG), we found that indolicidin interacts with these model membranes in one of two concentration-dependent manners. At low peptide concentrations, indolicidin forms an amorphous layer on the fluid domains when these domains contain anionic lipids. At high peptide concentrations, indolicidin appears to initiate a lowering of the gel-phase domains independent of the presence of an anionic lipid. Similar studies performed using membrane-raft mimetic bilayers comprising 30mol% cholesterol/1:1 DOPC/egg sphingomyelin revealed that indolicidin does not form a carpet-like layer on the zwitterionic DOPC domains at low peptide concentrations and does not induce membrane lowering of the liquid-ordered sphingomyelin/cholesterol-rich domains at high peptide concentration. Simultaneous AFM-confocal microscopy imaging did however reveal that indolicidin preferentially inserts into the fluid-phase DOPC domains. These data suggest that the indolicidin-membrane association is influenced greatly by specific electrostatic interactions, lipid fluidity, and peptide concentration. These insights provide a glimpse into the mechanism of the membrane selectivity of antibacterial peptides and suggest a powerful correlated approach for characterizing peptide-membrane interactions. PMID:16459101

Shaw, James E; Alattia, Jean-René; Verity, Jocelyne E; Privé, Gilbert G; Yip, Christopher M



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


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

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



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


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

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



Effects of ammonium sulfate aerosols on the gas-phase reactions of the hydroxyl radical with organic compounds  

NASA Astrophysics Data System (ADS)

Air quality modeling is of seminal importance to the assessment of air pollution control strategies. Traditionally, these models include four basic components: meteorology data, emissions data, transport mechanisms, and chemistry. The gas-phase chemistry portions have been based on kinetic and product laboratory studies in relatively pristine gas-phase environments. However, given the abundance of particles in the atmosphere, it is possible that aerosols can have catalytic effects on gas-phase reaction kinetics. These studies focus on elucidating those effects. Ultimately, the data gained can be used to improve regional air quality models. Relative rate studies of the OH radical initiated reactions of n-hexane, p-xylene, and 1-propanol were conducted in a Tedlar bag in the presence of ammonium sulfate aerosols. Results show that ammonium sulfate aerosols promote the reaction of 1-propanol with OH radicals compared to the reactions of n-hexane with OH radicals and p-xylene with OH radicals. The relative rate of the 1-propanol/·OH reaction versus the n-hexane/·OH reaction increased from 0.85±0.05 in the absence of (NH 4) 2SO 4 aerosols to 1.07±0.05 in the presence of aerosols. Also, the relative rate of the 1-propanol/·OH reaction versus the p-xylene/·OH reaction increased from 0.45±0.03 in the absence of (NH 4) 2SO 4 aerosols to 0.56±0.02 in the presence of aerosols.

Oh, Sewon; Andino, Jean M.


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

E-print Network

solution of 20% piperidine in DMF, which was carried out a total of 4-5 times, each lasting 10 minutes until the Kaiser test for the presence of a primary amine was positive (yielded a strong blue color). Note that for some residues, such as histidine...

Slaton, James Garrett



Molecular cloning of hamster brain and atrial natriuretic peptide cDNAs. Cardiomyopathic hamsters are useful models for brain and atrial natriuretic peptides.  

PubMed Central

Brain and atrial natriuretic peptides (BNP and ANP) are cardiac hormones with diuretic, natriuretic, and vasodilatory activities. Cardiomyopathic hamsters are widely used animal models of heart failure. Due to the structural divergence of BNP among species, examination on pathophysiological roles of BNP using cardiomyopathic hamsters is so far impossible. We therefore isolated hamster BNP and ANP cDNAs, and investigated synthesis and secretion of these peptides in normal and cardiomyopathic hamsters. The COOH-terminal 32-residue peptide of cloned hamster preproBNP with 122 amino acids, preceded by a single arginine residue, supposedly represents hamster BNP showing < 50% homology to rat BNP. Alpha-hamster ANP, 28-residue peptide, is identical to alpha-rat ANP. In hamsters, BNP and ANP occur mainly in the ventricle and the atrium, respectively. The 32-wk-old hypertrophic cardiomyopathic BIO14.6 strain exhibited ventricular hypertrophy. The 32-wk-old dilated cardiomyopathic BIO53.58 strain remained at the stage without apparent heart failure. In BIO14.6 and BIO53.58 strains at this age, ventricular BNP and ANP gene expressions are augmented, and the plasma BNP concentration is elevated to 136 and 108 fmol/ml, respectively, three times greater than the elevated plasma ANP concentration, which well mimics changes of the plasma BNP and ANP concentrations in human heart failure. Cardiomyopathic hamsters, therefore, are useful models to investigate the implication of BNP in human cardiovascular diseases. Images PMID:8083346

Tamura, N; Ogawa, Y; Itoh, H; Arai, H; Suga, S; Nakagawa, O; Komatsu, Y; Kishimoto, I; Takaya, K; Yoshimasa, T



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

NASA Technical Reports Server (NTRS)

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

Radhakrishnan, Krishnan; Bittker, David A.



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


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



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

Microsoft Academic Search

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

Leonor Saiz; Michael L. Klein



Energetics of Selected Gas Phase Ion-Molecule Reactions  

NASA Astrophysics Data System (ADS)

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

Paul, Gary John Charles



CS-AMPPred: An Updated SVM Model for Antimicrobial Activity Prediction in Cysteine-Stabilized Peptides  

PubMed Central

The antimicrobial peptides (AMP) have been proposed as an alternative to control resistant pathogens. However, due to multifunctional properties of several AMP classes, until now there has been no way to perform efficient AMP identification, except through in vitro and in vivo tests. Nevertheless, an indication of activity can be provided by prediction methods. In order to contribute to the AMP prediction field, the CS-AMPPred (Cysteine-Stabilized Antimicrobial Peptides Predictor) is presented here, consisting of an updated version of the Support Vector Machine (SVM) model for antimicrobial activity prediction in cysteine-stabilized peptides. The CS-AMPPred is based on five sequence descriptors: indexes of (i) ?-helix and (ii) loop formation; and averages of (iii) net charge, (iv) hydrophobicity and (v) flexibility. CS-AMPPred was based on 310 cysteine-stabilized AMPs and 310 sequences extracted from PDB. The polynomial kernel achieves the best accuracy on 5-fold cross validation (85.81%), while the radial and linear kernels achieve 84.19%. Testing in a blind data set, the polynomial and radial kernels achieve an accuracy of 90.00%, while the linear model achieves 89.33%. The three models reach higher accuracies than previously described methods. A standalone version of CS-AMPPred is available for download at and runs on any Linux machine. PMID:23240023

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



Exploring the free energy landscape of a model ?-hairpin peptide and its isoform.  


Secondary structural transitions from ?-helix to ?-sheet conformations are observed in several misfolding diseases including Alzheimer's and Parkinson's. Determining factors contributing favorably to the formation of each of these secondary structures is therefore essential to better understand these disease states. ?-hairpin peptides form basic components of anti-parallel ?-sheets and are suitable model systems for characterizing the fundamental forces stabilizing ?-sheets in fibrillar structures. In this study, we explore the free energy landscape of the model ?-hairpin peptide GB1 and its E2 isoform that preferentially adopts ?-helical conformations at ambient conditions. Umbrella sampling simulations using all-atom models and explicit solvent are performed over a large range of end-to-end distances. Our results show the strong preference of GB1 and the E2 isoform for ?-hairpin and ?-helical conformations, respectively, consistent with previous studies. We show that the unfolded states of GB1 are largely populated by misfolded ?-hairpin structures which differ from each other in the position of the ?-turn. We discuss the energetic factors contributing favorably to the formation of ?-helix and ?-hairpin conformations in these peptides and highlight the energetic role of hydrogen bonds and non-bonded interactions. PMID:24825659

Narayanan, Chitra; Dias, Cristiano L



Substrate-free gas-phase synthesis of graphene  

NASA Astrophysics Data System (ADS)

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

Dato, Albert Manglallan


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


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




E-print Network

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

Howk, Jay Christopher



EPA Science Inventory

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


Gas phase photolysis of pinonaldehyde in the presence of sunlight  

NASA Astrophysics Data System (ADS)

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

Jaoui, M.; Kamens, R. M.


CHAOS II: Gas-Phase Abundances in NGC 5194  

E-print Network

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

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



Experimental signals of a nuclear liquid-gas phase transition  

NASA Astrophysics Data System (ADS)

The critical phenomenon of the nuclear liquid-gas phase transition has been investigated in the reactions 64Zn+64Zn, 64Ni+64Ni and 70Zn+70Zn at beam energy of 35 MeV/nucleon. Yields of fragments arising from fragmenting quasi-projectiles (QPs) with different neutron-proton asymmetries were analyzed within the framework of the Landau free energy approach. Fits to the free energy of fragments as a function of fragment asymmetry showed three minima, indicating the system to be in a regime of a first-order phase transition. The QP temperature estimates were extracted from the analysis of N=Z fragment data. Additionally, we make use of a recent method based on quantum fluctuations of fermions to derive temperatures and densities of selected QPs. Critical scaling of these observables is found for systems which differ in neutron to proton asymmetry. The derived critical exponent ? = 0.35 ± 0.01, belongs to the liquid-gas universality class.

Mabiala, J.; Bonasera, A.; Zheng, H.; McIntosh, A. B.; Kohley, Z.; Cammarata, P.; Hagel, K.; Heilborn, L.; May, L. W.; Raphelt, A.; Souliotis, G. A.; Zarrella, A.; Yennello, S. J.



Gas phase production and loss of isoprene epoxydiols.  


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



Electron affinities, gas phase acidities, and potential energy curves: Benzene  

NASA Astrophysics Data System (ADS)

The experimental electron affinities of benzene, Ea(Bz), 0.4 to -4.8 eV, are evaluated. Multiple negative ion states are proposed to account for different electron affinities. The semi-empirical procedure known as ?configuration interaction or unrestricted orbitals to relate experimental quantities to self-consistent field values by estimating electron correlation? (CURES-EC) has several advantages: (i) supports multiple Ea(Bz), (ii) supports the Ea(phenyl) and the D(C bond H,Bz), (iii) supports the gas phase acidity of benzene from the latter, (iv) predicts the singlet-triplet split for the phenyl anion of 1.2(2) eV, and (v) predicts the existence of an excited quartet state of the benzene anion with an Ea(Bz), -2.5(2) eV. Nine ionic Morse curves are calculated from CURES-EC properties and experimental data. These are compared with quantum mechanical crossing ?c? potentials obtained using a subroutine in commercial software and ab initio and density functional theory (DFT) procedures. Curves are calculated for the proposed quartet state of the benzene anion.

Jalbout, A. F.; Trzaskowski, B.; Chen, E. C. M.; Chen, E. S.; Adamowicz, Ludwik


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




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.



Gas phase trichloroethylene removal at low concentration using activated carbon fiber.  


The breakthrough adsorption behaviors of gas phase trichloroethylene in a packed bed of activated carbon fibers (ACF) were investigated. The specific surface area of the ACF was 600 m2/g, 1400 m2/g and 1600 m2/g, respectively, and the concentration of trichloroethylene ranged from 270 mg/m3 to 2700 mg/m3. Results showed that the capacity of adsorption increased with increasing specific surface area, the relationship between the logarithms of 10% breakthrough time and concentration was approximately linear over the experimental range, the breakthrough time decreased with increasing temperature and humidity. The breakthrough curves at different inlet concentration or different temperature can be predicted by several simple theoretical models with good agreements. PMID:14971452

Liu, Jun; Huang, Zheng-hong; Wang, Zhan-sheng; Kang, Fei-yu



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

NASA Astrophysics Data System (ADS)

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

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



Conformational preferences of alpha,alpha-trehalose in gas phase and aqueous solution.  


This work presents an investigation on the conformational preferences of alpha,alpha-trehalose in gas phase and aqueous solution. Eighty-one systematically selected structures were studied at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level, giving rise to 40 unique conformers. The 19 lower energy structures and some selected other were further re-optimized at the B3LYP/6-311++G(d,p) level. The main factors accounting for the conformer's stability were pointed out and discussed. NBO and QTAIM analyses were performed in some selected conformers in order to address the anomeric and exo-anomeric effects as well as intramolecular hydrogen bonding. The effect of solvent water on the relative stability of the conformers was accounted for by applying the conductor-like polarizable continuum model, CPCM. PMID:20709315

Nunes, Sandra C C; Jesus, A J Lopes; Moreno, M João; Eusébio, M Ermelinda S



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

NASA Astrophysics Data System (ADS)

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

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



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

SciTech Connect

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

Garrison, W.M.



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

PubMed Central

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

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



Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results.  


Molecular dynamics simulations of a keratin/peptide complex have been conducted to predict the binding affinity of four different peptides toward human hair. Free energy calculations on the peptides' interaction with the keratin model demonstrated that electrostatic interactions are believed to be the main driving force stabilizing the complex. The molecular mechanics-Poisson-Boltzmann surface area methodology used for the free energy calculations demonstrated that the dielectric constant in the protein's interior plays a major role in the free energy calculations, and the only way to obtain accordance between the free energy calculations and the experimental binding results was to use the average dielectric constant. PMID:22275089

Azoia, Nuno G; Fernandes, Margarida M; Micaêlo, Nuno M; Soares, Cláudio M; Cavaco-Paulo, Artur



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



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.



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

PubMed Central

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

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



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


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



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.



Ion channel models based on self-assembling cyclic peptide nanotubes  

PubMed Central

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

Montenegro, Javier



Gas-Phase Combustion Synthesis of Aluminum Nitride Powder  

NASA Technical Reports Server (NTRS)

Due to its combined properties of high electrical resistivity and high thermal conductivity aluminum nitride (AlN) is a highly desirable material for electronics applications. Methods are being sought for synthesis of unagglomerated, nanometer-sized powders of this material, prepared in such a way that they can be consolidated into solid compacts having minimal oxygen content. A procedure for synthesizing these powders through gas-phase combustion is described. This novel approach involves reacting AlCl3, NH3, and Na vapors. Equilibrium thermodynamic calculations show that 100% yields can be obtained for these reactants with the products being AlN, NaCl, and H2. The NaCl by-product is used to coat the AlN particles in situ. The coating allows for control of AlN agglomeration and protects the powders from hydrolysis during post-flame handling. On the basis of thermodynamic and kinetic considerations, two different approaches were employed to produce the powder, in co-flow diffusion flame configurations. In the first approach, the three reactants were supplied in separate streams. In the second, the AlCl3 and NH3 were premixed with HCl and then reacted with Na vapor. X-ray diffraction (XRD) spectra of as-produced powders show only NaCl for the first case and NaCl and AlN for the second. After annealing at 775 C tinder dynamic vacuum, the salt was removed and XRD spectra of powders from both approaches show only AlN. Aluminum metal was also produced in the co-flow flame by reacting AlCl3 with Na. XRD spectra of as-produced powders show the products to be only NaCl and elemental aluminum.

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



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.



Measurement of Gas-phase Acids in Diesel Exhaust  

NASA Astrophysics Data System (ADS)

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

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



Proton irradiation of DNA nucleosides in the gas phase.  


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

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



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



Measurement of soil/dust arsenic by gas phase chemiluminescence.  


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

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



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

Microsoft Academic Search

Proton transfer energies of phenol and 14 chlorophenols with H2O as a base are analyzed in the gas phase and in solution using quantum chemical methods at the semiempirical and ab initio level of computation. The effect of aqueous solution was accounted for by applying the density functional theory (DFT) implementation of the conductor-like screening model (COSMO) as well as

Gerrit Schüürmann



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.



High resolution trapped ion mobility spectrometery of peptides.  


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

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



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



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


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



Photofragmentation of transition-metal-cluster carbonyls in the gas phase  

SciTech Connect

The available data are reviewed for gas-phase photofragmentation of transition-metal-cluster carbonyls. Several new and sophisticated techniques are discussed in relation to the photodissociation of carbonyls, with emphasis on multiphoton-dissociation/ionization methods. The data base obtained for the gas-phase photodissociation of transition-metal clusters is compared to the well-established body of work on cluster compounds in the condensed phase. The new gas-phase results are discussed in light of the predictions coming from electronic-structure theory concerning the photofragmentation of these cluster compounds. 66 references, 6 figures, 2 tables.

Hollingsworth, W.E.; Vaida, V.



Modeling and prediction of peptide drift times in ion mobility spectrometry using sequence-based and structure-based approaches.  


The mobile behavior of 1481 peptides in ion mobility spectrometry (IMS), which are generated by protease digestion of the Drosophila melanogaster proteome, is modeled and predicted based on two different types of characterization methods, i.e. sequence-based approach and structure-based approach. In this procedure, the sequence-based approach considers both the amino acid composition of a peptide and the local environment profile of each amino acid in the peptide; the structure-based approach is performed with the CODESSA protocol, which regards a peptide as a common organic compound and generates more than 200 statistically significant variables to characterize the whole structure profile of a peptide molecule. Subsequently, the nonlinear support vector machine (SVM) and Gaussian process (GP) as well as linear partial least squares (PLS) regression is employed to correlate the structural parameters of the characterizations with the IMS drift times of these peptides. The obtained quantitative structure-spectrum relationship (QSSR) models are evaluated rigorously and investigated systematically via both one-deep and two-deep cross-validations as well as the rigorous Monte Carlo cross-validation (MCCV). We also give a comprehensive comparison on the resulting statistics arising from the different combinations of variable types with modeling methods and find that the sequence-based approach can give the QSSR models with better fitting ability and predictive power but worse interpretability than the structure-based approach. In addition, though the QSSR modeling using sequence-based approach is not needed for the preparation of the minimization structures of peptides before the modeling, it would be considerably efficient as compared to that using structure-based approach. PMID:21439562

Zhang, Yiming; Jin, Quan; Wang, Shuting; Ren, Ren



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

E-print Network

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

Chenghao Li; Doru Constantin; Tim Salditt



Full membrane spanning self-assembled monolayers as model systems for UHV-based studies of cell-penetrating peptides.  


Biophysical studies of the interaction of peptides with model membranes provide a simple yet effective approach to understand the transport of peptides and peptide based drug carriers across the cell membrane. Herein, the authors discuss the use of self-assembled monolayers fabricated from the full membrane-spanning thiol (FMST) 3-((14-((4'-((5-methyl-1-phenyl-35-(phytanyl)oxy-6,9,12,15,18,21,24,27,30,33,37-undecaoxa-2,3-dithiahenpentacontan-51-yl)oxy)-[1,1'-biphenyl]-4-yl)oxy)tetradecyl)oxy)-2-(phytanyl)oxy glycerol for ultrahigh vacuum (UHV) based experiments. UHV-based methods such as electron spectroscopy and mass spectrometry can provide important information about how peptides bind and interact with membranes, especially with the hydrophobic core of a lipid bilayer. Near-edge x-ray absorption fine structure spectra and x-ray photoelectron spectroscopy (XPS) data showed that FMST forms UHV-stable and ordered films on gold. XPS and time of flight secondary ion mass spectrometry depth profiles indicated that a proline-rich amphipathic cell-penetrating peptide, known as sweet arrow peptide is located at the outer perimeter of the model membrane. PMID:25708639

Franz, Johannes; Graham, Daniel J; Schmüser, Lars; Baio, Joe E; Lelle, Marco; Peneva, Kalina; Müllen, Klaus; Castner, David G; Bonn, Mischa; Weidner, Tobias



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

NASA Technical Reports Server (NTRS)

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

Rhatigan, Jennifer L.



Structure and further fragmentation of significant [a3?+?Na?-?H]+ ions from sodium-cationized peptides.  


A good understanding of gas-phase fragmentation chemistry of peptides is important for accurate protein identification. Additional product ions obtained by sodiated peptides can provide useful sequence information supplementary to protonated peptides and improve protein identification. In this work, we first demonstrate that the sodiated a3 ions are abundant in the tandem mass spectra of sodium-cationized peptides although observations of a3 ions have rarely been reported in protonated peptides. Quantum chemical calculations combined with tandem mass spectrometry are used to investigate this phenomenon by using a model tetrapeptide GGAG. Our results reveal that the most stable [a3?+?Na?-?H](+) ion is present as a bidentate linear structure in which the sodium cation coordinates to the two backbone carbonyl oxygen atoms. Due to structural inflexibility, further fragmentation of the [a3?+?Na?-?H](+) ion needs to overcome several relatively high energetic barriers to form [b2?+?Na?-?H](+) ion with a diketopiperazine structure. As a result, low abundance of [b2?+?Na?-?H](+) ion is detected at relatively high collision energy. In addition, our computational data also indicate that the common oxazolone pathway to generate [b2?+?Na?-?H](+) from the [a3?+?Na?-?H](+) ion is unlikely. The present work provides a mechanistic insight into how a sodium ion affects the fragmentation behaviors of peptides. PMID:25601695

Wang, Huixin; Wang, Bing; Wei, Zhonglin; Zhang, Hao; Guo, Xinhua



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

SciTech Connect

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

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



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

NASA Astrophysics Data System (ADS)

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

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



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


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

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



Fluorescence resonance energy transfer of gas-phase ions under ultra high vacuum and ambient conditions.  


We report evidence for fluorescence resonance energy transfer (FRET) of gas-phase ions under ultra high vacuum conditions (10(-9) mbar) inside a mass spectrometer as well as under ambient conditions inside an electrospray plume. Two different FRET pairs based on carboxyrhodamine 6G (donor) and ATTO590 or Bodipy TR (acceptor) dyes were examined and their gas-phase optical properties were studied. Our measurements indicate a different behavior for the two FRET pairs, which can be attributed to their different conformations in the gas phase. Upon desolvation via electrospray ionization, one of the FRET pairs undergoes a conformational change that leads to disappearance of FRET. This study shows the promise of FRET to obtain a direct correlation between solution and gas-phase structures. PMID:24691138

Frankevich, Vladimir; Chagovets, Vitaliy; Widjaja, Fanny; Barylyuk, Konstantin; Yang, Zhiyi; Zenobi, Renato



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

PubMed Central

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

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




EPA Science Inventory

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


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

E-print Network

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

Wann, Derek A


Fourier transform vibrational-circular-dichroism studies of model peptide molecules  

Microsoft Academic Search

Vibrational circular dichroism (VCD) spectra have been recorded in the NH and C equals O stretching regions for a series of tripodal peptides and peptides containing an unsaturated residue, in order to obtain information about solution conformations.

Mario J. Citra; M. G. Paterlini; Teresa B. Freedman; Laurence A. Nafie; A. Shanzer; Y. Tor; Claudio Pratesi; Osvaldo Pieroni



Gas phase ion\\/molecule reactions and analytical applications by tandem mass spectrometry  

Microsoft Academic Search

Fundamental studies and analytical applications by tandem mass spectrometry are described in this thesis. Gas phase ion\\/molecule reactions involving W(CO)$\\\\sb6$ and perfluorohexane (C$\\\\sb6$F$\\\\sb{14})$ are used to study mechanisms related to ion\\/surface collisions. A single collision event is suggested to be responsible for multiple fluorine atoms pick-up during collisions of tungsten-containing ions with fluorinated self-assembled monolayer surfaces. Gas phase \\

Guodong Chen



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

SciTech Connect

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

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



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.



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


Triplet-state energy values obtained from the gas phase are still scarce. In this study, the triplet-state energies of 58 aroyl compounds, introduced as gas chromatographic peaks at atmospheric pressure and typically 473 K, have been determined from the 0-0 bands of their n --> pi* type phosphorescence spectra in excited nitrogen. Correlations of those gas-phase triplet-state energies with Hammett constants could be observed for substituted acetophenones, benzaldehydes and benzophenones. PMID:10728860

Lin, Z P; Aue, W A



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

NASA Technical Reports Server (NTRS)

A new type of gas phase flow reactor, designed to permit the study of gas phase reactions near 1 atm of pressure, is described. A general solution to the flow/diffusion/reaction equations describing reactor performance under pseudo-first-order kinetic conditions is presented along with a discussion of critical reactor parameters and reactor limitations. The results of numerical simulations of the reactions of ozone with monomethylhydrazine and hydrazine are discussed, and performance data from a prototype flow reactor are presented.

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



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

PubMed Central

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

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



Interactions of mast cell degranulating peptides with model membranes: A comparative biophysical study  

Microsoft Academic Search

In the last decade, there has been renewed interest in biologically active peptides in fields like allergy, autoimmune diseases and antibiotic therapy. Mast cell degranulating peptides mimic G-protein receptors, showing different activity levels even among homologous peptides. Another important feature is their ability to interact directly with membrane phospholipids, in a fast and concentration-dependent way. The mechanism of action of

Marcia Perez dos Santos Cabrera; Manoel Arcisio-Miranda; Laiana Cristina da Costa; Bibiana Monson de Souza; Sabrina Thaís Broggio Costa; Mario Sérgio Palma; João Ruggiero Neto; Joaquim Procopio



Thrombin related peptide TP508 promoted fracture repair in a mouse high energy fracture model  

PubMed Central

Background Thrombin related peptide (TP508) is a 23 amino-acid synthetic peptide that represents a portion of the receptor-binding domain of thrombin molecule. Previous studies have shown that TP508 can accelerate musculoskeletal tissue repair including fracture healing. Objectives The aim of this study was to investigate the effect of TP508 on fracture healing in a murine fracture model representing high energy fracture situation. Methods Eighty CD 1 mice underwent controlled quadriceps muscle crush and open transverse mid diaphyseal femoral fracture that was then fixed with an external fixator. Animals were randomised into four groups to receive an intra-operative dose of either 100 ?g TP508 into the fracture gap; 100 ?g TP508 into the surrounding damaged muscle tissues; 10 ?g TP508 into the fracture gap, or control equal amount of saline into the fracture gap. Radiographic assessment was performed weekly for 5 weeks; histological analysis was at 3 and 5 weeks post fracture and biomechanical testing of the fractured bone was performed at 5 weeks post fracture. Results Mechanical testing data showed that the fracture stiffness was significantly higher in the group receiving 100 ?g TP508 into the fracture gap than other groups. Histological and radiographic analysis revealed a trend of increase in bone formation in the 100 ?g TP508 injected into the fracture gap group compared to the saline control group. It was noted that the scar tissues was significantly less in Group II comparing with the saline control group and there was increased blood vessel formation in the crushed muscles and fracture gap areas in the groups receiving TP508 comparing to the saline control group. Conclusion The results from this study demonstrated the use of thrombin related peptide TP508 in the situation of a high energy fracture can promote fracture healing and reduce the potential complications such as muscle fibrosis and fracture delayed or non-union. PMID:19175943

Hanratty, Brain M; Ryaby, James T; Pan, Xiao-Hua; Li, Gang



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


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

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



[Calculation of flammability limits of gas phases with ethylene oxide in sterilisers].  


A calculation method for flammability limits of gas phases with ethylene oxide in sterilisers was developed. Using the Software GasEq and the newly developed Makro "SterEx" for MS-Excel, flammability limits of mixtures with ethylene oxide, air and inert gases at temperatures between 20 degrees C and 100 degrees C and pressures between 0.4 bar and 1.0 bar can be calculated. This method can be used to easily determine safe operating conditions. The used semi-empirical model is based upon the assumption of constant flame temperature profiles at the flammability limits subject to the EO-concentration for different mixtures. To collect model parameters and to validate the model, several experiments with mixtures of ethylene oxide, nitrogen, carbon dioxide, water vapour and air were carried out to determine flammability limits. To simulate the structural conditions of sterilisers, the experiments were conducted in accordance to DIN EN 1839-B in a closed autoclave with temperatures and pressures relevant for sterilisation processes. The calculation of flammability limits of process gas mixtures with "SterEx" provides good agreement with flammability limits that were determined in experiments. PMID:19037868

Askar, Enis; Schröder, Volkmar; Acikalin, Aydan; Steinbach, Jörg



Infrared spectroscopy of gas-phase PAH molecules. 1: Role of the physical environment  

NASA Astrophysics Data System (ADS)

In the PAH model, polycyclic aromatic hydrocarbons are responsible for the Unidentified IR (UIR) bands observed in emission in many astronomical objects. Although this model states that these molecules are isolated, and at high temperatures (T approximately 1000 K), most laboratory spectra have been obtained for condensed molecules at low temperatures. In this paper, we present the IR absorption spectra (3-20 micrometers), measured for gas phase molecules at high temperatures. For the three studied species, pyrene (C16H10), coronene (C24H12), and ovalene (C32H14), these spectra are compared to those obtained in condensed phases, solid state and rare gas matrices. The relative band intensities clearly depend on the molecular environment. We report absorption cross-sections for gaseous molecules which are better laboratory analogues for interstellar neutral PAHs. The interpretation of the UIR bands observed in strongly irradiated objects with the spectra of neutral gaseous PAHs, leads to a good spectral agreement. A mean number of about 100 atoms per molecule is derived for the PAH distributions in these objects. The determined hydrogen coverage is curiously low (a few %) in general although it can be higher (approximately 40%) in objects that show a strong plateau in the (11-13 micrometers) range. However, PAHs are predicted to be ionized in these regions by current models and our laboratory data may be more relevant for future observations of the diffuse interstellar medium where PAHs are expected to be neutral.

Joblin, C.; D'Hendecourt, L.; Leger, A.; Defourneau, D.



High-order structure and dissociation of gaseous peptide aggregates that are hidden in mass spectra  

Microsoft Academic Search

Injected-ion mobility and high-pressure ion mobility techniques have been used to examine the conformations of bradykinin,\\u000a insulin chain A, and several other peptide ions in the gas phase. Under the experimental conditions employed, evidence for\\u000a multimer formation in the mass spectra of peptides is minimal or absent altogether. However, ion mobility distributions show\\u000a that aggregates of peptides (containing a single

Anne E. Counterman; Stephen J. Valentine; Catherine A. Srebalus; Sheila C. Henderson; Cherokee S. Hoaglund; David E. Clemmer



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



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


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

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



Multifragmentation and the liquid-gas phase transition: an experimental overview  

NASA Astrophysics Data System (ADS)

Two roads are presently being followed in order to establish the existence of a liquid- gas phase transition in finite nuclear systems from nuclear reactions at high energy. The clean experiment of observing the thermodynamic properties of a finite number of nucleons in a container is presently only possible with the computer. Performed with advanced nuclear transport models, it has revealed the first-order character of the transition and allowed the extraction of the pertinent thermodynamic parameters. The validity of the applied theory is being confirmed by comparing its predictions for heavy-ion reactions with exclusive experiments. The second approach is experimentally more direct. Signals of the transition are searched for by analysing reaction data within the framework of thermodynamics of small systems. A variety of potential signals has been investigated and found to be qualitatively consistent with the expectations for the phase transition. Many of them are well reproduced with percolation models which places the nuclear fragmentation into the more general context of partitioning phenomena in finite systems. A wealth of new data on this subject has been obtained in recent experiments, some of them with a new generation of multi-detector devices aiming at higher resolutions, isotopic identification of the fragments, and the coincident detection of neutrons. Isotopic effects in multifragmentation were addressed quite intensively, with particular attention being given to their relation to the symmetry energy and its dependence on density.

Trautmann, W.



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



In vivo Gold Nanoparticle Delivery of Peptide Vaccine Induces Anti-Tumor Immune Response in Prophylactic and Therapeutic Tumor Models.  


Gold nanoparticles (AuNPs) are promising vehicles for cancer immunotherapy, with demonstrated efficacy in immune delivery and innate cell stimulation. Nevertheless, their potential has yet to be assessed in the in vivo application of peptide cancer vaccines. In this study, it is hypothesized that the immune distribution and adjuvant qualities of AuNPs could be leveraged to facilitate delivery of the ovalbumin (OVA) peptide antigen and the CpG adjuvant and enhance their therapeutic effect in a B16-OVA tumor model. AuNP delivery of OVA (AuNP-OVA) and of CpG (AuNP-CpG) enhanced the efficacy of both agents and induced strong antigen-specific responses. In addition, it is found that AuNP-OVA delivery alone, without CpG, is sufficient to promote significant antigen-specific responses, leading to subsequent anti-tumor activity and prolonged survival in both prophylactic and therapeutic in vivo tumor models. This enhanced therapeutic efficacy is likely due to the adjuvant effect of peptide coated AuNPs, as they induce inflammatory cytokine release when cultured with bone marrow dendritic cells. Overall, AuNP-mediated OVA peptide delivery can produce significant therapeutic benefits without the need of adjuvant, indicating that AuNPs are effective peptide vaccine carriers with the potential to permit the use of lower and safer adjuvant doses during vaccination. PMID:25354691

Almeida, Joao Paulo Mattos; Lin, Adam Yuh; Figueroa, Elizabeth Raquel; Foster, Aaron Edward; Drezek, Rebekah Anna



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

PubMed Central

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



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

SciTech Connect

The apparent dissolution rates of gas phase in the co-presence of solid phase were examined by in-room experiments in this study. The apparent dissolution rate of gas phase q (mol/m{sup 3}.s) was generally defined by q=aK{sub L}(?P{sub g}-c), where a (1/m) is specific surface area of the interface between gas and liquid phases, K{sub L} (m/s) is overall mass transfer coefficient, ? (mol/(Pa.m{sup 3})) is reciprocal number of Henry constant, P{sub g} (Pa) is partial pressure of gas phase, and c (mol/m{sup 3}) is the concentration of gas component in liquid phase. As a model gas, CO{sub 2} gas was used. For evaluating the values of K{sub L}, this study monitored pH or the migration rate of the interface between water/gas phases, using some experiments such as the packed beds and the micro channel consisting of granite chip and rubber sheet including a slit. In the results, the values of K{sub L} were distributed in the range from 5.0x10{sup -6} m/s to 5.0x10{sup -7} m/s. These values were small, in comparison with that (7.8x10{sup -4} m/s) obtained from the bubbling test where gas phase was continually injected into deionized water without solid phase. This means that the solid phase limits the local mixing of water phase near gas-liquid interfaces. (authors)

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



What happens to hydrophobic interactions during transfer from the solution to the gas phase? The case of electrospray-based soft ionization methods.  


The disappearance of the hydrophobic effect in the gas phase due to the absence of an aqueous surrounding raises a long-standing question: can noncovalent complexes that are exclusively bound by hydrophobic interactions in solution be preserved in the gas phase? Some reports of successful detection by mass spectrometry of complexes largely stabilized by hydrophobic effect are questionable by the presence of electrostatic forces that hold them together in the gas phase. Here, we report on the MS-based analysis of model supramolecular complexes with a purely hydrophobic association in solution, ?-cyclodextrin, and synthetic adamantyl-containing ligands with several binding sites. The stability of these complexes in the gas phase is investigated by quantum chemical methods (DFT-M06). Compared with the free interaction partners, the inclusion complex between ?-cyclodextrin and adamantyl-containing ligand is shown to be stabilized in the gas phase by ?G = 9.6 kcal mol(-1). The host-guest association is mainly enthalpy-driven due to strong dispersion interactions caused by a large nonpolar interface and a high steric complementarity of the binding partners. Interference from other types of noncovalent binding forces is virtually absent. The complexes are successfully detected via electrospray ionization mass spectrometry, although a high dissociation yield is also observed. We attribute this pronounced dissociation of the complexes to the collisional activation of ions in the atmospheric interface of mass spectrometer. The comparison of several electrospray-based ionization methods reveals that cold spray ionization provides the softest ion generation conditions for these complexes. PMID:21953099

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



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

NASA Astrophysics Data System (ADS)

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

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



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



Synthetic peptides corresponding to protective epitopes of Escherichia coli digalactoside-binding pilin prevent infection in a murine pyelonephritis model.  

PubMed Central

Synthetic peptides corresponding to five segments of a globoside (Gal-Gal)-binding pilin sequence [residues 5-12 (R5-12), R65-75, R93-104, R103-116, and R131-143], cyanogen bromide fragment II (CNBr-II, R53-163), and purified, intact Gal-Gal pili were prepared as vaccines and tested for their efficacy in a BALB/c murine model of pyelonephritis. Intact Gal-Gal pili, CNBr-II, and synthetic peptides R5-12 and R65-75 engendered antibodies that bound the homologous pilin protein and prevented urine and renal colonization in most vaccine recipients. Protection correlated with serum anti-pilus IgG ELISA titers greater than or equal to 1:250. The efficacy afforded by synthetic peptides R5-12 and R65-75 in vaccinated mice indicates that linear "antigenic" determinants in separate cyanogen bromide fragments encode "protective" epitopes. Peptides R93-104, R103-116, and R131-143 lacked efficacy, indicating that not all regions of the sequence are serologically equivalent. The crossreactivity of the peptide antisera for different Gal-Gal pilins was also assessed and correlated with the sequence homology of the corresponding regions. Antiserum to peptide R65-75, which corresponds to a region of unconserved sequence in heterologous pilins, bound only the homologous pilin. Thus, it specifies a type-specific protective epitope. Antiserum to synthetic peptide R5-12, which corresponds to a region of conserved sequence, bound Gal-Gal pilins from seven of eight pyelonephritis strains, indicating that it specifies a crossreacting protective epitope. Images PMID:2448796

Schmidt, M A; O'Hanley, P; Lark, D; Schoolnik, G K



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

Microsoft Academic Search

We studied antitumor effects of peptide extracts from plants on slowly growing mammary adenocarcinoma in CBRB-Rb(8.17)1Iem\\u000a mice used as a model of breast cancer in humans. The antitumor effect of a single injection of the test peptides was evaluated\\u000a by the delay of the appearance and growth of palpable breast cancer in mice over 4 weeks. Peptides from Hypericum perforatum

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



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

PubMed Central

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

Bhowmick, Manishabrata; Fields, Gregg B.



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


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

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



Theoretical study on the properties of linear and cyclic amides in gas phase and water solution.  


The structural and energetic properties of a group of selected amides, of well-known importance for the design of efficient clathrate inhibitors, are calculated with Hartree-Fock and density functional theory, B3LYP, theoretical levels, and a 6-311++g** basis set in the gas phase and a water solution. The conformational behavior of the molecules is studied through the scanning of the torsional potential energy surfaces and by the analysis of the differences in the energetic and structural properties between the isomers. The properties of the amides in water solution are determined within a self-consistent reaction field approach with a polarizable continuum model that allows the calculation of the different contributions to the free energy of solvation. The calculated barriers to rotation are in good agreement with the available experimental data and the comparison of the gas and water results shows the strong effect of the solute polarization. The properties of different amide-water complexes are calculated and compared with available experimental information. PMID:16854032

Aparicio-Martínez, S; Hall, K R; Balbuena, P B



Gas-phase kinetics of hydroxyl radical reactions with alkenes: experiment and theory.  


Reactions of the hydroxyl radical with propene and 1-butene are studied experimentally in the gas phase in a continuous supersonic flow reactor over the range 50?T/K?224. OH radicals are produced by pulsed laser photolysis of H(2)O(2) at 266 nm in the supersonic flow and followed by laser-induced fluorescence in the (1, 0) A(2)?(+)?X(2)?(3/2) band at about 282 nm. These reactions are found to exhibit negative temperature dependences over the entire temperature range investigated, varying between (3.1-19.2) and (4.2-28.6)×10(-11) cm(3) molecule(-1) s(-1) for the reactions of OH with propene and 1-butene, respectively. Quantum chemical calculations of the potential energy surfaces are used as the basis for energy- and rotationally resolved Rice-Ramsperger-Kassel-Marcus calculations to determine the rate constants over a range of temperatures and pressures. The negative temperature dependences of the rate constants are explained by competition between complex redissociation and passage to the adducts by using a model with two transition states. The results are compared and contrasted with earlier studies and discussed in terms of their potential relevance to the atmosphere of Saturn. PMID:20839269

Daranlot, Julien; Bergeat, Astrid; Caralp, Françoise; Caubet, Philippe; Costes, Michel; Forst, Wendell; Loison, Jean-Christophe; Hickson, Kevin M



Probing the reactivity of microhydrated ?-nucleophile in the anionic gas-phase SN 2 reaction.  


To probe the kinetic performance of microsolvated ?-nucleophile, the G2(+)M calculations were carried out for the gas-phase SN 2 reactions of monohydrated and dihydrated ?-oxy-nucleophiles XO(-) (H2 O)n ?=?1,2 (X?=?HO, CH3 O, F, Cl, Br), and ?-sulfur-nucleophile, HSS(-) (H2 O)n ?=?1,2 , toward CH3 Cl. We compared the reactivities of hydrated ?-nucleophiles to those of hydrated normal nucleophiles. Our calculations show that the ?-effect of monohydrated and dihydrated ?-oxy-nucleophiles will become weaker than those of unhydrated ones if we apply a plot of activation barrier as a function of anion basicity. Whereas the enhanced reactivity of monohydrated and dihydrated ROO(-) (R?=?H, Me) could be observed if compared them with the specific normal nucleophiles, RO(-) (R?=?H, Me). This phenomena can not be seen in the comparisons of XO(-) (H2 O)n ?=?1,2 (X?=?F, Cl, Br) with ClC2 H4 O(-) (H2 O)n ?=?1,2 , a normal nucleophile with similar gas basicity to XO(-) (H2 O)n ?=?1,2 . These results have been carefully analyzed by natural bond orbital theory and activation strain model. Meanwhile, the relationships between activation barriers with reaction energies and the ionization energies of ?-nucleophile are also discussed. © 2015 Wiley Periodicals, Inc. PMID:25760852

Zhao, Wen-Yang; Yu, Jie; Ren, Si-Jia; Wei, Xi-Guang; Qiu, Fang-Zhou; Li, Peng-Hui; Li, He; Zhou, Yi-Peng; Yin, Chang-Zhen; Chen, An-Pu; Li, Hao; Zhang, Lei; Zhu, Jun; Ren, Yi; Lau, Kai-Chung



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.



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

NASA Astrophysics Data System (ADS)

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

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



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

NASA Technical Reports Server (NTRS)

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

Powell, Michael R.



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


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

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



Identification of lipopolysaccharide-binding peptide regions within HMGB1 and their effects on subclinical endotoxemia in a mouse model  

PubMed Central

Lipopolysaccharide (LPS) triggers deleterious systemic inflammatory responses when released into the circulation. LPS-binding protein (LBP) in the serum plays an important role in modifying LPS toxicity by facilitating its interaction with LPS signaling receptors, which are expressed on the surface of LPS-responsive cells. We have previously demonstrated that high mobility group box 1 (HMGB1) can bind to and transfer LPS, consequently increasing LPS-induced TNF-? production in human peripheral blood mononuclear cells (PBMCs). We report here on the identification of two LPS-binding domains within HMGB1. Furthermore, using 12 synthetic HMGB1 peptides, we define the LPS-binding regions within each domain. Among them, synthetic peptides HPep1 and HPep6, which are located in the A and B box domains of HMGB1, bind to the polysaccharide and lipid A moieties of LPS respectively. Both HPep1 and HPep6 peptides inhibited binding of LPS to LBP and HMGB1, LBP-mediated LPS transfer to CD14, and cellular uptake of LPS in RAW264.7 cells. These peptides also inhibited LPS-induced TNF-? release in human PBMCs and induced lower levels of TNF-? in the serum in a subclinical endotoxemia mouse model. These results indicate that HMGB1 has two LPS-binding peptide regions that can be utilized to design anti-sepsis or LPS-neutralizing therapeutics. PMID:21660935

Youn, Ju Ho; Kwak, Man Sup; Wu, Jie; Kim, Eun Sook; Ji, Yeounjung; Min, Hyun Jin; Yoo, Ji-Ho; Choi, Ji Eun; Cho, Hyun-Soo; Shin, Jeon-Soo



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


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

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



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.



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

PubMed Central

Our previous finding and the given mechanism of charge and electron transfer in polypeptides are here integrated in a bifunctional model involving electronic charge transfer coupled to special internal rotations. Present molecular dynamics simulations that describe these motions in the chain result in the mean first passage times for the hopping process of an individual step. This “rest and fire” mechanism is formulated in detail—i.e., individual amino acids are weakly coupled and must first undergo alignment to reach the special strong coupling. This bifunctional model contains the essential features demanded by our prior experiments. The molecular dynamics results yield a mean first passage time distribution peaked at about 140 fs, in close agreement with our direct femtosecond measurements. In logic gate language this is a strongly conducting ON state resulting from small firing energies, the system otherwise being a quiescent OFF state. The observed time scale of about 200 fs provides confirmation of our simulations of transport, a model of extreme transduction efficiency. It explains the high efficiency of charge transport observed in polypeptides. We contend that the moderate speed of weak coupling is required in our model by the bifunctionality of peptides. This bifunctional mechanism agrees with our data and contains valuable features for a general model of long-range conductivity, final reactivity, and binding at a long distance. PMID:10655485

Schlag, E. W.; Sheu, Sheh-Yi; Yang, Dah-Yen; Selzle, H. L.; Lin, S. H.



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

Microsoft Academic Search

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

Dalit Bechor; Nir Ben-Tal



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

NASA Astrophysics Data System (ADS)

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 a globally complete picture. In the European projects GEMS and MACC two major reanalyses have been carried out using state-of-the-art chemistry transport models coupled to the ECMWF integrated forecasting system and its sophisticated data assimilation modules. In the reanalyses satellite data from various sensors were assimilated in order to constrain tropospheric (and stratospheric) ozone and CO. In the MACC reanalysis tropospheric NO2 retrievals were also assimilated.The reanalysis simulations were evaluated with independent in-situ data from MOZAIC, the GAW network, the NOAA cooperative sampling network and others. Independent NO2 retrievals from SCIAMACHY were compared with model-derived NO2 columns. The reanalysis simulations are consistently superior to uncoupled model simulations with MOZART, TM5 and MOCAGE and generally yield satisfactory results, even though a number of problems have been identified. Important conclusions from both reanalyses are the lack of constraints in the planetary boundary layer from assimilating only satellite data and the relatively strong sensitivity of reanalysis results to small changes in the model formulation and the input data. This highlights the need to include surface and airborne measurements in the data assimilation framework in the future. Furthermore it becomes evident that accurate up-to-date emission estimates for ozone and aerosol precursors from anthropogenic and biomass burning sources are essential prerequisites.

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



Chiral analyses of peptides by ion/molecule reactions  

NASA Astrophysics Data System (ADS)

Protonated complexes comprised of guest peptides with permethylated hosts ([beta]-cyclodextrin and maltoheptaose) were produced in the gas phase by electrospray ionization and reacted with a gaseous amine in a Fourier transform ion cyclotron resonance mass spectrometer. An exchange reaction was observed whereby the guest peptide was replaced by the gaseous alkyl amine. The exchange reaction was enantioselective and was used to determine enantiomeric excess in mixtures of enantiomers. The nature of the recognition is probed by the selection of the peptides and the use of molecular dynamics calculations.

Grigorean, Gabriela; Cong, Xin; Lebrilla, Carlito B.



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


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



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

SciTech Connect

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

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



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.



The relative importance of gas-phase and heterogeneous processes for polar chlorine activation and subsequent ozone depletion  

NASA Astrophysics Data System (ADS)

Polar stratospheric cloud (PSC) particles are composed of different compounds and exist both in crystalline and in liquid form. Heterogeneous reactions occur on the surfaces and in the bulk of PSCs; these reactions are a prerequisite of polar halogen catalysed ozone loss. Both the formation of PSC particles and their heterogeneous reactivity is strongly temperature dependent. Here we discuss under which conditions the heterogeneous reactivity, and thus the composition of PSC particles, is important for polar ozone loss and under which conditions the speed of gas-phase reactions is rate limiting for chlorine activation and polar ozone loss. We discuss different cases of chlorine activation, both for the Arctic and the Antarctic. We find that for a variety of conditions, including the onset of chlorine activation in early winter, the subsequent completion of chlorine in the course of winter, and in the period of very rapid ozone loss in Antarctic spring, the speed of heterogeneous reactions is not a controlling factor for activation and subsequent ozone loss. However, we present also a case in Arctic spring, where gas-phase and heterogeneous reactions compete. Further, a sensitivity simulation is performed with the chemistry-climate model EMAC; it can be shown that the significance of heterogeneous reactions on ice particles, in comparison to liquid particles, is subordinate regarding chlorine activation and ozone depletion in Antarctic spring.

Müller, Rolf; Wegner, Tobias; Grooß, Jens-Uwe; Kirner, Ole; Drdla, Katja



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.



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.



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.



Characterizing the structures and folding of free proteins using 2-D gas-phase separations: observation of multiple unfolded conformers.  


Understanding the 3-D structure and dynamics of proteins and other biological macromolecules in various environments is among the central challenges of chemistry. Electrospray ionization can often transfer ions from solution to gas phase with only limited structural distortion, allowing their profiling using mass spectrometry and other gas-phase approaches. Ion mobility spectrometry (IMS) can separate and characterize macroion conformations with high sensitivity and speed. However, IMS separation power is generally insufficient for full resolution of major structural variants of protein ions and elucidation of their interconversion dynamics. Here we report characterization of macromolecular conformations using field asymmetric waveform IMS (FAIMS) coupled to conventional IMS in conjunction with mass spectrometry. The collisional heating of ions in the electrodynamic funnel trap between FAIMS and IMS stages enables investigating the structural evolution of particular isomeric precursors as a function of the intensity and duration of activation that can be varied over large ranges. These new capabilities are demonstrated for ubiquitin and cytochrome c, two common model proteins for structure and folding studies. For nearly all charge states, two-dimensional FAIMS/IMS separations distinguish many more conformations than either FAIMS or IMS alone, including some with very low abundance. For cytochrome c in high charge states, we find several abundant "unfolded" isomer series not distinguishable by IMS, possibly corresponding to different "string of beads" geometries. The unfolding of specific ubiquitin conformers selected by FAIMS has been studied by employing their heating in the FAIMS/IMS interface. PMID:16689531

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



Two-dimensional simulation of an oxy-acetylene torch diamond reactor with a detailed gas-phase and surface mechanism  

NASA Astrophysics Data System (ADS)

A two-dimensional model is presented for the hydrodynamics and chemistry of an oxy-acetylene torch reactor for chemical vapor deposition of diamond, and it is validated against spectroscopy and growth rate data from the literature. The model combines the laminar equations for flow, heat, and mass transfer with combustion and deposition chemistries, and includes multicomponent diffusion and thermodiffusion. A two-step solution approach is used. In the first step, a lumped chemistry model is used to calculate the flame shape, temperatures and hydrodynamics. In the second step, a detailed, 27 species / 119 elementary reactions gas phase chemistry model and a 41 species / 67 elementary reactions surface chemistry model are used to calculate radicals and intermediates concentrations in the gas phase and at the surface, as well as growth rates. Important experimental trends are predicted correctly, but there are some discrepancies. The main problem lies in the use of the Miller-Melius hydrocarbon combustion mechanism for rich oxy-acetylene flames. [J. A. Miller and C. F. Melius, Combustion and Flame 91, 21 (1992)]. Despite this problem, some aspects of the diamond growth process are clarified. It is demonstrated that gas-phase diffusion limitations play a minor role in the diamond growth process, which is determined by surface kinetics. Except for atomic hydrogen, gas phase diffusion is also of minor importance for the transport of species in and behind the flame front. Finally, it is shown that penetration of nitrogen from the ambient air into the flame cannot explain the observed changes at the center of the diamond films as reported in the literature.

Okkerse, M.; Kleijn, C. R.; van den Akker, H. E. A.; de Croon, M. H. J. M.; Marin, G. B.



Shallow n(+) junctions in silicon by arsenic gas-phase doping  

NASA Astrophysics Data System (ADS)

Shallow arsenic junctions were formed in short processing times using gas-phase rapid thermal diffusion with arsine or tertiarybutylarsine (TBA). A 60 s gas-phase diffusion at 1100 C using 3.6% arsine in helium at 760 Torr formed 150 nm junctions with a measured sheet resistance of 100 Omega /d'Alembertian . Shallow junctions were also formed with a 12 min diffusion at 900 C using 10% TBA in argon at 10 Torr. These TBA-formed junctions have arsenic concentration at the silicon surface greater than 1 x 10(sup 20) atms/cu cm and a sheet resistance of 244 Omega /d'Alembertian . In addition, TEM cross sections show no process-induced damage at the junction for gas-phase doping.

Ransom, C. M.; Jackson, T. N.; Degelormo, J. F.; Zeller, C.; Kotecki, D. E.; Graimann, C.; Sadana, D. K.; Benedict, J.



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


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)



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

PubMed Central

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



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


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

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



A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates.  

PubMed Central

There is now convincing evidence that the proteasome contributes to the generation of most of the peptides presented by major histocompatibility complex class I molecules. Here we present a model-based kinetic analysis of fragment patterns generated by the 20S proteasome from 20 to 40 residues long oligomeric substrates. The model consists of ordinary first-order differential equations describing the time evolution of the average probabilities with which fragments can be generated from a given initial substrate. First-order rate laws are used to describe the cleavage of peptide bonds and the release of peptides from the interior of the proteasome to the external space. Numerical estimates for the 27 unknown model parameters are determined across a set of five different proteins with known cleavage patterns. Testing the validity of the model by a jack knife procedure, about 80% of the observed fragments can be correctly identified, whereas the abundance of false-positive classifications is below 10%. From our theoretical approach, it is inferred that double-cleavage fragments of length 7-13 are predominantly cut out in "C-N-order" in that the C-terminus is generated first. This is due to striking differences in the further processing of the two fragments generated by the first cleavage. The upstream fragment exhibits a pronounced tendency to escape from second cleavage as indicated by a large release rate and a monotone exponential decline of peptide bond accessibility with increasing distance from the first scissile bond. In contrast, the release rate of the downstream fragment is about four orders of magnitude lower and the accessibility of peptide bonds shows a sharp peak in a distance of about nine residues from the first scissile bond. This finding strongly supports the idea that generation of fragments with well-defined lengths is favored in that temporary immobilization of the downstream fragment after the first cleavage renders it susceptible for a second cleavage. PMID:10968984

Holzhütter, H G; Kloetzel, P M



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

PubMed Central

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

Atkinson, R; Arey, J



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

NASA Astrophysics Data System (ADS)

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

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



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

NASA Technical Reports Server (NTRS)

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

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



Determination of doubly labeled water by gas-phase Fourier transform infrared spectroscopy.  


Both 2H (deuterium) and 18O (oxygen 18) in isotopically enriched water have been detected by gas-phase Fourier transform infrared (FTIR) spectroscopy at 2,720 and 3,661.8 cm-1, respectively. A linear relationship between varying concentrations of each of these isotopes and their absorbance at the above frequencies indicates that gas-phase FTIR may provide a rapid and potentially less expensive approach to measure doubly labeled water in biological fluids for the estimation of energy expenditure and total body water. PMID:7854152

Khaled, M A; Krumdieck, C L; Ong, J L



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

NASA Astrophysics Data System (ADS)

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

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



Biofiltration of mixtures of gas-phase styrene and acetone with the fungus Sporothrix variecibatus  

Microsoft Academic Search

The biodegradation performance of a biofilter, inoculated with the fungus Sporothrix variecibatus, to treat gas-phase styrene and acetone mixtures under steady-state and transient conditions was evaluated. Experiments were carried out by varying the gas-flow rates (0.05–0.4m3h?1), leading to empty bed residence times as low as 17.1s, and by changing the concentrations of gas-phase styrene (0.01–6.3gm?3) and acetone (0.01–8.9gm?3). The total

Eldon R. Rene; Radka Špa?ková; María C. Veiga; Christian Kennes



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.



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

NASA Astrophysics Data System (ADS)

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

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



Model of voluntary ethanol intake in zebrafish: Effect on behavior and hypothalamic orexigenic peptides.  


Recent studies in zebrafish have shown that exposure to ethanol in tank water affects various behaviors, including locomotion, anxiety and aggression, and produces changes in brain neurotransmitters, such as serotonin and dopamine. Building on these investigations, the present study had two goals: first, to develop a method for inducing voluntary ethanol intake in individual zebrafish, which can be used as a model in future studies to examine how this behavior is affected by various manipulations, and second, to characterize the effects of this ethanol intake on different behaviors and the expression of hypothalamic orexigenic peptides, galanin (GAL) and orexin (OX), which are known in rodents to stimulate consumption of ethanol and alter behaviors associated with alcohol abuse. Thus, we first developed a new model of voluntary intake of ethanol in fish by presenting this ethanol mixed with gelatin, which they readily consume. Using this model, we found that individual zebrafish can be trained in a short period to consume stable levels of 10% or 20% ethanol (v/v) mixed with gelatin and that their intake of this ethanol-gelatin mixture leads to pharmacologically relevant blood ethanol concentrations which are strongly, positively correlated with the amount ingested. Intake of this ethanol-gelatin mixture increased locomotion, reduced anxiety, and stimulated aggressive behavior, while increasing expression of GAL and OX in specific hypothalamic areas. These findings, confirming results in rats, provide a method in zebrafish for investigating with forward genetics and pharmacological techniques the role of different brain mechanisms in controlling ethanol intake. PMID:25257106

Sterling, M E; Karatayev, O; Chang, G-Q; Algava, D B; Leibowitz, S F



Fluid dynamic numerical simulation of a gas phase polymerization reactor  

Microsoft Academic Search

SUMMARY This article presents preliminaryuid dynamic simulation results of ethylene polymerization dense ?uidized bed using the two-phaseow numerical code ESTET-ASTRID developed by Electricited e France for CFB boilers and based on the two-?uid modelling approach. The continuous phase consists of gas and the dispersed phase consists of catalyst particles. The particleuctuating motion is modelled using two-separate transport equations, on the

Anne Gobin; Hervé Neau; Olivier Simonin; Jean-Richard Llinas; Vince Reiling; Jean-Lofc Sélo



Pegylation of Antimicrobial Peptides Maintains the Active Peptide Conformation, Model Membrane Interactions, and Antimicrobial Activity while Improving Lung Tissue Biocompatibility following Airway Delivery  

PubMed Central

Antimicrobial peptides (AMPs) have therapeutic potential, particularly for localized infections such as those of the lung. Here we show that airway administration of a pegylated AMP minimizes lung tissue toxicity while nevertheless maintaining antimicrobial activity. CaLL, a potent synthetic AMP (KWKLFKKIFKRIVQRIKDFLR) comprising fragments of LL-37 and cecropin A peptides, was N-terminally pegylated (PEG-CaLL). PEG-CaLL derivatives retained significant antimicrobial activity (50% inhibitory concentrations [IC50s] 2- to 3-fold higher than those of CaLL) against bacterial lung pathogens even in the presence of lung lining fluid. Circular dichroism and fluorescence spectroscopy confirmed that conformational changes associated with the binding of CaLL to model microbial membranes were not disrupted by pegylation. Pegylation of CaLL reduced AMP-elicited cell toxicity as measured using in vitro lung epithelial primary cell cultures. Further, in a fully intact ex vivo isolated perfused rat lung (IPRL) model, airway-administered PEG-CaLL did not result in disruption of the pulmonary epithelial barrier, whereas CaLL caused an immediate loss of membrane integrity leading to pulmonary edema. All AMPs (CaLL, PEG-CaLL, LL-37, cecropin A) delivered to the lung by airway administration showed limited (<3%) pulmonary absorption in the IPRL with extensive AMP accumulation in lung tissue itself, a characteristic anticipated to be beneficial for the treatment of pulmonary infections. We conclude that pegylation may present a means of improving the lung biocompatibility of AMPs designed for the treatment of pulmonary infections. PMID:22430978

Morris, Christopher J.; Beck, Konrad; Fox, Marc A.; Ulaeto, David; Clark, Graeme C.



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

NASA Astrophysics Data System (ADS)

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

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



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


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

El-Shall, M Samy



Computational study of Peptide plane stacking with polar and ionizable amino Acid side chains.  


Parallel and T-shaped stacking interactions of the peptide plane with polar and ionizable amino acid side chains (including aspartic/glutamic acid, asparagine/glutamine, and arginine) are investigated using the quantum mechanical MP2 and CCSD computational methods. It is found that the electrostatic interaction plays an essential role in determining the optimal stacking configurations for all investigated stacking models. For certain complexes, the dispersion interaction also contributes considerably to stacking. In the gas phase, the stacking interaction of the charged system is stronger than that of the neutral system, and T-shaped stacking is generally more preferred than parallel stacking, with the stacking energy in the range of -4 to -18 kcal/mol. The solvation effect overall weakens stacking, especially for the charged system and the T-shaped stacking configurations. In water, the interaction energies of different stacking models are comparable. PMID:25826573

Wang, Yefei; Wang, Jia; Yao, Lishan



Terahertz Time Domain Gas-phase Spectroscopy of Carbon Monoxide  

NASA Astrophysics Data System (ADS)

Free induction decay signals emitted from Carbon Monoxide (CO) excited by sub-picosecond pulses of Terahertz (THz) radiation are directly measured in the time domain and compared to model calculations using a linear dispersion model to good agreement. Best fitting techniques of the data using the model allow the self-pressure broadening of CO to be measured across a range of absolute pressures, and the rotational constant to be determined. We find B V = 5.770 ± 0.003 × 1010 Hz in agreement with previous measurements. A partial pressure limit of detection for CO of 7900 ppm is estimated at atmosphere through extrapolating the calculated commensurate echo peaks down to low pressures with respect to the RMS noise floor of our THz time domain spectroscopy (THz-TDS) apparatus, which implies a limit of detection in the range of 40 ppm for commercial THz-TDS systems.

Kilcullen, Patrick; Hartley, I. D.; Jensen, E. T.; Reid, M.



Terahertz Time Domain Gas-phase Spectroscopy of Carbon Monoxide  

NASA Astrophysics Data System (ADS)

Free induction decay signals emitted from Carbon Monoxide (CO) excited by sub-picosecond pulses of Terahertz (THz) radiation are directly measured in the time domain and compared to model calculations using a linear dispersion model to good agreement. Best fitting techniques of the data using the model allow the self-pressure broadening of CO to be measured across a range of absolute pressures, and the rotational constant to be determined. We find B V = 5.770 ± 0.003 × 1010 Hz in agreement with previous measurements. A partial pressure limit of detection for CO of 7900 ppm is estimated at atmosphere through extrapolating the calculated commensurate echo peaks down to low pressures with respect to the RMS noise floor of our THz time domain spectroscopy (THz-TDS) apparatus, which implies a limit of detection in the range of 40 ppm for commercial THz-TDS systems.

Kilcullen, Patrick; Hartley, I. D.; Jensen, E. T.; Reid, M.



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.



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



Comparison of collision-induced dissociation and electron-induced dissociation of singly protonated aromatic amino acids, cystine and related simple peptides using a hybrid linear ion trap–FT-ICR mass spectrometer  

Microsoft Academic Search

The gas-phase fragmentation reactions of singly protonated aromatic amino acids, their simple peptides as well as simple models for intermolecular disulfide bonds have been examined\\u000a using a commercially available hybrid linear ion trap–Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer.\\u000a Low-energy collision-induced dissociation (CID) reactions within the linear ion trap are compared with electron-induced dissociation\\u000a (EID) reactions within the FT-ICR

Hadi Lioe; Richard A. J. O’Hair



Gas phase pulse etching of silicon for MEMS with xenon difluoride  

Microsoft Academic Search

Xenon difluoride is an isotropic gas-phase etchant of silicon which has advantages in some aspects over anisotropic etchants such as KOH, EDP, and TMAH. An inexpensive, small, vacuum system is described for `pulse etching' single crystal silicon wafers (standard CMOS substrates) for releasing microelectromechanical systems (MEMS) devices. Results are presented of etching protocols from several silicon substrates which had been

I. W. T. Chan; K. B. Brown; R. P. W. Lawson; A. M. Robinson; Yuan Ma; D. Strembicke



The ozonizer discharge as a gas-phase advanced oxidation process  

Microsoft Academic Search

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




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


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

Zhu, Hongying; Huang, Guangming




EPA Science Inventory

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



EPA Science Inventory

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



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...



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...



EPA Science Inventory

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



EPA Science Inventory

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


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

Microsoft Academic Search

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

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



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

E-print Network

Methane-to-Methanol Conversion by Gas-Phase Transition Metal Oxide Cations: Experiment and Theory-phase transition metal oxide cations can convert methane to methanol. Methane activation by MO+ is discussed such as methanol has attracted great experimental and theoretical interest due to its importance as an industrial

Metz, Ricardo B.


Specific and reproducible gas sensors utilizing gas-phase chemical reaction on organic transistors.  


Utilizing a textbook reaction on the surface of an organic active channel, achieves sensitive detection of HCl, NH3 and NO2, with good selectivity, excellent reproducibility, and satisfactory stability. These results reveal gas-phase reaction assisted detection as a unique and promising approach to construct practical applicable gas sensors with typical organic transistors. PMID:24510689

Zang, Yaping; Zhang, Fengjiao; Huang, Dazhen; Di, Chong-an; Meng, Qing; Gao, Xike; Zhu, Daoben



Bond-specific dissociation following excitation energy transfer for distance constraint determination in the gas phase.  


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

Hendricks, Nathan G; Lareau, Nichole M; Stow, Sarah M; McLean, John A; Julian, Ryan R



Gas phase dispersion in compost as a function of different water contents and air flow rates  

Microsoft Academic Search

Gas phase dispersion in a natural porous medium (yard waste compost) was investigated as a function of gas flow velocity and compost volumetric water content using oxygen and nitrogen as tracer gases. The compost was chosen because it has a very wide water content range and because it represents a wide range of porous media, including soils and biofilter media.

Prabhakar Sharma; Tjalfe G. Poulsen



Evaluated Gas Phase Basicities and Proton Affinities of Molecules: An Update  

Microsoft Academic Search

The available data on gas-phase basicities and proton affinities of approximately 1700 molecular, radical and atomic neutral species are evaluated and compiled. Tables of the data are sorted (1) according to empirical formula and (2) according to evaluated gas basicity. This publication constitutes an update of a similar evaluation published in 1984.

Edward P. L. Hunter; Sharon G. Lias



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

Microsoft Academic Search

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

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



Supporting Information First detection of methylgermylene in the gas-phase and time resolved study of  

E-print Network

1 Supporting Information First detection of methylgermylene in the gas-phase and time resolved anhydrous magnesium sulphate, filtered, and the solvent removed by distillation. Vacuum distillation as reference. Low resolution mass spectra were determined by GC/MS, using a Hewlett-Packard 5890II gas

Leigh, William J.


Kinetics of the initial stage of isothermal gas phase formation D. Kashchiev and A. Firoozabadi  

E-print Network

other and coalescenceis of no importance.The kinetics of the initial stageof the processKinetics of the initial stage of isothermal gas phase formation D. Kashchiev and A. Firoozabadi December 1992) A theoretical description is proposedof the kinetics of the initial stageof

Firoozabadi, Abbas



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...


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

E-print Network

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

Davis, Ben G.


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

SciTech Connect

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

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



Gas Phase Catalytic Oxidation of ?-Picoline to Nicotinic Acid: Catalysts, Mechanism and Reaction Kinetics  

Microsoft Academic Search

An overview of the fundamental studies on a new method of nicotinic acid synthesis by the gas phase catalytic oxidation of ?-picoline by oxygen is presented. The nature of active component in vanadia catalysts and reactivity of vanadium species are considered. Common features and differences in the mechanistic steps of nicotinic acid formation on various catalysts investigated by in situ

Tamara V. Andrushkevich; Elena V. Ovchinnikova




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,


The control of gas phase kinetics to maximize densification during chemical vapor infiltration  

Microsoft Academic Search

A serious problem during the fabrication of composite materials by isothermal chemical vapor infiltration is that the matrix forms more rapidly at the external edges of the body and traps a large amount of porosity inside. In theory, this problem can be eliminated by controlling the gas-phase kinetics to obtain densification which is more rapid in the center of a

Brian W. Sheldon



DOI: 10.1002/chem.200901830 Hydration of Sugars in the Gas Phase: Regioselectivity and Conformational  

E-print Network

DOI: 10.1002/chem.200901830 Hydration of Sugars in the Gas Phase: Regioselectivity and Conformational Choice in N-Acetyl Glucosamine and Glucose Emilio J. Cocinero,[a] E. Cristina Stanca-Kaposta,[a, c*[a] Introduction N-Acetyl glucosamine (GlcNAc) and glucose (Glc) are the primary building blocks of many

Davis, Ben G.


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

E-print Network

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

Wysocki, Vicki H.


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

NASA Technical Reports Server (NTRS)

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

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




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...



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...


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


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

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



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



Rate constants for the homogeneous gas-phase Al/HCl combustion chemistry  

E-print Network

Rate constants for the homogeneous gas-phase Al/HCl combustion chemistry Mark T. Swiharta Engineering, University at Buffalo (SUNY), Buffalo, NY 14260-4200, USA b Laboratoire de Combustion et Syste Orleans cedex 2, France c Laboratoire de Combustion et Syste`mes Re´actifs (LCSR), CNRS, 1C, av. de la

Swihart, Mark T.


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

E-print Network

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

Schlegel, H. Bernhard


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

E-print Network

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


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

E-print Network

Assembling gas-phase reaction mechanisms for high temperature inorganic systems based on quantum chemistry calculations and reaction rate theories Mark T. Swihart* Department of Chemical Engineering quantum chemistry and reaction rate theories. In addition, for both of these cases there is a database

Swihart, Mark T.



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...



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...


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

ERIC Educational Resources Information Center

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

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



Source reconciliation of atmospheric gas-phase and particle-phase pollutants during a severe photochemical smog episode.  


A comprehensive organic compound-based receptor model is developed that can simultaneously apportion the source contributions to atmospheric gas-phase organic compounds, semivolatile organic compounds, fine particle organic compounds, and fine particle mass. The model is applied to ambient data collected at four sites in the south coast region of California during a severe summertime photochemical smog episode, where the model determines the direct primary contributions to atmospheric pollutants from 11 distinct air pollution source types. The 11 sources included in the model are gasoline-powered motor vehicle exhaust, diesel engine exhaust, whole gasoline vapors, gasoline headspace vapors, organic solvent vapors, whole diesel fuel, paved road dust, tire wear debris, meat cooking exhaust, natural gas leakage, and vegetative detritus. Gasoline engine exhaust plus whole gasoline vapors are the predominant sources of volatile organic gases, while gasoline and diesel engine exhaust plus diesel fuel vapors dominate the emissions of semivolatile organic compounds from these sources during the episode studied at all four air monitoring sites. The atmospheric fine particle organic compound mass was composed of noticeable contributions from gasoline-powered motor vehicle exhaust, diesel engine exhaust, meat cooking, and paved road dust with smaller but quantifiable contributions from vegetative detritus and tire wear debris. In addition, secondary organic aerosol, which is formed from the low-vapor pressure products of gas-phase chemical reactions, is found to be a major source of fine particle organic compound mass under the severe photochemical smog conditions studied here. The concentrations of secondary organic aerosol calculated in the present study are compared with previous fine particle source apportionment results for less intense photochemical smog conditions. It is shown that estimated secondary organic aerosol concentrations correlate fairly well with the concentrations of 1,2-benzenedicarboxylic acid in the atmospheric fine particle mass, indicating that aromatic diacids may be useful in the quantification of certain sources of secondary organic aerosol in the atmosphere. PMID:12322754

Schauer, James J; Fraser, Matthew P; Cass, Glen R; Simoneit, Bernd R T



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

NASA Astrophysics Data System (ADS)

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

Cunningham, Joy; English, Douglas



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



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


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

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



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

SciTech Connect

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

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



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



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



The interstellar gas-phase chemistry of HCN and HNC  

NASA Astrophysics Data System (ADS)

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

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



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

NASA Astrophysics Data System (ADS)

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

Miller, Joseph Daniel


Conformations and spectroscopic properties of laccaic acid A in the gas phase and in implicit water  

NASA Astrophysics Data System (ADS)

Conformations and spectroscopic properties of laccaic acid A (lacA) were studied by means of the experimental and theoretical approaches. The minimum energy conformers of lacA in the gas phase and in implicit water obtained from the B3LYP/6-311G(d,p) calculations displayed the same orientation of the COOH and OH groups on the anthraquinone-based component. The intramolecular hydrogen bonds (H-bonds) formed between the COOH, Cdbnd O and OH groups are very strong. In contrast, the orientations of the Ph(OH)CH2CH2NHCOCH3 substituent moiety on the anthraquinone-based component in the gas phase and in implicit water are completely different. The substituent prefers to bind with the anthraquinone-based component in the gas phase while it moves away from the anthraquinone-based component in implicit water. The calculated IR spectra of the two lowest-lying energy conformers of lacA in the gas phase fit to the experimental FTIR spectrum. The full assignments of the vibrational modes with the correlated vibrational wavenumbers of those conformers were proposed here, for the first time. The intramolecular H-bond formations in lacA can cause the shift of the vibrational wavenumber for the COOH, Cdbnd O, OH and NH groups as compared to the normal vibrations of these groups. The NMR spectra showed that the stabilities of the two lowest-lying energy conformers of lacA in the gas phase are comparable and this is consistent with their computational energies. The UV-Vis spectra of the lowest-lying energy conformers of lacA in implicit water were compared with the experimental UV-Vis spectrum. The calculations suggested that the electronic transition in the visible region involves with the singlet ? ? ?* excitation which the electron density transfers to a COOH group on the anthraquinone ring.

Dokmaisrijan, Supaporn; Payaka, Apirak; Tantishaiyakul, Vimon; Chairat, Montra; Nimmanpipug, Piyarat; Lee, Vannajan Sanghiran



Gas-phase Reactions of Hydride Anion, H-  

NASA Astrophysics Data System (ADS)

Rate constants were measured at 300 K for the reactions of the hydride anion, H-, with neutral molecules C2H2, H2O, CH3CN, CH3OH, (CH3)2CO, CH3CHO, N2O, CO2, O2, CO, CH3Cl, (CH3)3CCl, (CH3CH2)2O, C6H6, and D2 using a flowing-afterglow instrument. Experimental work was supplemented by ab initio calculations to provide insight into the viability of reaction pathways. Our reported rate constants should prove useful to models of astrophysical environments where conditions prevail for the existence of both H- and neutral species. The variety of neutral reactants studied includes representative species from prototypical chemical groups, effectively mapping reactivity trends for the hydride anion.

Martinez, Oscar, Jr.; Yang, Zhibo; Demarais, Nicholas J.; Snow, Theodore P.; Bierbaum, Veronica M.



Identification of gas phase alkali species released during biomass combustion  

SciTech Connect

Direct sampling, molecular beam, mass spectrometry has been used to monitor alkali metal-containing vapors released during the combustion of a wide variety of biomass feedstocks that have potential use for power generation. Interpretation of the mass spectral data has revealed correlations between alkali metal release and feedstock composition. Alkali chlorides are the primary form of alkali metal vapor released during the combustion of grasses and straws. Alkali hydroxides are the most abundant alkali species released during the combustion of feedstocks with high alkali metal and low chlorine. Primary alkali metal release during the combustion of relatively low alkali metal woody feedstocks is from alkali sulfates. The chlorine content of biomass has been identified as an important parameter that facilitates alkali metal release. These results will ultimately be used to develop a predictive model that relates feedstock composition to fouling and slagging behavior in power generating facilities.

Dayton, D.C.; French, R.J.; Milne, T.A. [National Renewable Energy Lab., Golden, CO (United States)



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


Peptide nucleic acid (PNA): A model structure for the primordial genetic material?  

Microsoft Academic Search

It is proposed that the primordial genetic material could have been peptide nucleic aicds,i.e., DNA analogues having a peptide backbone. PNA momomers based on the amino acid, a, ?-diaminobutyric acid or ornithine are suggested as compounds that could have been formed in the prebiotic soup. Finally, the possibility of a PNA\\/RNA world is presented, in which PNA constitutes the stable

Peter Egil Nielsen



Radiolabeled RGD Peptides to Image Angiogenesis in Swine Model of Hibernating Myocardium  

PubMed Central

Objectives To image angiogenesis produced by endomyocardial injection of phVEGF165 in a swine model of hibernating myocardium using [123I]Gluco-RGD targeting the ?v?3 integrins. Background A non-invasive test to monitor the efficacy of therapy inducing angiogenesis is needed. The interaction between extracellular matrix and endothelial cells in sprouting capillaries is effected primarily by ?v?3 integrins that bind through RGD motifs. Methods At 21±4 days after LCx ameroid constrictor (AM) placement, 8 swine received endomyocardial injection of 1.2 mg phVEGF165 divided into 6 sites and 6 swine received saline (S) using non-fluoroscopic 3D endocardial mapping system (Noga) guided delivery. After 20±6 days 13 animals were injected with 6.4±1.7 mCi [123I]Gluco-RGD, one VEGF injected animal with I-123 labeled peptide control and all animals with 2.5±0.4 mCi of Tl-201 and underwent SPECT imaging. Blood flow and echocardiographic measurements were made at both time points and tissue analyzed for fibrosis and capillary density by lectin staining. Results Hibernating myocardium in the AM territory at time of injections was documented by reduced wall thickening compared to remote. Ratio of MBF in LCx/LAD territories increased by 15±11% in the VEGF animals and fell 13±12% in S injected (p<0.01). There was a small increase in wall thickening (WT) in AM territory following VEGF (8 ± 17%) while in S injected WT fell by 23 ± 31% (p=0.01vs.VEGF). Lectin staining as % positive tissue staining for ameroid territory was higher in VEGF injected compared to S injected (2.5±0.1.5 vs. 0.87±0.52%, p=0.01). Focal uptake of [123I]Gluco-RGD corresponding to Tl-201 defects was seen in VEGF injected but not in S injected animals. [123I]Gluco-RGD uptake in the ameroid territory as % ID correlated with lectin staining (R2=0.80, p=0.002). Conclusions These data suggest that SPECT imaging of radiolabeled RGD peptides may be useful non-invasive method to monitor therapy that induces angiogenesis in the heart. PMID:19198663

Johnson, Lynne L; Schofield, Lorraine; Donahay, Tammy; Bouchard, Mark; Poppas, Athena; Haubner, Roland



Activity of Potent and Selective Host Defense Peptide Mimetics in Mouse Models of Oral Candidiasis  

PubMed Central

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

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



Peptide-Mediated Liposomal Doxorubicin Enhances Drug Delivery Efficiency and Therapeutic Efficacy in Animal Models  

PubMed Central

Lung cancer ranks among the most common malignancies, and is the leading cause of cancer-related mortality worldwide. Chemotherapy for lung cancer can be made more specific to tumor cells, and less toxic to normal tissues, through the use of ligand-mediated drug delivery systems. In this study, we investigated the targeting mechanism of the ligand-mediated drug delivery system using a peptide, SP5-2, which specifically binds to non-small cell lung cancer (NSCLC) cells. Conjugation of SP5-2 to liposomes enhanced the amount of drug delivered directly into NSCLC cells, through receptor-mediated endocytosis. Functional SP5-2 improved the therapeutic index of Lipo-Dox by enha