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1

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

Microsoft Academic Search

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

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

2001-01-01

2

Modelling peptide-metal dication interactions: formamide-Ca2+ reactions in the gas phase.  

PubMed

The collision induced dissociation of formamide-Ca(2+) complexes produced in the gas phase through nanoelectrospray ionization yields as main products ions [CaOH](+), [HCNH](+), [Ca(NH(2))](+), HCO(+) and [Ca(NH(3))](2+) and possibly [Ca(H(2)O)](2+) and [C,O,Ca](2+), the latter being rather minor. The mechanisms behind these fragmentation processes have been established by analyzing the topology of the potential energy surface by means of B3LYP calculations carried out with a core-correlated cc-pWCVTZ basis set. The Ca(2+) complexes formed by formamide itself and formimidic acid play a fundamental role. The former undergoes a charge separation reaction yielding [Ca(NH(2))](+) + HCO(+), and the latter undergoes the most favorable Coulomb explosion yielding [Ca-OH](+) + [HCNH](+) and is the origin of a multistep mechanism which accounts for the observed loss of water and HCN. Conversely, the other isomer of formamide, amino(hydroxyl)carbene, does not play any significant role in the unimolecular reactivity of the doubly charged molecular cation. PMID:22892540

Eizaguirre, Ane; Mó, Otilia; Yáñez, Manuel; Salpin, Jean-Yves; Tortajada, Jeanine

2012-10-01

3

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

4

Modeling the interactions between peptide functions and Sr2+: formamide-Sr2+ reactions in the gas phase.  

PubMed

The interactions between formamide, which can be considered a prototype of a peptide function, and Sr(2+) have been investigated by combining nanoelectrospray ionization/mass spectrometry techniques and G96LYP DFT calculations. For Sr an extended LANL2DZ basis set was employed, together with a 6-311+G(3df,2p) basis set expansion for the remaining atoms of the system. The observed reactivity seems to be dominated by the Coulomb explosion process yielding [SrOH](+) + [HNCH](+), which are the most intense peaks in the MS/MS spectra. Nevertheless, additional peaks corresponding to the loss of HNC and CO indicate that the association of Sr(2+) to water or to ammonia leads to long-lived doubly charged species detectable in the timescale of these experimental techniques. The topology of the calculated potential energy surface permits us to establish the mechanisms behind these processes. Although the interaction between the neutral base and Sr(2+) is essentially electrostatic, the polarization triggered by the doubly charged metal ion results in the activation of several bonds, and favors different proton transfer mechanisms required for the formation of the [SrOH](+), [SrOH(2)](2+) and [SrNH(3)](2+) products. PMID:21901223

Eizaguirre, Ane; Mó, Otília; Yáñez, Manuel; Salpin, Jean-Yves

2011-09-08

5

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

PubMed Central

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

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

2011-01-01

6

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.

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

2005-01-01

7

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

NASA Astrophysics Data System (ADS)

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

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

2005-02-01

8

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

PubMed

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

Tao, Yuanqi; Julian, Ryan R

2013-07-09

9

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

NASA Astrophysics Data System (ADS)

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

Tao, Yuanqi; Julian, Ryan R.

2013-11-01

10

A condensed gas–phase chemical model and its application  

Microsoft Academic Search

Using the “lumped mechanism” and “counting species” methods, we developed a condensed gas-phase chemical model based on a\\u000a simplified one. The modified quasi-steady-state approximation (QSSA) scheme and the error redistribution mass conservation\\u000a technique are adopted to solve the atmospheric chemistry kinetic equations. Results show that the condensed model can well\\u000a simulate concentration variations of gas species such as SO2, NOX,

Tijian Wang; Zhaobo Sun; Zongkai Li

1999-01-01

11

Modeling Gas-Phase Chemistry in Cometary Atmospheres  

NASA Astrophysics Data System (ADS)

Gas-phase chemistry is central to understand the physics and chemistry of comets. Photochemistry is a major source of ions and electrons that further initiate key gas-phase reactions, leading to the plethora of molecules and atoms seen in cometary atmospheres. The relevant physico-chemical processes are identified within a modeling framework to understand observations and in situ measurements of comets (e.g., Halley, Borrelly, Hyakutake, Hale-Bopp, Tempel 1, Wild 2) and to provide valuable insights into the intrinsic properties of their nuclei. Details of these processes are presented, from the collision-dominated inner coma to the solar wind interaction region. This extensive modeling effort to investigate these important cometary processes is highly relevant to ground-based observations of comets and past, on going, and future spacecraft missions to these primitive objects.Gas-phase chemistry is central to understand the physics and chemistry of comets. Photochemistry is a major source of ions and electrons that further initiate key gas-phase reactions, leading to the plethora of molecules and atoms seen in cometary atmospheres. The relevant physico-chemical processes are identified within a modeling framework to understand observations and in situ measurements of comets (e.g., Halley, Borrelly, Hyakutake, Hale-Bopp, Tempel 1, Wild 2) and to provide valuable insights into the intrinsic properties of their nuclei. Details of these processes are presented, from the collision-dominated inner coma to the solar wind interaction region. This extensive modeling effort to investigate these important cometary processes is highly relevant to ground-based observations of comets and past, on going, and future spacecraft missions to these primitive objects.

Boice, D. C.

12

Model of boron diffusion from gas phase in silicon carbide  

SciTech Connect

Boron diffusion from the gas phase in silicon carbide is described on the basis of a two-component model. 'Shallow' boron, i.e., boron at silicon sites, is a slow component with a high surface concentration. Its diffusivity is proportional to the concentration of positively charged intrinsic point defects, which are presumably interstitial silicon atoms. 'Deep' boron, i.e., impurity-defect pairs of boron-carbon vacancy, is a fast component with lower surface concentration. The ratio between the surface concentrations of the components depends on the pressure of silicon or carbon vapors in the gas phase. The diffusion and interaction of components are described by the set of diffusion-reaction equations. The diffusion retardation observed on the concentration-profile tail is related to the capture of impurity-defect pairs and excess vacancies by traps of background impurities and defects.

Aleksandrov, O. V., E-mail: Aleksandr_ov@mail.ru [St. Petersburg State Electrotechnical University, 'LETI' (Russian Federation); Mokhov, E. N., E-mail: Mokhov@mail.ioffe.ru [Russian Academy of Sciences, Ioffe Physical Technical Institute (Russian Federation)

2011-06-15

13

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

14

On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions  

PubMed Central

Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation.

Marchese, Roberto; Grandori, Rita; Carloni, Paolo; Raugei, Simone

2010-01-01

15

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

PubMed Central

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

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

2009-01-01

16

Computational study of peptide bond formation in the gas phase through ion-molecule reactions.  

PubMed

A computational study of peptide bond formation from gas-phase ion-molecule reactions has been carried out. We have considered the reaction between protonated glycine and neutral glycine, as well as the reaction between two neutral glycine molecules for comparison purposes. Two different mechanisms, concerted and stepwise, were studied. Both mechanisms show significant energy barriers for the neutral reaction. The energy requirements for peptide bond formation are considerably reduced upon protonation of one of the glycine molecules. For the reaction between neutral glycine and N-protonated glycine the lowest energy barrier is observed for the concerted mechanism. For the reaction between neutral glycine and protonated glycine at carbonyl oxygen, the preferred mechanism is the stepwise one, with a relatively small energy barrier (23 kJ mol(-1) at 0 K) and leading to the lowest-lying protonated glycylglycine isomer. In the case that the reaction could be initiated by protonated glycine at hydroxyl oxygen the process would be barrier-free and clearly exothermic. In that case peptide bond formation could take place even under interstellar conditions if glycine is present in space. PMID:23817675

Redondo, Pilar; Martínez, Henar; Cimas, Alvaro; Barrientos, Carmen; Largo, Antonio

2013-08-21

17

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

PubMed Central

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

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

2011-01-01

18

Development of Peptide Nanotube-Modified Biosensors for Gas-Phase Organophosphate Detection.  

National Technical Information Service (NTIS)

Vapor-phase detection of the model organophosphate malathion was achieved using enzymes encapsulated in peptide nanotubes and attached to gold screen-printed electrodes. Malathion was chosen as the model for this experiment because its binding mechanism w...

P. A. Baker

2013-01-01

19

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

PubMed

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

20

Dissociation Behavior of Doubly-Charged Tryptic Peptides: Correlation of Gas-Phase Cleavage Abundance with Ramachandran Plots  

SciTech Connect

Large numbers of gas-phase dissociation spectra of protonated peptides are obtained daily and used in protein identification studies. Yet fundamental knowledge of the factors that influence their unimolecular dissociation branching ratios is relatively poor. It is still not possible to predict dissociation branching ratios from peptide sequence. Clearly, several chemicals factors must influence dissociation patterns, includes y, f angles determined by the residues involved in an amide bond, the propensities for certain side chains to interact each other or with the backbone, the tendency for added protons to be intramolecularly solvated, and the stability of the fragment ions once formed.

Huang, Yingying; Triscari, Joseph M.; Pasa-Tolic, Liljiana; Anderson, Gordon A.; Lipton, Mary S.; Smith, Richard D.; Wysocki, Vicki H.

2004-03-17

21

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

Microsoft Academic Search

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

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

2005-01-01

22

Modelling nongrey gas-phase and soot radiation in luminous turbulent nonpremixed jet flames  

Microsoft Academic Search

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

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

2005-01-01

23

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

SciTech Connect

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

Malandra, J.

1993-05-01

24

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

PubMed Central

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

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

2005-01-01

25

Structural and conformational aspects of gas phase peptides probed by electron capture dissociation  

Microsoft Academic Search

Mass spectrometry (MS) is a major player in the field of structural characterization of peptides and proteins. MS-based proteomics is nowadays routinely carried out at universities, research institutes and hospitals. Often, fragmentation techniques are applied to generate information about the molecular architecture. One way to obtain peptide fragments is by making use of reactions between multiply charged polypeptide cations in

R. Mihalca

2007-01-01

26

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

NASA Astrophysics Data System (ADS)

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

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

2012-06-01

27

Gas-Phase Peptide Sulfinyl Radical Ions: Formation and Unimolecular Dissociation  

NASA Astrophysics Data System (ADS)

A variety of peptide sulfinyl radical (RSO•) ions with a well-defined radical site at the cysteine side chain were formed at atmospheric pressure (AP), sampled into a mass spectrometer, and investigated via collision-induced dissociation (CID). The radical ion formation was based on AP reactions between oxidative radicals and peptide ions containing single inter-chain disulfide bond or free thiol group generated from nanoelectrospray ionization (nanoESI). The radical induced reactions allowed large flexibility in forming peptide radical ions independent of ion polarity (protonated or deprotonated) or charge state (singly or multiply charged). More than 20 peptide sulfinyl radical ions in either positive or negative ion mode were subjected to low energy collisional activation on a triple-quadrupole/linear ion trap mass spectrometer. The competition between radical- and charge-directed fragmentation pathways was largely affected by the presence of mobile protons. For peptide sulfinyl radical ions with reduced proton mobility (i.e., singly protonated, containing basic amino acid residues), loss of 62 Da (CH2SO), a radical-initiated dissociation channel, was dominant. For systems with mobile protons, this channel was suppressed, while charge-directed amide bond cleavages were preferred. The polarity of charge was found to significantly alter the radical-initiated dissociation channels, which might be related to the difference in stability of the product ions in different ion charge polarities.

Tan, Lei; Xia, Yu

2012-11-01

28

Gas phase IR spectra of tri-peptide Z-Pro-Leu-Gly: Effect of C-terminal amide capping on secondary structure  

NASA Astrophysics Data System (ADS)

Three-residue peptides capped with benzyloxycarbonyl (Z-) group, Z-Pro-Leu-Gly-NH2 and Z-Pro-Leu-Gly-OH, are investigated by infrared (IR) spectroscopy, using supersonic-jet laser desorption technique, in the N-H and O-H stretching frequency ranges. The IR spectra show clear evidence of the formation of different hydrogen-bonding network in the two peptides. The possible gas phase structure is proposed from density functional theory calculations using cc-pVDZ basis set. The Z-Pro-Leu-Gly-OH in the gas phase forms successive ?-turn structure with free C-terminal carboxyl group whereas main structural element in Z-Pro-Leu-Gly-NH2 is ?-turn with C-terminal sbnd NH2 group forming hydrogen bond. Structural information is employed to predict their binding capability in gas phase.

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

2012-04-01

29

Modeling of inducing gas?phase advective transport of voc in the unsaturated zone  

Microsoft Academic Search

A multi?phase, multi?component model which describes contaminant transport in the unsaturated zone is developed in this work. The model incorporates the heterogeneity of pore fluid distribution and inducing gas?phase advective transport. The numerical approximation scheme consists of finite difference method and the method of characteristics. For solving the system of equations, the method of over?relaxation is employed. This model has

1995-01-01

30

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

SciTech Connect

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

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

1992-06-01

31

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

NASA Astrophysics Data System (ADS)

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

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

2012-11-01

32

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

PubMed

The salt bridge formation and stability in the terminated lysine-glutamate dipeptide is investigated in water clusters of increasing size up to the limit of bulk water. Proton transfer dynamics between the acidic and basic side chains is described by DFT-based Born-Oppenheimer molecular dynamics simulations. While the desolvated peptide prefers to be in its neutral state, already the addition of a single water molecule can trigger proton transfer from the glutamate side chain to the lysine side chain, leading to a zwitterionic salt bridge state. Upon adding more water molecules we find that stabilization of the zwitterionic state critically depends on the number of hydrogen bonds between side chain termini, the water molecules, and the peptidic backbone. Employing classical molecular dynamics simulations for larger clusters, we observed that the salt bridge is weakened upon additional hydration. Consequently, long-lived solvent shared ion pairs are observed for about 30 water molecules while solvent separated ion pairs are found when at least 40 or more water molecules hydrate the dipeptide. These results have implications for the formation and stability of salt bridges at partially dehydrated surfaces of aqueous proteins. PMID:23163393

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

2012-11-14

33

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

SciTech Connect

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

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

2010-11-17

34

Radio-frequency glow discharges in methane gas: modelling of the gas-phase physics and chemistry  

Microsoft Academic Search

A methane discharge fluid model is developed, and subsequently combined with a simple gas-phase chemical kinetics model. The aim is to provide better understanding of the charged species dynamics, and their interaction with the gas-phase kinetics in a CH4 plasma. Swarm data are used as input in the fluid model, which predicts the ion and electron densities, electric fields and

E. Gogolides; C. Buteau; A. Rhallabi; G. Turban

1994-01-01

35

Dissociation Behavior of Tryptic and Intramolecular Disulfide-linked Peptide Ions Modified in the Gas Phase via Ion/Ion Reactions  

PubMed Central

Protonated tryptic peptides, somatostatin-14, and oxytocin have been subjected to reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas phase. The major product is a negatively-charged complex comprised of the peptide and the reagent. Upon dehydration of the complex, all peptides show evidence for Schiff base formation involving a primary amine of the peptide. Some peptides also show evidence for the formation of a relatively strong electrostatic interaction without Schiff base formation (i.e., a mixture of isomeric precursor ions is generated upon dehydration of the complex). Ion trap collision-induced dissociation of the dehydration products from all peptides examined gave distinct product ion spectra relative to the deprotonated and protonated forms of the peptides. The distinct behavior of the modified ions is attributed to the highly stable charge carrying sulfonate group, which tends to inhibit intramolecular proton transfer in negatively charged species. Modified anions of the peptides with an intramolecular disulfide linkage show evidence for cleavage of both the disulfide linkage and an amide bond in the loop defined by the disulfide bond. Modification of protonated peptides via charge inversion with FBDSA is a useful means for generating novel and distinct ion-types that can provide complementary structural information upon subsequent activation to that obtained from dissociation of protonated or deprotonated forms of the peptide.

Stutzman, John R.; Hassell, Kerry M.; McLuckey, Scott A.

2011-01-01

36

Dissociation Behavior of Tryptic and Intramolecular Disulfide-linked Peptide Ions Modified in the Gas Phase via Ion/Ion Reactions.  

PubMed

Protonated tryptic peptides, somatostatin-14, and oxytocin have been subjected to reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas phase. The major product is a negatively-charged complex comprised of the peptide and the reagent. Upon dehydration of the complex, all peptides show evidence for Schiff base formation involving a primary amine of the peptide. Some peptides also show evidence for the formation of a relatively strong electrostatic interaction without Schiff base formation (i.e., a mixture of isomeric precursor ions is generated upon dehydration of the complex). Ion trap collision-induced dissociation of the dehydration products from all peptides examined gave distinct product ion spectra relative to the deprotonated and protonated forms of the peptides. The distinct behavior of the modified ions is attributed to the highly stable charge carrying sulfonate group, which tends to inhibit intramolecular proton transfer in negatively charged species. Modified anions of the peptides with an intramolecular disulfide linkage show evidence for cleavage of both the disulfide linkage and an amide bond in the loop defined by the disulfide bond. Modification of protonated peptides via charge inversion with FBDSA is a useful means for generating novel and distinct ion-types that can provide complementary structural information upon subsequent activation to that obtained from dissociation of protonated or deprotonated forms of the peptide. PMID:22408389

Stutzman, John R; Hassell, Kerry M; McLuckey, Scott A

2012-02-15

37

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

2013-04-01

38

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

39

Gas phase photo-formation and vacuum UV photofragmentation spectroscopy of tryptophan and tyrosine radical-containing peptides.  

PubMed

Tryptophan (Trp(•)) and tyrosyl (Tyr(•)) radical containing peptides were produced by UV laser-induced electron detachment from a suitable precursor. Vacuum ultraviolet (VUV) action spectra of these radical peptides were recorded with synchrotron radiation in the 4.5-16 eV range, from which fragmentation pathways and yields are measured as a function of the VUV photon energy. An enhancement in photofragmentation yields of radical species by 1 order of magnitude with respect to nonradical peptides is demonstrated here for the first time. Photofragmentation spectra are compared with absorption spectra for model chromophores calculated in the frame of the time-dependent density functional theory (TDDFT). A qualitative agreement in the position of bands in the 6-8 eV region is observed between experimental photofragmentation and calculated absorption spectra. Photofragmentation spectra of peptide radicals can be useful to better assess the complex deactivation pathways that occur following the absorption of a VUV photon in biomolecular radical anions. PMID:21744817

Brunet, Claire; Antoine, Rodolphe; Allouche, Abdul-Rahman; Dugourd, Philippe; Canon, Francis; Giuliani, Alexandre; Nahon, Laurent

2011-07-25

40

Models of Gas-phase and Surface Chemistry for Plasma Enhanced Chemical Vapor Deposition  

NASA Astrophysics Data System (ADS)

Plasma enhanced chemical vapor deposition for inter-metal-layer gap-fill processes are increasingly important in semiconductor device manufacture, as the devices include increasing numbers of metal layers with decreasing linewidth and spacing. Optimization of these processes requires knowledge of the microscopic consequences of variations in reactor operating conditions. Topographical simulation can address the gap-fill performance of a depositing film, but the predictive capabiliities are limited by the ability of the model user to accurately supply ion and radical fluxes at a gas/surface interface. Critical to determining this information are the chemical kinetics between gas-phase species and the deposition surfaces. Recent improvements and extensions to the CHEMKIN and Surface CHEMKIN software allow general inclusion of detailed chemical mechanisms in plasma simulations and in models of plasma-surface interactions. In the results presented here (This work represents a collaboration with R. Larson and P. Ho at Sandia, J. Rey and J. Li at TMA, S. M. Han and E. Aydil of UCSB, and S. Huang at Lam Research Corporation), we have used a CHEMKIN-based well mixed reactor model of a high-density SiH_4/O_2/Ar plasma to predict and characterize species fluxes, oxide-deposition rates, and ion-milling rates on a flat surface. These calculated rates can be used as direct input to a topographical simulator. The gas-phase chemistry in the plasma reactor model is comprised of electron impact reactions with silane, oxygen, hydrogen, and argon, as well as neutral radical recombination, abstraction, and oxidation reactions. The surface reaction mechanism contains four classes of reactions: silicon-containing radical deposition, radical abstraction, ion-induced desorption, and physical ion sputtering. We include relative thermochemistry of the surface and gas species to allow reversible reaction dynamics. The plasma model results show good agreement with measured ion densities, as well as with measured net deposition rates.

Meeks, Ellen

1996-10-01

41

Impacts of Gas-phase Chemical Mechanisms on Modeled Responses of Ozone and Fine Particulate Matter to Emission Changes  

NASA Astrophysics Data System (ADS)

Two air pollutants of most concern are ozone and fine particulate matter (i.e., PM2.5; particulate matter with an aerodynamic diameter less than 2.5 ?m) due to their adverse human health effects. Gas-phase chemical mechanisms are one of the important components in regional air quality models and applied to describe the formation of air pollutants such as ozone and secondary PM2.5. Modeled responses of air pollutant concentrations to precursor emission changes (i.e., sensitivities) provide useful information for developing air pollution mitigation strategies and are expected to be affected by gas-phase chemical mechanisms chosen for air quality simulations. The goal of this study is to investigate impacts of gas-phase chemical mechanisms on modeled responses of ozone and PM2.5 concentrations to emission reductions over the eastern United States. We used the U.S. Environmental Protection Agency's regional air quality model, Community Multiscale Air Quality Model (CMAQ) version 4.7.1, to simulate three-dimensional gridded concentrations of ambient ozone, PM2.5 and other air pollutants during three summer months (June, July and August) in 2007. A uniform grid of 12 by 12 km horizontal cells with 34 vertical layers was employed in the air quality simulations. Two gas-phase chemical mechanisms (CB-05; Carbon Bond Mechanism, version V and SAPRC-99; Statewide Air Pollution Research Center, version 99) were used in the regional air quality simulations. The preliminary results show that modeled responses of peak ozone levels to emission changes could be affected by the gas-phase chemical mechanism chosen in air quality modeling. The effects of gas-phase chemical mechanisms on modeled responses of PM2.5 to emission changes are small. Final results of this modeling study and related discussion will be presented at the conference.

Liao, Kuo-Jen

2013-04-01

42

Gas-phase noncovalent interactions between vancomycin-group antibiotics and bacterial cell-wall precursor peptides probed by hydrogen\\/deuterium exchange  

Microsoft Academic Search

Gas-phase structures of noncovalent complexes between the glycopeptide antibiotics vancomycin, eremomycin, ristocetin, and\\u000a pseudo aglyco-ristocetin and the cell-wall mimicking peptides N-acetyl-D-Alanyl-D-Alanine, N-acetyl-Glycyl-D-Alanine, and\\u000a N,N?-di-acetyl L-Lysyl-D-Alanyl-D-Alanine have been probed by hydrogen\\/deuterium (H\\/D) exchange using ND3 as reagent gas. The noncovalent complexes were transferred from solution to the vacuum using electrospray ionization. The\\u000a H\\/D exchange of the solvent-free ions was studied in

Albert J. R. Heck; Thomas J. D. Jørgensen; Mary O’Sullivan; Markus von Raumer; Peter J. Derrick

1998-01-01

43

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.

44

Gas Phase Bio-conjugation of Peptides via Ion/Ion Charge Inversion: Schiff Base Formation on the Conversion of Cations to Anions  

PubMed Central

The selective covalent modification of singly protonated peptides in the gas-phase via ion/ion charge inversion reactions is demonstrated. Doubly deprotonated 4-formyl-1,3-benzene disulfonic acid serves as a reagent anion for forming a Schiff base via the reaction of a primary amine on the peptide and the aldehyde functionality of the reagent anion. The process is initiated by the formation of an ion/ion complex comprised to the two reactants. Ion trap collisional activation of the complex results in loss of water from the intermediate that gives rise to Schiff base formation. N-terminally acetylated peptides with no lysine residues do not undergo covalent bond formation upon reaction with the reagent anion. Rather, the adduct species simply loses the reagent either as a neutral species or as a deprotonated species. The ability to modify singly protonated peptide ions covalently and selectively opens up new possibilities for the analysis of peptides, and, possibly, other analyte species with primary amine functionalities.

Hassell, Kerry M.; Stutzman, John R.; McLuckey, Scott A.

2010-01-01

45

The gas-phase dipeptide analogue acetyl-phenylalanyl-amide: a model for the study of side chain/backbone interactions in proteins.  

PubMed

The issue of the influence of the side chain/backbone interaction on the local conformational preferences of a phenylalanine residue in a peptide chain is addressed. A synergetic approach is used, which combines gas-phase UV spectroscopy as well as gas-phase IR/UV double-resonance experiments with DFT and post Hartree-Fock calculations. N-Acetyl-Phe-amide was chosen as a model system for which three different conformers were observed. The most stable conformer has been identified as an extended beta(L) conformation of the peptide backbone. It is stabilized by a weak but significant NH-pi interaction bridging the aromatic ring on the residue (i) with the NH group on residue (i+1), with the aromatic side chain being in an anti conformation. This stable conformation corresponds to the common NH(i+1)-aromatic(i) interaction encountered in proteins for the three aromatic residues (phenylalanine, tyrosine, and tryptophan), which illustrates the relevance of gas-phase investigations to structural biology issues. The two other less abundant conformers have been assigned to two gamma-folded backbone conformations that differ by the orientation of the side chain. In all cases, the IR data provided spectroscopic fingerprints of these interactions. Finally, the strong conformational dependence of the fluorescence yield found for N-acetyl-Phe-amide illustrates the role of the environment on the excited-state dynamics of these species, which is often exploited by biochemists to monitor protein structural changes from tryptophan lifetime measurements. PMID:16839051

Chin, Wutharath; Mons, Michel; Dognon, Jean-Pierre; Mirasol, Reinard; Chass, Gregory; Dimicoli, Iliana; Piuzzi, François; Butz, Patrick; Tardivel, Benjamin; Compagnon, Isabelle; von Helden, Gert; Meijer, Gerard

2005-06-23

46

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

NASA Astrophysics Data System (ADS)

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

Bird, G. A.

2011-10-01

47

Caloric curve for nuclear liquid-gas phase transition in relativistic mean-field hadronic model  

NASA Astrophysics Data System (ADS)

The main thermodynamical properties of the first order phase transition of the relativistic mean-field (RMF) hadronic model were explored in the isobaric, the canonical and the grand canonical ensembles on the basis of the method of the thermodynamical potentials and their first derivatives. It was proved that the first order phase transition of the RMF model is the liquid-gas type one associated with the Gibbs free energy G. The thermodynamical potential G is the piecewise smooth function and its first order partial derivatives with respect to variables of state are the piecewise continuous functions. We have found that the energy in the caloric curve is discontinuous in the isobaric and the grand canonical ensembles at fixed values of the pressure and the chemical potential, respectively, and it is continuous, i.e. it has no plateau, in the canonical and microcanonical ensembles at fixed values of baryon density, while the baryon density in the isotherms is discontinuous in the isobaric and the canonical ensembles at fixed values of the temperature. The general criterion for the nuclear liquid-gas phase transition in the canonical ensemble was identified.

Parvan, A. S.

2012-08-01

48

Model for the catalytic oxidation of CO, including gas-phase impurities and CO desorption.  

PubMed

We present results of kinetic Monte Carlo simulations of a modified Ziff-Gulari-Barshad model for the reaction CO+O ? CO_{2} on a catalytic surface. Our model includes impurities in the gas phase, CO desorption, and a modification known to eliminate the unphysical O poisoned phase. The impurities can adsorb and desorb on the surface, but otherwise remain inert. In a previous work that did not include CO desorption [Buendía and Rikvold, Phys. Rev. E 85, 031143 (2012)], we found that the impurities have very distinctive effects on the phase diagram and greatly diminish the reactivity of the system. If the impurities do not desorb, once the system reaches a stationary state, the CO_{2} production disappears. When the impurities are allowed to desorb, there are regions where the CO_{2} reaction window reappears, although greatly reduced. Following experimental evidence that indicates that temperature effects are crucial in many catalytic processes, here we further analyze these effects by including a CO desorption rate. We find that the CO desorption has the effect to smooth the transition between the reactive and the CO rich phase, and most importantly it can counteract the negative effects of the presence of impurities by widening the reactive window such that now the system remains catalytically active in the whole range of CO pressures. PMID:23944439

Buendía, G M; Rikvold, P A

2013-07-25

49

Gas-Phase Fragmentation of [M + nH + OH]n•+ Ions Formed from Peptides Containing Intra-Molecular Disulfide Bonds  

NASA Astrophysics Data System (ADS)

In this study, we systematically investigated gas-phase fragmentation behavior of [M + nH + OH]n•+ ions formed from peptides containing intra-molecular disulfide bond. Backbone fragmentation and radical initiated neutral losses were observed as the two competing processes upon low energy collision-induced dissociation (CID). Their relative contribution was found to be affected by the charge state (n) of [M + nH + OH]n•+ ions and the means for activation, i.e., beam-type CID or ion trap CID. Radical initiated neutral losses were promoted in ion-trap CID and for lower charge states where mobile protons were limited. Beam-type CID and dissociation of higher charge states of [M + nH + OH]n•+ ions generally gave abundant backbone fragmentation, which was highly desirable for characterizing peptides containing disulfide bonds. The amount of sequence information obtained from CID of [M + nH + OH]n•+ ions was compared with that from CID of disulfide bond reduced peptides. For the 11 peptides studied herein, similar extent of sequence information was obtained from these two methods.

Ma, Xiaoxiao; Love, Chasity B.; Zhang, Xinrong; Xia, Yu

2011-05-01

50

Modeling particle growth and morphology of impact polypropylene produced in the gas phase  

NASA Astrophysics Data System (ADS)

A gas phase reactor system using on-line FTIR for controlled composition olefin polymerization experiments with gaseous or liquid monomers has been designed and constructed in this work. Using this equipment, a comprehensive study of the kinetics, particle growth and morphological development of impact polypropylene produced in-situ with a TiClsb4/MgClsb2 catalyst has been conducted. The catalyst was found exhibiting a decay type behavior for ethylene and propylene homopolymerization but an activation effect was observed when both monomers were present together. Hydrogen was also seen to boost the rate of propylene polymerization but not ethylene, and increased the rate of catalyst deactivation during propylene polymerization. Microscopy analysis of the particles over a range of copolymer content (up to 70 wt. %), copolymer composition, reaction temperature and hydrogen levels reveal how the copolymer phase segregates from the homopolymer and grows within the homopolymer matrix. A model for particle growth is proposed. A computer model for the study of the effects of changing morphology for polyolefins produced in multistage processes has been developed and used to investigate the role of monomer diffusion limitations during polymerization using the experimental data found in this work. To study the effects of residence time distribution in multistage continuous processes for impact polypropylene, population balance models have been developed for multistage processes consisting of gas and liquid phase reactors. The effects of catalyst size distribution and monomer diffusion limitations can be incorporated into the models. It is shown that commercial impact polypropylene consists of a broad distribution of polymer properties as a consequence of reactor residence time distribution issues. Implications for product homogeneity, particle sticking and process productivity are discussed.

Debling, Jon A.

51

CHEMICAL TRANSFORMATION MODULES FOR EULERIAN ACID DEPOSITION MODELS. VOLUME 1. THE GAS-PHASE CHEMISTRY  

EPA Science Inventory

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

52

The gas phase reaction between CO 2 and lanthanide atoms. A test of a model for the isokinetic effect  

Microsoft Academic Search

Summary Using literature data on the gas phase reaction between free lanthanide atoms and carbon dioxide,  we have found an isokinetic relation for seven  of the twelve investigated elements with an isokinetic temperature, Tiso, of 2500±330 K. This value is analyzed in the framework of the model of selective energy transfer, SET, indicating that metal-CO2 complexes are formed as pre-reaction

Ragnar Larsson; Joëlle Mascetti

2005-01-01

53

Comparisons between a gas-phase model of silane chemical vapor deposition and laser-diagnostic measurements  

Microsoft Academic Search

Theoretical modeling and experimental measurements have been used to study gas-phase chemistry in the chemical vapor deposition (CVD) of silicon from silane. Pulsed laser Raman spectroscopy was used to obtain temperature profiles and to obtain absolute density profiles of silane during deposition at atmospheric and 6-Torr total pressures for temperatures ranging from 500 to 800°C. Laser-excited fluorescence was used to

William G. Breiland; Michael E. Coltrin; Pauline Ho

1986-01-01

54

Comparisons between a gas-phase model of silane chemical vapor deposition and laser-diagnostic measurements  

Microsoft Academic Search

Theoretical modeling and experimental measurements have been used to study gas-phase chemistry in the chemical vapor deposition (CVD) of silicon from silane. Pulsed laser Raman spectroscopy was used to obtain temperature profiles and to obtain absolute density profiles of silane during deposition at atmospheric and 6-Torr total pressures for temperatures ranging from 500 to 800 °C. Laser-excited fluorescence was used

William G. Breiland; Michael E. Coltrin; Pauline Ho

1986-01-01

55

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

PubMed Central

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

Flicker, T M; Green, S A

2001-01-01

56

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

2007-01-01

57

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

Microsoft Academic Search

Electrosprayed multi-protein complexes can be dissociated by collisional activation in the gas phase. Typically, these processes\\u000a follow a mechanism whereby a single subunit gets ejected with a disproportionately high amount of charge relative to its mass.\\u000a This asymmetric behavior suggests that the departing subunit undergoes some degree of unfolding prior to being separated from\\u000a the residual complex. These structural changes

Stephen V. Sciuto; Jiangjiang Liu; Lars Konermann

2011-01-01

58

Comparison of gas-phase mechanisms applied to RDX combustion model  

Microsoft Academic Search

Two detailed gas-phase chemical mechanisms for RDX – Yetter and coworkers, herein ‘Y2’ [K. Prasad, R.A. Yetter, M.D. Smooke, Combust. Sci. Technol. 124 (1997) p. 35.]; Cal. Tech. group, herein ‘CTM’ [(a) A.D. Chakraborty, R.P. Muller, S. Dasgupta, W.A. Goddard, III, J. Phys. Chem. A 104 (2000) 2261. (b) D. Chakraborty, R.P. Muller, S. Dasgupta, W.A. Goddard, III, J. Comput.

William R. Anderson; Clint B. Conner

2009-01-01

59

Gas-phase spectroscopy of protonated 3-OH kynurenine and argpyrimidine. comparison of experimental results to theoretical modeling.  

PubMed

The aging process of the human lens is associated with accumulation of chromophores and fluorophores that impair visual function. In the present study, we examined the photodissociation of 3-OH-kynurenine and argpyrimidine. Furthermore, absorption spectra obtained in gas phase using an electrostatic ion storage ring were studied as gas phase absorption have been shown to be more similar to the in vivo condition than absorption spectra obtained in the liquid phase. Experimental results were compared to theoretical modeling using the multistate, multireference perturbation theory approach combined with advanced molecular modeling tools to account for the solvent effects and to provide direct support for band assignments. Absorption maxima were determined both experimentally and theoretically and significant differences between the two chromophores were found. In particular, 3-OH-kynurenine demonstrated a blue-shift of more than 130 nm in the aqueous phase compared to the gas-phase due to the existence of different 3-OH-kynurenine conformers, which are stable under different conditions and originate from the interplay between intra- and intermolecular interactions. Photodissociation of argpyrimidine and 3-OH-kynurenine was observed in vacuum thus confirming the results previously obtained in liquid phase demonstrating that the photodestruction takes place in both media. PMID:17914773

Kessel, Line; Nielsen, Iben B; Bochenkova, Anastasia V; Bravaya, Ksenia B; Andersen, Lars H

2007-10-03

60

Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H\\/D exchange (SORI-HDX) in fourier transform ion-cyclotron resonance (FT-ICR) instruments  

Microsoft Academic Search

The usefulness of gas-phase H\\/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly\\u000a and multiply protonated peptides\\/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation\\u000a (SORI-CID). The fragments and the surviving precursor ions then all undergo H\\/D exchange in the gas-phase with either D2O or CD3OD under the same experimental conditions. Usually, 10 to 60

Árpád Somogyi

2008-01-01

61

Quantitative reproducibility of mass spectra in matrix-assisted laser desorption ionization and unraveling of the mechanism for gas-phase peptide ion formation.  

PubMed

In a previous study on matrix-assisted laser desorption ionization (MALDI) of peptides using ?-cyano-4-hydroxycinnamic acid (CHCA) as a matrix, we found that the patterns of single-shot spectra obtained under different experimental conditions became similar upon temperature selection. In this paper, we report that absolute ion abundances are also similar in temperature-selected MALDI spectra, even when laser fluence is varied. The result that has been obtained using CHCA and 2,5-dihydroxybenzoic acid as matrices is in disagreement with the hypothesis of laser-induced ionization of matrix as the mechanism for primary ion formation in MALDI. We also report that the total number of ions in such a spectrum is unaffected by the identity, concentration and number of analytes, i.e. it is the same as that in the spectrum of pure matrix. We propose that the generation of gas-phase ions in MALDI can be explained in terms of two thermal reactions, i.e. the autoprotolysis of matrix molecules and the matrix-to-analyte proton transfer, both of which are in quasi-equilibrium in the early matrix plume. PMID:23494784

Ahn, Sung Hee; Park, Kyung Man; Bae, Yong Jin; Kim, Myung Soo

2013-03-01

62

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

SciTech Connect

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

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

1992-06-01

63

Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments.  

PubMed

The usefulness of gas-phase H/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly and multiply protonated peptides/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The fragments and the surviving precursor ions then all undergo H/D exchange in the gas-phase with either D(2)O or CD(3)OD under the same experimental conditions. Usually, 10 to 60 s of reaction time is adequate to monitor characteristic differences in the H/D exchange kinetic rates. These differences are then correlated to isomeric ion structures. The SORI-HDX method can be used to rapidly test fragment ion structures and provides useful insights into peptide fragmentation mechanisms. PMID:18848466

Somogyi, Arpád

2008-08-26

64

Gas-phase models for catalysis: alkane activation and olefin epoxidation by the triatomic cation Ag2O+.  

PubMed

Electrospray ionization of aqueous silver nitrate is used for the preparation of the disilver-oxide cation Ag2O+ in the gas phase. The mass-selected cation is capable of activating C-H bonds of simple alkanes other than methane via H-atom abstraction, i.e., Ag2O+ + R-H --> Ag2OH+ + R* (R = C2H5, C3H7, C4H9). Clean O-atom transfer from Ag2O+ is observed with ethene as a neutral reagent, whereas oxygenation and allylic C-H abstraction compete in the case of propene. The gaseous Ag2O+ cation can thus be regarded as a minimalist model for the problems associated with the silver-mediated epoxidation of olefins more complex than ethene itself. The experimental findings are fully supported by the results of quantum chemical studies, thereby providing deep mechanistic insight into the reactions in the idealized gas phase, which also might have implications for further improvements in applied catalysis. PMID:18020337

Roithova, Jana; Schröder, Detlef

2007-11-17

65

Effects of peptide chain length on the gas-phase proton transfer properties of doubly-protonated ions from bradykinin and its N-terminal fragment peptides  

Microsoft Academic Search

Proton transfer properties were studied for doubly-protonated ions from bradykinin and seven smaller peptides whose sequences have C-terminal residues successively removed from bradykinin. Ions were generated by electrospray ionization (ESI) and their deprotonation reactions were investigated in a Fourier transform ion cyclotron resonance mass spectrometer. Sustained off-resonance irradiation (SORI)-collision-induced dissociation (CID) was used to obtain information on sites of protonation,

Giovanni A Pallante; Carolyn J Cassady

2002-01-01

66

Emergence of tricritical point and liquid-gas phase in the massless 2+1 dimensional Gross-Neveu model  

SciTech Connect

A complete thermodynamical analysis of the 2+1 dimensional massless Gross-Neveu model is performed using the optimized perturbation theory. This is a nonperturbative method that allows us to go beyond the known large-N results already at lowest order. Our results, for a finite number of fermion species, N, show the existence of a tricritical point in the temperature and chemical potential phase diagram for a discrete chiral phase transition allowing us precisely to locate it. By studying the phase diagram in the pressure and inverse density plane, we also show the existence of a liquid-gas phase, which, so far, was unknown to exist in this model. Finally, we also derive N dependent analytical expressions for the order parameter, critical temperature, and critical chemical potential.

Kneur, Jean-Loiec [Laboratoire de Physique Theorique et Astroparticules-CNRS-UMR 5207, Universite Montpellier II (France); Pinto, Marcus Benghi; Staudt, Ederson [Departamento de Fisica, Universidade Federal de Santa Catarina, 88040-900 Florianopolis, Santa Catarina (Brazil); Ramos, Rudnei O. [Departamento de Fisica Teorica, Universidade do Estado do Rio de Janeiro, 20550-013 Rio de Janeiro, Rio de Janeiro (Brazil)

2007-08-15

67

Recent developments in modeling gas-phase catalyzed olefin polymerization fluidized-bed reactors: The effect of bubble size variation on the reactor's performance  

Microsoft Academic Search

In the present study recent developments in modeling gas-phase catalyzed olefin polymerization fluidized-bed reactors (FBR) are critically reviewed. A new FBR model is developed to account for the effect of varying bubble size with the bed height on the reactor dynamics and the molecular properties of the polymer product. A comprehensive kinetic model for ethylene copolymerization in the presence of

H. Hatzantonis; H. Yiannoulakis; A. Yiagopoulos; C. Kiparissides

2000-01-01

68

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

Microsoft Academic Search

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

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

2000-01-01

69

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

NASA Astrophysics Data System (ADS)

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

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

2012-05-01

70

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

Microsoft Academic Search

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

G. A. Bird

2011-01-01

71

Two-phase modeling of a gas phase polyethylene fluidized bed reactor  

Microsoft Academic Search

A two-phase model is proposed for describing the behavior of a fluidized bed reactor used for polyethylene production. In the proposed model, the bed is divided into several sequential sections where flow of the gas is considered to be plug flow through the bubbles and perfectly mixed through the emulsion phase. Polymerization reactions occur not only in the emulsion phase

Ali Kiashemshaki; Navid Mostoufi; Rahmat Sotudeh-Gharebagh

2006-01-01

72

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

NASA Astrophysics Data System (ADS)

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

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

2011-11-01

73

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

NASA Astrophysics Data System (ADS)

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

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

2009-03-01

74

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

EPA Science Inventory

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

75

Computer Construction of Detailed Chemical Kinetic Models for Gas-Phase Reactors  

Microsoft Academic Search

The combustion, oxidation, and pyrolysis chemistry of even simple light hydrocarbons can be extremely complex, involving hundreds or thousands of kinetically significant species. Even relatively minor species can play an important role in the formation of undesirable emissions and byproducts, and their properties and reactions need to be modeled in some detail in order to make accurate predictions. In many

W. H. Green; P. I. Barton; B. Bhattacharjee; D. M. Matheu; D. A. Schwer; J. Song; R. Sumathi; H.-H. Carstensen; A. M. Dean; J. M. Grenda

2001-01-01

76

Mass transport models for a single particle in gas-phase propylene polymerisation  

Microsoft Academic Search

Olefin polymerisation on heterogeneous catalysts is gaining importance due to widening of the polymer properties window. The supported active catalyst on the heterogeneous particle reacts with the monomer and produces polymer. Polymeric flow (PF) model is relatively simple and assume that particle morphology develops as the catalyst active sites move outwards along with the polymer formed thus leading to PF

U. Parasu Veera

2003-01-01

77

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.

2003-04-01

78

Modeling Gas-Phase Transport in Polymer-Electrolyte FuelCells  

SciTech Connect

In this transaction, the equations and methodology for modeling convection and ordinary, Knudsen, and pressure diffusion of gases in a fuel-cell gas-diffusion layer are described. Some results examining the magnitudes of the various terms are also made. This derivation results in a self-consistent description of the various transport mechanisms and is robust for numerical solutions, especially for conditions involving different flow regimes or where the regime is not known a priori.

Weber, A.Z.; Newman, J.

2006-08-17

79

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

NASA Astrophysics Data System (ADS)

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

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

2011-05-01

80

H\\/D exchange kinetics: Experimental evidence for formation of different b fragment ion conformers\\/isomers during the gas-phase peptide sequencing  

Microsoft Academic Search

Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with H\\/D exchange\\u000a reactions was utilized to explore the existence of different b5+ and b4+ fragment ion conformers\\/isomers of hexapeptide WHWLQL in the gas phase. Distinct H\\/D exchange trends for protonated WHWLQL\\u000a ([M + H]+) and its b5+ and b4+ fragment ions (with ND3) were observed. Isolated

Alireza Fattahi; Behrooz Zekavat; Touradj Solouki

2010-01-01

81

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

82

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

NASA Astrophysics Data System (ADS)

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

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

83

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

National Technical Information Service (NTIS)

Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes as they are advected and/or dispersed. Furthermore, parent and daughter radionuclides may dec...

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

1992-01-01

84

Free radical-induced site-specific peptide cleavage in the gas phase: Low-energy collision-induced dissociation in ESI and MALDI mass spectrometry  

Microsoft Academic Search

Protein identification is routinely accomplished by peptide sequencing using mass spectrometry (MS) after enzymatic digestion.\\u000a Site-specific chemical modification may improve peptide ionization efficiency or sequence coverage in mass spectrometry. We\\u000a report herein that amino group of lysine residue in peptides can be selectively modified by reaction with a peroxycarbonate\\u000a and the resulting lysine peroxycarbamates undergo homolytic fragmentation under conditions of

Huiyong Yin; Almary Chacon; Ned A. Porter; Douglas S. Masterson

2007-01-01

85

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

NASA Astrophysics Data System (ADS)

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

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

86

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

Microsoft Academic Search

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

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

2006-01-01

87

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

PubMed

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

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

2011-06-24

88

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

NASA Astrophysics Data System (ADS)

Tropospheric chemistry and air quality processes were implemented on-line in the Global Environmental Multiscale weather prediction model. The integrated model, GEM-AQ, was developed as a platform to investigate chemical weather at scales from global to urban. The current chemical mechanism is comprised of 50 gas-phase species, 116 chemical and 19 photolysis reactions, and is complemented by a sectional aerosol module with 5 aerosols types. All tracers are advected using the semi-Lagrangian scheme native to GEM. The vertical transport includes parameterized subgrid-scale turbulence and large scale deep convection. Dry deposition is included as a flux boundary condition in the vertical diffusion equation. Wet deposition of gas-phase species is treated in a simplified way, and only below-cloud scavenging is considered. The emissions used include yearly-averaged anthropogenic, and monthly-averaged biogenic, ocean, soil, and biomass burning emission fluxes, as well as NOx from lightning. In order to evaluate the ability to simulate seasonal variations and regional distributions of trace gases such as ozone, nitrogen dioxide and carbon monoxide, the model was run for a period of five years (2001 2005) on a global uniform 1.5°×1.5° horizontal resolution domain and 28 hybrid levels extending up to 10 hPa. Model results were compared with observations from satellites, aircraft measurement campaigns and balloon sondes. We find that GEM-AQ is able to capture the spatial details of the chemical fields in the middle and lower troposphere. The modelled ozone consistently shows good agreement with observations, except over tropical oceans. The comparison of carbon monoxide and nitrogen dioxide with satellite measurements emphasizes the need for more accurate, year-specific emissions fluxes for biomass burning and anthropogenic sources. Other species also compare well with available observations.

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

2008-06-01

89

Gas-phase diffusion in porous media: Evaluation of an advective- dispersive formulation and the dusty-gas model including comparison to data for binary mixtures  

SciTech Connect

Two models for gas-phase diffusion and advection in porous media, the Advective-Dispersive Model (ADM) and the Dusty-Gas Model (DGM), are reviewed. The ADM, which is more widely used, is based on a linear addition of advection calculated by Darcy`s Law and ordinary diffusion using Fick`s Law. Knudsen diffusion is often included through the use of a Klinkenberg factor for advection, while the effect of a porous medium on the diffusion process is through a porosity-tortuosity-gas saturation multiplier. Another, more comprehensive approach for gas-phase transport in porous media has been formulated by Evans and Mason, and is referred to as the Dusty- Gas Model (DGM). This model applies the kinetic theory of gases to the gaseous components and the porous media (or ``dust``) to develop an approach for combined transport due to ordinary and Knudsen diffusion and advection including porous medium effects. While these two models both consider advection and diffusion, the formulations are considerably different, especially for ordinary diffusion. The various components of flow (advection and diffusion) are compared for both models. Results from these two models are compared to isothermal experimental data for He-Ar gas diffusion in a low-permeability graphite. Air-water vapor comparisons have also been performed, although data are not available, for the low-permeability graphite system used for the helium-argon data. Radial and linear air-water heat pipes involving heat, advection, capillary transport, and diffusion under nonisothermal conditions have also been considered.

Webb, S.W.

1996-05-01

90

Modeling the role of HONO in the plume gas phase and aerosol chemistry of boreal forest biomass burning emissions during the summer 2009 ARCTAS campaign  

NASA Astrophysics Data System (ADS)

Approximately 3-20% of NOy in the flame front of biomass burning, as determined from field and lab studies, is HONO. Because HONO is readily photolyzed, it serves as a short-term reservoir for HOx and NOx. As the HONO is lost to photolysis, it affects NOy partitioning as well as O3 formation/loss. Using data from the NASA DC-8 payload during the summer 2008 ARCTAS campaign for model initialization, we have previously implemented a gas phase chemical model to evaluate the impact of HONO on the chemical evolution of one plume on 1 July 2008. We present results incorporating the ARCTAS particle phase data with the Aerosol Simulation Program and a Lagrangian parcel model to more completely represent the plume evolution.

St Clair, J. M.; Alvarado, M. J.; Wennberg, P. O.; Crounse, J.; Cohen, R. C.; Dibb, J. E.; Kuerten, A.; Diskin, G. S.; Sachse, G. W.; Ren, X.; Brune, W. H.; Apel, E. C.; Knapp, D. J.; Jimenez, J. L.; Cubison, M.; Vay, S. A.; Huey, L. G.; Weinheimer, A. J.; Wisthaler, A.; Scheuer, E. M.; Fried, A.; Weibring, P.; Walega, J.; Hall, S. R.; Blake, D. R.; Anderson, B. E.; Kondo, Y.; Cantrell, C. A.; Ullmann, K.

2010-12-01

91

EPA GAS PHASE CHEMISTRY CHAMBER STUDIES  

EPA Science Inventory

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

92

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...

93

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.

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

2009-01-01

94

Atomic-scale modeling of chemical vapor deposition processes from new complicated gas-phase mixtures for micro- and nanoelectronic applications  

NASA Astrophysics Data System (ADS)

Low-pressure chemical vapor deposition (CVD) is one of the most important processes for obtaining thin films widely used in semiconductor and in IC technology. Because of the baffling complexity of deposition process the usually-used approaches in CVD modeling include a great number of empiric non-calculated parameters, and this drawback becomes a grave disadvantage if one needs to model the process with new reagents and materials which were not used before. So we place primary emphasis upon the development of non-empirical deposition models that rely on phenomenological theories and experimental data only to a minimal extent. We are presenting the atomistic-scale models and software package throughout the entire deposition process that are based mainly on the first principles and ab initio methods. The main modeling stages are studied and discussed in detail, namely: atomistic modeling of gas-phase and surface reactions, determination of the basic chemical and physical mechanisms for the considered gas mixtures, calculations of the reactions rates for elementary reactions and acts, Monte Carlo and/or molecular dynamics simulation of the thin film growth, and modeling of macrokinetic processes in realistic deposition flow-reactor chamber. The modeling results for thin films deposition from actual gas mixtures are given. The physical properties of films as well as their stoichiometric composition and structure in dependence of process conditions are discussed.

Makhviladze, T. M.; Sarychev, M. E.

2009-01-01

95

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

PubMed

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. PMID:23902028

Bhaskaran, Renjith; Sarma, Manabendra

2013-07-28

96

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

EPA Science Inventory

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

97

Approaching complete peroxisome characterization by gas-phase fractionation  

Microsoft Academic Search

We examined the utility of gas-phase fractionation (GPF) in the m\\/z dimension to increase proteome coverage and reproducibility of peptide ion selection by direct microliquid chromatography\\/electrospray ionization-tandem mass spectrometry (LC\\/ESI-MS\\/MS) analysis of the peptides produced by proteolytic digestion of un- fractionated proteins from a yeast whole-cell lysate and in a peroxisomal membrane protein fraction derived from isolated yeast peroxisomes. We

Eugene C. Yi; Marcello Marelli; Hookeun Lee; Samuel O. Purvine; Ruedi Aebersold; John D. Aitchison; David R. Goodlett

2002-01-01

98

Development of expanded and core kinetic models for the gas phase formation of dioxins from chlorinated phenols.  

PubMed

Expanded, 45 reaction, and core, 12 reaction, kinetic models have been developed that account for the major features in the homogeneous formation of polychlorinated dibenzo-p-dioxins (PCDD) from the oxidation of 2,4,6-trichlorophenol (P). The expanded and core schemes provide good agreement between experimental and calculated yields of PCDDs using the CHEMKIN combustion package or the React kinetic program, respectively. Steady-state approximations of the reaction kinetic models including radical-molecule and radical-radical formation pathways of PCDD, as well as oxidative destruction pathways of chlorinated phenoxyl radicals, reveal a competition between reactions of chlorinated phenoxyl radicals with chlorinated phenols, recombination reactions of chlorinated phenoxyl mesomers, and destruction/decomposition of phenoxyl radicals. PMID:12738283

Khachatryan, L; Asatryan, R; Dellinger, Barry

2003-07-01

99

Modeling of plasma-etch processes using well stirred reactor approximations and including complex gas-phase and surface reactions  

Microsoft Academic Search

A 0-D or well stirred reactor model determines spatially and time-averaged species composition in plasma-etch reactors, through solution of species, mass, and electron-energy balance equations. The use of well stirred reactor approximations reduces the computational expense of detailed kinetics calculations and allows investigation of the dependence of plasma chemistry on etch-process parameters. The reactor is characterized by a chamber volume,

E. Meeks; Jong Won Shon

1995-01-01

100

Emergence of tricritical point and liquid-gas phase in the massless 2+1 dimensional Gross-Neveu model  

Microsoft Academic Search

A complete thermodynamical analysis of the 2+1 dimensional massless Gross-Neveu model is performed using the optimized perturbation theory. This is a nonperturbative method that allows us to go beyond the known large-N results already at lowest order. Our results, for a finite number of fermion species, N, show the existence of a tricritical point in the temperature and chemical potential

Jean-Loïc Kneur; Marcus Benghi Pinto; Rudnei O. Ramos; Ederson Staudt

2007-01-01

101

Development of expanded and core kinetic models for the gas phase formation of dioxins from chlorinated phenols  

Microsoft Academic Search

Expanded, 45 reaction, and core, 12 reaction, kinetic models have been developed that account for the major features in the homogeneous formation of polychlorinated dibenzo-p-dioxins (PCDD) from the oxidation of 2,4,6-trichlorophenol (P). The expanded and core schemes provide good agreement between experimental and calculated yields of PCDDs using the CHEMKIN combustion package or the React kinetic program, respectively. Steady-state approximations

L. Khachatryan; R. Asatryan; Barry Dellinger

2003-01-01

102

Gas-phase polar cycloadditions  

NASA Astrophysics Data System (ADS)

The dilute gas-phase environment of mass spectrometers provides versatile and convenient medium in which chemists can form a great variety of ionic species and study their intrinsic reactivity exploring reaction mechanisms and screening for new reactions and their applications. Recent and illustrative examples of gas-phase polar cycloadditions of even and odd-electrons ions, which have been observed (some for the first time) in the solvent- and counter ion-free environment of mass spectrometers, are presented. Synthetic and analytical applications of such reactions and correlations with analogous reactions observed in solution are also discussed.

Eberlin, Marcos N.

2004-07-01

103

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

SciTech Connect

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

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

1997-12-31

104

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.

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

2009-01-01

105

Modeling peptide binding to anionic membrane pores.  

PubMed

Peptide-induced pore formation in membranes can be dissected into two steps: pore formation and peptide binding to the pore. A computational method is proposed to study the second step in anionic membranes. The electrostatic potential is obtained from numerical solutions to the Poisson-Boltzmann equation and is then used in conjunction with IMM1 (implicit membrane model 1). A double charge layer model is used to incorporate the effects of the membrane dipole potential. Inhomogeneity of the charge density in the pore, characterized by explicit membrane simulations of toroidal pores, is included in the model. This approach was applied to two extensively studied peptides, magainin and melittin. In agreement with previous work, binding to toroidal pores is more favorable than binding to the flat membrane. The dependence of binding energy on anionic content exhibits different patterns for the two peptides, in correlation with the different lipid selectivity that has been observed experimentally. PMID:23580260

He, Yi; Prieto, Lidia; Lazaridis, Themis

2013-04-11

106

Gas phase kinetic and quantum chemical studies of the reactions of silylene with the methylsilanes. Absolute rate constants, temperature dependences, RRKM modelling and potential energy surfaces.  

PubMed

Time resolved studies of silylene, SiH2, generated by the 193 nm laser flash photolysis of phenylsilane, have been carried out to obtain rate coefficients for its bimolecular reactions with methyl-, dimethyl- and trimethyl-silanes in the gas phase. The reactions were studied over the pressure range 3-100 Torr with SF6 as bath gas and at five temperatures in the range 300-625 K. Only slight pressure dependences were found for SiH2+MeSiH3(485 and 602 K) and for SiH2+Me2SiH2(600 K). The high pressure rate constants gave the following Arrhenius parameters: [TABLE: SEE TEXT]. These are consistent with fast, near to collision-controlled, association processes. RRKM modelling calculations are consistent with the observed pressure dependences (and also the lack of them for SiH2+Me3SiH). Ab initio calculations at both second order perturbation theory (MP2) and coupled cluster (CCSD(T)) levels, showed the presence of weakly-bound complexes along the reaction pathways. In the case of SiH2+MeSiH3 two complexes, with different geometries, were obtained consistent with earlier studies of SiH2+SiH4. These complexes were stabilised by methyl substitution in the substrate silane, but all had exceedingly low barriers to rearrangement to product disilanes. Although methyl groups in the substrate silane enhance the intrinsic SiH2 insertion rates, it is doubtful whether the intermediate complexes have a significant effect on the kinetics. A further calculation on the reaction MeSiH+SiH4 shows that the methyl substitution in the silylene should have a much more significant kinetic effect (as observed in other studies). PMID:17464393

Becerra, Rosa; Carpenter, Ian W; Gordon, Mark S; Roskop, Luke; Walsh, Robin

2007-03-06

107

Spectroscopic studies of cold, gas-phase biomolecular ions  

NASA Astrophysics Data System (ADS)

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

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

108

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

SciTech Connect

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

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

1995-12-01

109

Nonextensive nuclear liquid-gas phase transition  

NASA Astrophysics Data System (ADS)

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

Lavagno, A.; Pigato, D.

2013-10-01

110

Gas-Phase Reactivity of Carboxylic Acid Functional Groups with Carbodiimides  

NASA Astrophysics Data System (ADS)

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

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

2013-01-01

111

In silico models for designing and discovering novel anticancer peptides.  

PubMed

Use of therapeutic peptides in cancer therapy has been receiving considerable attention in the recent years. Present study describes the development of computational models for predicting and discovering novel anticancer peptides. Preliminary analysis revealed that Cys, Gly, Ile, Lys, and Trp are dominated at various positions in anticancer peptides. Support vector machine models were developed using amino acid composition and binary profiles as input features on main dataset that contains experimentally validated anticancer peptides and random peptides derived from SwissProt database. In addition, models were developed on alternate dataset that contains antimicrobial peptides instead of random peptides. Binary profiles-based model achieved maximum accuracy 91.44% with MCC 0.83. We have developed a webserver, which would be helpful in: (i) predicting minimum mutations required for improving anticancer potency; (ii) virtual screening of peptides for discovering novel anticancer peptides, and (iii) scanning natural proteins for identification of anticancer peptides (http://crdd.osdd.net/raghava/anticp/). PMID:24136089

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

2013-10-18

112

In Silico Models for Designing and Discovering Novel Anticancer Peptides  

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

113

Gas-Phase Protein Sequenator.  

National Technical Information Service (NTIS)

The major research conducted with this machine has been the proposed characterization of opioid and non-opioid peptides secreted by the adrenal medulla. To date the sequencer has run 110 samples of which 75 have been adrenal medullary peptides. The other ...

R. V. Lewis

1984-01-01

114

SVOC partitioning between the gas phase and settled dust indoors  

NASA Astrophysics Data System (ADS)

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

Weschler, Charles J.; Nazaroff, William W.

2010-09-01

115

Synthesis of carbon nanbotubes by plasma-enhanced CVD process: gas phase study of synthesis conditions  

NASA Astrophysics Data System (ADS)

To support experimental investigations, a model based on Chemkin^TM software was used to simulate gas phase and surface chemistry during plasma-enhanced catalytic CVD of carbon nanotubes. According to these calculations, gas phase composition, etching process and growth rates are calculated. The role of several carbon species, hydrocarbon molecules and ions in the growth mechanism of carbon nanotubes is presented in this study. Study of different conditions of gas phase activation sources and pressure is performed.

Guláš, M.; Cojocaru, C. S.; Fleaca, C. T.; Farhat, S.; Veis, P.; Le Normand, F.

2008-09-01

116

Activated carbon for gas phase arsenic capture  

Microsoft Academic Search

Investigation of activated carbon as a multifunctional sorbent for trace metal capture is the focus of this study. In addition to mercury and halides, selenium and arsenic represent two of the most volatile trace species that remain in gas phase in substantial amounts. In this work, fundamental sorption characteristics of the activated carbon for arsenic removal from the gas phase

R. Jadhav; H. Gupta; S. Misro; R. Agnihotri; L. S. Fan

1999-01-01

117

Gas-phase NO+ affinities  

PubMed Central

A scale of relative gas-phase NO+ binding energies (BEs) has been constructed by evaluation of NO+-transfer equilibria L1NO+ + L2 ? L2NO+ + L1 by Fourier-transform ion cyclotron resonance mass spectrometry and by application of the kinetic method, based on the metastable fragmentation of L1(NO+)L2 nitryl-ion bound dimers. The relative scale, anchored to the NO+ affinity of water, for 52 ligands, including alkyl halides, alkyl nitrates, alcohols, nitroalkanes, nitriles, aldehydes, ketones, and aromatic and heterocyclic compounds, led to an absolute NO+ affinity scale. The results are compared with those of an earlier study, and the apparent discrepancies are traced to a different choice of the absolute BE value used as the reference standard. The NO+ BEs fit a satisfactorily linear correlation when plotted versus the corresponding proton affinities (PAs). The NO+ BEs, while much lower than the PAs, are nevertheless higher than the corresponding BEs of the strictly related NO2+ cation, a result consistent with the experimental and theoretical results currently available on the structure and the stability of NO+ and NO2+ complexes. The NO+ BE vs. PA correlation allows one to estimate within 1–2 kcal·mol?1 the NO+ BE of the molecules included in the comprehensive PA compilations currently available. For example, the correlation gives the following NO+ affinities of the DNA bases, in kcal·mol?1 (1 kcal = 4.18 kJ): adenine, 40.3; cytosine, 40.4; guanine, 40.1; and thymine, 34.9. The experimental NO+ BE of thymine, the only one accessible to direct measurement, amounts to 35.6 ± 2 kcal·mol?1, which underlines the predictive value of the correlation. This study reports the second successful extension of the kinetic method to the evaluation of the absolute BEs of polyatomic cations, following our recent application to the strictly related NO2+ ion.

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

1997-01-01

118

Gas-phase ion-molecule reactions in mass spectrometric studies of phenyl radical-induced damage on peptides and in the characterization of functional groups in unknown compounds  

Microsoft Academic Search

Some biomolecules, such as DNA, RNA and proteins, undergo aggregation and degradation upon phenyl radical attack. However, the mechanisms of these reactions still remain unknown. Therefore, the reactivity and susceptibility of di-, tri-, tetra-, and larger peptides toward phenyl radical attack was examined via ion-molecule reactions in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer coupled with the laser-induced

Sen Li

2008-01-01

119

Atomic and Molecular Gas Phase Spectrometry.  

National Technical Information Service (NTIS)

The research involves an extensive investigation of analytical and physical aspects of gas phase spectroscopy. The goal of these studies is the development of high sensitivity, high selectivity, precise, accurate methods of analysis of elements in real sa...

J. D. Winefordner

1987-01-01

120

Intramolecular photoelectron diffraction in the gas phase  

NASA Astrophysics Data System (ADS)

We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

Ueda, K.; Miron, C.; Plésiat, E.; Argenti, L.; Patanen, M.; Kooser, K.; Ayuso, D.; Mondal, S.; Kimura, M.; Sakai, K.; Travnikova, O.; Palacios, A.; Decleva, P.; Kukk, E.; Martín, F.

2013-09-01

121

Formation and dissociation processes of gas-phase detergent micelles.  

PubMed

Growing interest in micelles to protect membrane complexes during the transition from solution to gas phase prompts a better understanding of their properties. We have used ion mobility mass spectrometry to separate and assign detergent clusters formed from the n-trimethylammonium bromide series of detergents. We show that cluster size is independent of detergent concentration in solution, increases with charge state, but surprisingly decreases with alkyl chain length. This relationship contradicts the thermodynamics of micelle formation in solution. However, the liquid drop model, which considers both the surface energy and charge, correlates extremely well with the experimental cluster size. To explore further the properties of gas-phase micelles, we have performed collision-induced dissociation on them during tandem mass spectrometry. We observed both sequential asymmetric charge separation and neutral evaporation from the precursor ion cluster. Interestingly, however, we also found markedly different dissociation pathways for the longer alkyl chain detergents, with significantly fewer intermediate ions formed than for those with a shorter alkyl chain. These experiments provide an essential foundation for understanding the process of the gas-phase analysis of membrane protein complexes. Moreover they imply valuable mechanistic details of the protection afforded to protein complexes by detergent clusters during gas-phase activation processes. PMID:22512598

Borysik, Antoni J; Robinson, Carol V

2012-04-26

122

Reaction mechanisms in peptide synthesis. Part 1. Semiquantitative characteristics of the reactivity of 2-methyl-5(4H)-oxazolone with water and ammonia in the gas phase and weakly polar media.  

PubMed

2,4-Dialkyl-5(4H)-oxazolones are well-recognized intermediates in some aminolysis reactions in peptide synthesis. Using the MOPAC molecular orbital programs, detailed geometric and energetic characteristics of the elementary reaction pathways for the additions of water and ammonia to 2-methyl-5(4H)-oxazolone have been determined at the AM1 level. The results demonstrate that the additions must be parsed into a two-step mechanism involving formation of the alpha-hydroxyimine followed by tautomerization to the parent N-acetylamino acid or amide. PMID:1818092

Ciarkowski, J; Chen, F M; Benoiton, N L

1991-12-01

123

Aerosol formation by gas-phase-ozonolysis of small vinylethers  

NASA Astrophysics Data System (ADS)

Secondary organic aerosol (SOA) is formed in the troposphere by ozonolysis of biogenic VOC. The gas-phase processes however, which follow the ozonolysis reaction and lead to the formation of the nucleating compounds are so far poorly understood. A wide range of different primary or secondary products of gas-phase ozonolyses has so far been suggested as potential precursor of nucleation, such as secondary ozonides, dicarboxylic acids and their dimers, and peroxy compounds, such as peroxyhemiacetales or diacylperoxides. In order to assess the influences of oxygen groups in the neighborhood of the alkene double bond on reaction products and particle formation, gas-phase ozonolysis reactions of small vinylethers are investigated in this work. The observations might allow to draw conclusion on the likelihood of potential particle precursors to be formed in the gas phase and to have a sufficiently low vapour pressure for nucleation. Experiments have been carried out in a flow reactor of 1 m length in order to observe SOA formation during the first minute of the reaction, and in a 570 l spherical glass reactor in order to study nucleation or product formation dependent on the reaction time longer than 1 min. Particle size distributions are measured with a scanning mobility particle analyser (SMPS, Model 3936, TSI Inc.), product formation in the gas-phase is analysed by FTIR, and in the particle phase by LC-MS-MS. Threshold alkene conversions necessary for nucleation and initial particle formation are determined in the flow reactor by varying alkene concentrations at constant ozone concentrations and reaction times. Moreover, the influence of experimental conditions, such as relative humidity, is studied.

Sadezky, A.; Mellouki, A.; Winterhalter, R.; Römpp, A.; Moortgat, G.

2003-04-01

124

Gas-phase radiation-chemical oxidation of naphthalene  

Microsoft Academic Search

A kinetic model for the gas-phase radiation-chemical oxidation of naphthalene was developed on the basis of published data.\\u000a The principal routes of naphthalene conversion were studied with the use of the model. It was shown that the main product\\u000a of naphthalene radiolysis under the electron-beam dry scrubbing (EBDS) conditions of the removal of NO and SO2 from industrial gases is

G. V. Nichipor; G. Ya. Gerasimov

2008-01-01

125

Molecular Tagging Velocimetry (MTV) measurements in gas phase flows  

NASA Astrophysics Data System (ADS)

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

Stier, B.; Koochesfahani, M. M.

126

Gas-phase entropy generation during transient methanol droplet combustion  

Microsoft Academic Search

A numerical model was used to investigate gas-phase entropy generation during transient methanol droplet combustion in a low-pressure, zero-gravity, air environment.A comprehensive formulation for the entropy generation in a multi-component reacting flow is derived. Stationary methanol droplet combustion in a low ambient temperature (300 K) and a nearly quiescent atmosphere was studied and the effect of surface tension on entropy generation

Daniel N. Pope; Vasudevan Raghavan; George Gogos

2010-01-01

127

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

SciTech Connect

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

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

2005-03-15

128

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

NASA Astrophysics Data System (ADS)

Tropospheric chemistry and air quality processes were implemented on-line in the Global Environmental Multiscale model. The integrated model, GEM-AQ, has been developed as a platform to investigate chemical weather at scales from global to urban. The model was exercised for five years (2001-2005) to evaluate its ability to simulate seasonal variations and regional distributions of trace gases such as ozone, nitrogen dioxide and carbon monoxide on the global scale. The model results presented are compared with observations from satellites, aircraft measurement campaigns and balloon sondes.

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

2007-10-01

129

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

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

130

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

Microsoft Academic Search

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

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

2002-01-01

131

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

PubMed

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

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

2010-11-16

132

Experimental Thermochemistry of Gas Phase Cytosine Tautomers  

NASA Astrophysics Data System (ADS)

Enthalpies of interconversion are measured for the three lowest energy tautomers of isolated cytosine. The equilibrium distribution of tautomers near 600 K is frozen upon the capture of the gas phase species by low temperature helium nanodroplets. The temperature dependence of the gas phase cytosine tautomer populations is determined with infrared laser spectroscopy of the helium solvated species. The interconverison enthalpies obtained from the van't Hoff relation are 1.14 ± 0.21 and 1.63 ± 0.12 for the C31 rightleftharpoons C32 and C31 rightleftharpoons C1 equilibria, respectively. C31 and C32 are rotamers of an enol tautomer, and C1 is a keto tautomer. The interconversion enthalpies are compared to recent CCSD(T) thermochemistry calculations of cytosine tautomers.

Morrison, A. M.; Douberly, G. E.

2011-06-01

133

Activated carbon for gas phase arsenic capture  

SciTech Connect

Investigation of activated carbon as a multifunctional sorbent for trace metal capture is the focus of this study. In addition to mercury and halides, selenium and arsenic represent two of the most volatile trace species that remain in gas phase in substantial amounts. In this work, fundamental sorption characteristics of the activated carbon for arsenic removal from the gas phase are investigated. Activated carbons with different structural properties are studied for their usefulness in removing arsenic species from flue gas. Arsenic oxide (As{sub 2}O{sub 3}) is used as the source of arsenic. Preliminary sorption studies indicate that arsenic removal occurs by physical adsorption, with increased capture by carbons with higher surface areas.

Jadhav, R.; Gupta, H.; Misro, S.; Agnihotri, R.; Fan, L.S.

1999-07-01

134

A peptide model of insulin folding intermediate with one disulfide  

PubMed Central

Insulin folds into a unique three-dimensional structure stabilized by three disulfide bonds. Our previous work suggested that during in vitro refolding of a recombinant single-chain insulin (PIP) there exists a critical folding intermediate containing the single disulfide A20–B19. However, the intermediate cannot be trapped during refolding because once this disulfide is formed, the remaining folding process is very quick. To circumvent this difficulty, a model peptide ([A20-B19]PIP) containing the single disulfide A20–B19 was prepared by protein engineering. The model peptide can be secreted from transformed yeast cells, but its secretion yield decreases 2–3 magnitudes compared with that of the wild-type PIP. The physicochemical property analysis suggested that the model peptide adopts a partially folded conformation. In vitro, the fully reduced model peptide can quickly and efficiently form the disulfide A20–B19, which suggested that formation of the disulfide A20–B19 is kinetically preferred. In redox buffer, the model peptide is reduced gradually as the reduction potential is increased, while the disulfides of the wild-type PIP are reduced in a cooperative manner. By analysis of the model peptide, it is possible to deduce the properties of the critical folding intermediate with the single disulfide A20–B19.

Yan, Han; Guo, Zhan-Yun; Gong, Xiao-Wen; Xi, Dan; Feng, You-Min

2003-01-01

135

Analysis of gas phase compounds in chemical vapor deposition of carbon from light hydrocarbons  

Microsoft Academic Search

Product distributions in the pyrolysis of ethylene, acetylene, and propylene are studied to obtain an experimental database for a detailed kinetic modeling of gas phase reactions in chemical vapor deposition of carbon from these light hydrocarbons. Experiments were performed with a vertical flow reactor at 900°C and pressures from 2 to 15kPa. Gas phase components were analyzed by both on-line

Koyo Norinaga; Olaf Deutschmann; Klaus J. Hüttinger

2006-01-01

136

The gas-phase acidity of nitrocyclopropane  

NASA Astrophysics Data System (ADS)

Nitrocyclopropane is 10.5 kcal mol-1 weaker as an acid in the gas phase than its open-chain analog, 2-nitropropane. This is attributed to the conflicting hybridization requirements for carbanion stabilization by the cyclopropyl ring and by the nitro group. Based on reactivities, the deprotonated form does not ring-open to either the 2-nitroallyl anion or the 1-nitroallyl anion.

Bartmess, John E.; Wilson, Burton; Sorensen, Daniel N.; Bloor, John E.

1992-09-01

137

Gas-phase chemical sensing using electrochemiluminescence  

Microsoft Academic Search

Tris (2,2?-bipyridine) ruthenium (III) (Ru(bpy)33+), an electrogenerable, chemiluminescent reagent which is electrochemically reversible, has been demonstrated to be a suitable reagent for the sensitive detection of gas-phase hydrazine, and its derivatives dimethyl hydrazine and monomethyl hydrazine. The electrochemical oxidation of Ru(bpy)32+ to Ru(bpy)33+ creates a strong oxidizer, whose reduction back down to Ru(bpy)32+ by reaction with areducing analyte is typified

Greg E Collins

1996-01-01

138

Gas-Phase Photoionization Of A Protein  

NASA Astrophysics Data System (ADS)

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

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

2010-07-01

139

Kinetics of the initial stage of isothermal gas phase formation  

Microsoft Academic Search

at least one nucleus bubble and of the total volume V, of the newly formed gas phase in the case of progressive or instantaneous bubble nucleation. Different definitions of the critical supersaturation for gas phase formation are considered and their experimental applicability is discussed. The general results are applied to the particular cases of gas phase formation at constant and

D. Kashchiev; A. Firoozabadi

1993-01-01

140

Selective Covalent Bond Formation in Polypeptide Ions via Gas-Phase Ion/Ion Reaction Chemistry  

PubMed Central

Primary amines present in protonated polypeptides can be covalently modified via gas-phase ion/ion reactions using bifunctional reagent ions. The use of reagent anions with a charge bearing site that leads to strong interactions with the polypeptide, such as sulfonic acid, gives rise to the formation of a long-lived adduct. A distinct reactive functional group, an aldehyde in the present case, can then undergo a reaction with the peptide. Collisional activation of the adduct ion formed from a reagent with an aldehyde group and a peptide ion with a primary amine gives rise to water loss in conjunction with imine (Schiff base) formation. The covalently-bound modification is retained upon subsequent collisional activation. This work demonstrates the ability to selectively modify polypeptide ions in the gas-phase within the context of a multi-stage mass spectrometry experiment.

Han, Hongling; McLuckey, Scott A.

2009-01-01

141

Gas-phase purification enables accurate, large-scale, multiplexed proteome quantification with isobaric tagging  

PubMed Central

We describe a mass spectrometry method, QuantMode, which improves the accuracy of isobaric tag–based quantification by alleviating the pervasive problem of precursor interference—co-isolation of impurities—through gas-phase purification. QuantMode analysis of a yeast sample ‘contaminated’ with interfering human peptides showed substantially improved quantitative accuracy compared to a standard scan, with a small loss of spectral identifications. This technique will allow large-scale, multiplexed quantitative proteomics analyses using isobaric tagging.

Wenger, Craig D; Lee, M Violet; Hebert, Alexander S; McAlister, Graeme C; Phanstiel, Douglas H; Westphall, Michael S; Coon, Joshua J

2011-01-01

142

Helix versus sheet formation in a small peptide  

NASA Astrophysics Data System (ADS)

Segments with the amino acid sequence EKAYLRT (glutamine-lysine-alanine-tyrosine-leucine-arginine-threonine) appear in naturally occurring proteins both in ?-helices and ?-sheets. For this reason, we have used this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both the solvated molecule and EKAYLRT in gas phase form an ?-helix when not interacting with other molecules. However, in the vicinity of a ?-strand, the peptide forms a ?-strand. Because of this change in secondary structure our peptide may provide a simple model for the ??? transition that is supposedly related to the outbreak of prion diseases and similar illnesses.

Peng, Yong; Hansmann, Ulrich H.

2003-10-01

143

Gas-phase metalloprotein complexes interrogated by ion mobility-mass spectrometry  

NASA Astrophysics Data System (ADS)

Gas-phase biomolecular structure may be explored through a number of analytical techniques. Ion mobility-mass spectrometry (IM-MS) continues to prove itself as a sensitive and reliable bioanalytical tool for gas-phase structure determination due to intense study and development over the past 15 years. A vast amount of research interest, especially in protein and peptide conformational studies has generated a wealth of structural information for biological systems from small peptides to megadalton-sized biomolecules. In this work, linear low field IM-MS has been used to study gas-phase conformations and determine rotationally averaged collision cross-sections of three metalloproteins--cytochrome c, haemoglobin and calmodulin. Measurements have been performed on the MoQToF, a modified QToF 1 instrument (Micromass UK Ltd., Manchester, UK) modified in house. Gas-phase conformations and cross-sections of multimeric cytochrome c ions of the form [xM + nH+]n+ for x = 1-3 (monomer to trimer) have been successfully characterised and measured. We believe these to be the first reported collision cross-sections of higher order multimeric cytochrome c. Haemoglobin is investigated to obtain structural information on the associative mechanism of tetramer formation. Haemoglobin molecules, comprising apo- and holo-monomer chains, dimer and tetramer are transferred to the gas phase under a range of solution conditions. Structural information on the proposed critical intermediate, semi-haemoglobin, is reported. Cross-sections of the calcium binding protein calmodulin have been obtained under a range of calcium-bound conditions. Metalloprotein collision cross-sections from ion mobility measurements are compared with computationally derived values from published NMR and X-ray crystallography structural data. Finally we consider the change in the density of the experimentally measured rotationally averaged collision cross-section for compact geometries of the electrosprayed proteins.

Faull, Peter A.; Korkeila, Karoliina E.; Kalapothakis, Jason M.; Gray, Andrew; McCullough, Bryan J.; Barran, Perdita E.

2009-06-01

144

Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone  

PubMed Central

A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins.

Ponomarev, Sergei Y.; Kaminski, George A.

2011-01-01

145

PeptideBuilder: A simple Python library to generate model peptides.  

PubMed

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

2013-05-21

146

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.

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

2013-01-01

147

Hydrogen atoms and gas phase chemical dynamics  

SciTech Connect

This thesis describes the applications of Doppler spectroscopy of hydrogen atoms to gas phase chemical dynamics. Hydrogen atoms are generated in the electronic ground state (1s) either from photodissociation or from chemical reactions. They are then excited to the 2p state by 121.6 nm light. The fluorescence intensity (2p [yields] 1s) of the H atoms is monitored by a photomultiplier tube. The measurement of the H atom velocity helps us to follow chemical reactions in the gas phase occurring in a very short time. There are three experimental works described here. The first one shows how the Walden inversion, previously observed indirectly by organic chemists, is followed in the reaction of H atoms with CD[sub 4]. The reactions of electronically excited Xe and Kr atoms with H[sub 2] is illustrated in the next work. The indirect evidence for the formation of XeD and KrD is presented. In the third work, the photodissociation dynamics of small molecules like HCl, HCN and C[sub 2]H[sub 2] is discussed.

Chattopadhyay, A.

1992-01-01

148

NMR-derived model for a peptide-antibody complex  

SciTech Connect

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

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

1990-10-01

149

Gas phase methylation of methyl acetoacetate. Experimental and theoretical study  

NASA Astrophysics Data System (ADS)

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

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

1992-04-01

150

Gas-phase thermochemistry of chloropyridines  

NASA Astrophysics Data System (ADS)

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

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

2005-04-01

151

Gas phase hyper-Rayleigh scattering measurements  

NASA Astrophysics Data System (ADS)

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

Shelton, David P.

2012-07-01

152

Femtosecond lasers in gas phase chemistry.  

PubMed

This critical review is intended to provide an overview of the state-of-the-art in femtosecond laser technology and recent applications in ultrafast gas phase chemical dynamics. Although "femtochemistry" is not a new subject, there have been some tremendous advances in experimental techniques during the last few years. Time-resolved photoelectron spectroscopy and ultrafast electron diffraction have enabled us to observe molecular dynamics through a wider window. Attosecond laser sources, which have so far only been exploited in atomic physics, have the potential to probe chemical dynamics on an even faster timescale and observe the motions of electrons. Huge progress in pulse shaping and pulse characterisation methodology is paving the way for exciting new advances in the field of coherent control. PMID:16239996

Carley, R E; Heesel, E; Fielding, H H

2005-09-29

153

Modelling the effect of osmolytes on peptide mechanical unfolding  

NASA Astrophysics Data System (ADS)

Osmolyte molecules can be classified in two different groups with respect to their effect on protein stability: osmoprotectants, which stabilize the protein or peptide folded state, and denaturants, which favor the denaturated state. Mechanical unfolding free energy of a model peptide has been obtained from umbrella sampling and weighted histogram analysis method, and the effect of four different osmolytes on the free energy difference between the folded and the denaturated state have been calculated. The observed trend mirrors the expected behavior of the studied osmolytes and unfolding pathways analysis allows an insight in the osmolyte action mechanism.

Pieraccini, Stefano; Conti, Simone; Chaurasia, Shilpi; Sironi, Maurizio

2013-07-01

154

Gas-Phase Ion/Ion Reactions of Multiply Protonated Polypeptides with Metal Containing Anions  

PubMed Central

Gas-phase reactions of multiply protonated polypeptides and metal containing anions represent a new methodology for manipulating the cationizing agent composition of polypeptides. This approach affords greater flexibility in forming metal containing ions than commonly used methods, such as electrospray ionization of a metal salt/peptide mixture and matrix-assisted laser desorption. Here, the effects of properties of the polypeptide and anionic reactant on the nature of the reaction products are investigated. For a given metal, the identity of the ligand in the metal containing anion is the dominant factor in determining product distributions. For a given polypeptide ion, the difference between the metal ion affinity and the proton affinity of the negatively charged ligand in the anionic reactant is of predictive value in anticipating the relative contributions of proton transfer and metal ion transfer. Furthermore, the binding strength of the ligand anion to charge sites in the polypeptide correlates with the extent of observed cluster ion formation. Polypeptide composition, sequence, and charge state can also play a notable role in determining the distribution of products. In addition to their usefulness in gas-phase ion synthesis strategies, the reactions of protonated polypeptides and metal containing anions represent an example of a gas-phase ion/ion reaction that is sensitive to polypeptide structure. These observations are noteworthy in that they allude to the possibility of obtaining information, without requiring fragmentation of the peptide backbone, about ion structure as well as the relative ion affinities associated with the reactants.

Newton, Kelly A.; Amunugama, Ravi; McLuckey, Scott A.

2005-01-01

155

Uncertainties in gas-phase atmospheric iodine chemistry  

NASA Astrophysics Data System (ADS)

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

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

2012-09-01

156

Transition metal complex cations as reagents for gas-phase transformation of multiply deprotonated polypeptides.  

PubMed

Triply deprotonated DGAILDGAILD was reacted in the gas-phase with doubly charged copper, cobalt, and iron metal complexes containing either two or three phenanthroline ligands. Reaction products result from two major pathways. The first pathway involves the transfer of an electron from the negatively charged peptide to the transition-metal complex. The other major pathway consists of the displacement of the phenanthroline ligands by the peptide resulting in the incorporation of the transition-metal into the peptide to form [M - 3H + X(II)](-) ions, where X is Cu, Co, or Fe, respectively. The extent to which each pathway contributes is dependent on the nature of transition-metal complex. In general, bis-phen complexes result in more electron-transfer than the tris-phen complexes, while the tris-phen complexes result in more metal insertion. The metal in the complex plays a large role as well, with the Cu containing complexes giving rise to more electron transfer than the corresponding complexes of Co and Fe. The results show that a single reagent solution can be used to achieve two distinct sets of products (i.e., electron-transfer products and metal insertion products). These results constitute the demonstration of novel means for the gas-phase transformation of peptide anions from one ion type to another via ion/ion reactions using reagents formed via electrospray ionization. PMID:19535265

Crizer, David M; Xia, Yu; McLuckey, Scott A

2009-05-20

157

Gas-Phase Chemistry of Multiply Charged Bioions in Analytical Mass Spectrometry  

PubMed Central

Ion chemistry has long played an important role in molecular mass spectrometry (MS), as it is central to the use of MS as a structural characterization tool. With the advent of ionization methods capable of producing gaseous ions from large biomolecules, the chemistry of gaseous bioions has become a highly active area of research. Gas-phase biomolecule-ion reactions are usually driven by interactions with neutral molecules, photons, electrons, ions, or surfaces. Ion dissociation or transformation into different ion types can be achieved. The types of reaction products observed depend on the characteristics of the ions, the transformation methods, and the time frame of observation. This review focuses on the gas-phase chemistries of ions derived from the electrospray ionization of peptides, proteins, and oligonucleotides, with particular emphasis on their utility in bioanalysis. Various ion-transformation strategies, which further facilitate structural interrogation by converting ions from one type to another, are also summarized.

Huang, Teng-Yi; McLuckey, Scott A.

2011-01-01

158

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

Microsoft Academic Search

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 sink

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

2007-01-01

159

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

2007-01-01

160

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

SciTech Connect

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

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

1997-07-01

161

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

NASA Astrophysics Data System (ADS)

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

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

2012-11-01

162

Gas-Phase Spectroscopy of Biomolecular Building Blocks  

Microsoft Academic Search

Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from

Mattanjah S. de Vries; Pavel Hobza

2007-01-01

163

How Ubiquitin Unfolds after Transfer into the Gas Phase  

NASA Astrophysics Data System (ADS)

The structural evolution of ubiquitin after transfer into the gas phase was studied by electron capture dissociation. Site-specific fragment yields show that ubiquitin's solution fold is overall unstable in the gas phase, but unfolding caused by loss of solvent is slowest in regions stabilized by salt bridges.

Skinner, Owen S.; McLafferty, Fred W.; Breuker, Kathrin

2012-06-01

164

Gas Phase Ignition of a Hypergolic Propellant System  

Microsoft Academic Search

A method of measuring ignition delay of a gas phase hypergolic propellant system in quasi steady flow and low pressure conditions is described. The effects of ambient pressure, flow parameters and propellant temperature on the gas phase ignition delay of the system nitrogen tetroxide-UDMH are investigated. An empirical equation relating the ignition delay to ambient pressure and temperature is obtained

HIROSHI MIYAJIMA; HIROSHI SAKAMOTO

1971-01-01

165

Gas-phase basicity of 2-furaldehyde.  

PubMed

2-Furaldehyde (2-FA), also known as furfural or 2-furancarboxaldehyde, is an heterocyclic aldehyde that can be obtained from the thermal dehydration of pentose monosaccharides. This molecule can be considered as an important sustainable intermediate for the preparation of a great variety of chemicals, pharmaceuticals and furan-based polymers. Despite the great importance of this molecule, its gas-phase basicity (GB) has never been measured. In this work, the GB of 2-FA was determined by the extended Cooks's kinetic method from electrospray ionization triple quadrupole tandem mass spectrometric experiments along with theoretical calculations. As expected, computational results identify the aldehydic oxygen atom of 2-FA as the preferred protonation site. The geometries of O-O-cis and O-O-trans 2-FA and of their six different protomers were calculated at the B3LYP/aug-TZV(d,p) level of theory; proton affinity (PA) values were also calculated at the G3(MP2, CCSD(T)) level of theory. The experimental PA was estimated to be 847.9 ± 3.8 kJ mol(-1), the protonation entropy 115.1 ± 5.03 J mol(-1) K(-1) and the GB 813.6 ± 4.08 kJ mol(-1) at 298 K. From the PA value, a ?H°(f) of 533.0 ± 12.4 kJ mol(-1) for protonated 2-FA was derived. PMID:23147827

Ricci, Andreina; Piccolella, Simona; Pepi, Federico; Patsilinakos, Alexandros; Ragno, Rino; Garzoli, Stefania; Giacomello, Pierluigi

2012-11-01

166

Transferring pharmaceuticals into the gas phase  

NASA Astrophysics Data System (ADS)

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

Christen, Wolfgang; Krause, Tim; Rademann, Klaus

2008-11-01

167

Gas phase protonation of trifluoromethyl sulfur pentafluoride.  

PubMed

The gas phase protonation of SF5CF3, a potent new greenhouse gas recently discovered in stratospheric air samples, was studied by the joint application of mass spectrometric and ab initio theoretical methods. The reaction is essentially dissociative leading to the formation of HF, CF4 and SF3+ as main fragmentation products. Consistent with collisionally activated dissociation (CAD) mass spectrometric results, theoretical calculations identified the loosely bounded ion-molecule complex [HF-SF4 CF3], I, as the most stable isomer on the [SF5CF3]H+ potential energy surface. The proton affinity of SF5CF3 estimated from FT-ICR 'bracketing' experiments was found to be 152.5 +/- 3 kcal mol(-1) which agrees with the values obtained from theoretical calculations at B3LYP and CCSD(T) levels of theory, 154.0 +/- 3 and 153.4 +/- 3 kcal mol(-1), respectively. These results suggest that the basicity of SF5CF3 is higher than that of atmospheric cations such as H2O+; they need to be considered when evaluating the lifetime of SF5CF3 since it can be destroyed by proton transfer reactions. PMID:19791331

Pepi, Federico; Ricci, Andreina; Di Stefano, Marco; Rosi, Marzio

2005-03-21

168

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

PubMed

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

Balucani, Nadia; Casavecchia, Piergiorgio

2006-12-01

169

Peptide neuromodulation in invertebrate model systems  

PubMed Central

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

Taghert, Paul H.; Nitabach, Michael N.

2012-01-01

170

Effect of liquid inhibitors on PCDD/F formation. Prediction of particle-phase PCDD/F concentrations using PLS modelling with gas-phase chlorophenol concentrations as independent variables.  

PubMed

Emissions of polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) from municipal waste incineration are currently a subject of considerable public concern because of their extreme toxicity. PCDD/F formation in incineration processes is being studied widely, but little work has been done on their inhibition. We studied the effect of two liquid inhibitors, sodium ammonium hydrogen phosphate (NAHF) and urea (H2NCONH2), on PCDD/F formation in the combustion of liquid fuel doped with copper and chlorine using a pilot-scale plant. The inhibitors were injected into the flue gas stream at a temperature of 725 degrees C, whereupon both the chlorophenol and PCDD/F concentrations decreased. Particle-phase PCDD/F concentrations in particular decreased by up to 90% with NAHF and 70% with urea, but gas phase reduction took place only with urea. The results suggest that the formation of PCDD/Fs is hindered in the particle phase at the early stages of the PCDD/F formation chain, probably even before precursors such as chlorophenols have been formed. As a consequence, particle-phase PCDD/F concentrations can be predicted by a PLS (partial least-squares) approach with the gas-phase chlorophenol concentrations as independent variables. The structure and partial charges of Cu(+)-urea complex were calculated by the HF/3-21G basis set. PMID:10101863

Tuppurainen, K; Aatamila, M; Ruokojärvi, P; Halonen, I; Ruuskanen, J

1999-04-01

171

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

PubMed

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

Fang, Yigang; Bennett, Andrew; Liu, Jianbo

2010-12-07

172

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.

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

1995-01-01

173

Probing aerosol formation by comprehensive measurements of gas phase oxidation products  

NASA Astrophysics Data System (ADS)

A comprehensive suite of chemical ionization mass spectrometers (CIMS) were deployed for chamber studies of monoterpene oxidation. The CIMS instruments were able to detect several different groups of compounds ranging from volatile to practically non-volatile. The compound groups showed very different behavior and correlations with aerosol number and mass. Results suggest that major gas phase contributors are not considered in current models.

Ehn, Mikael; Kleist, Einhard; Junninen, Heikki; Sipilä, Mikko; Petäjä, Tuukka; Pullinen, Iida; Springer, Monika; Andres, Stefanie; Rissanen, Matti; Kontkanen, Jenni; Schobesberger, Siegfried; Rubach, Florian; Tillman, Ralf; Lee, Ben H.; Lopez-Hilfiker, Felipe; Kerminen, Veli-Matti; Kulmala, Markku; Worsnop, Douglas R.; Thornton, Joel; Wildt, Jürgen; Mentel, Thomas F.

2013-05-01

174

Titania formation by TiCl 4 gas phase oxidation, surface growth and coagulation  

Microsoft Academic Search

Titania particle formation by TiCl4 gas phase oxidation, surface growth and coagulation is investigated by a moving sectional population balance model. The dynamic evolution of the detailed particle size distribution is studied accounting for and neglecting the effect of surface growth. The effects of process temperature, T, and precursor volume fraction, ?, on the average diameter, dp, and geometric standard

Patrick T. Spicer; Olivier Chaoul; Stavros Tsantilis; Sotiris E. Pratsinis

2002-01-01

175

Reactions of an aromatic ?,?-biradical with amino acids and dipeptides in the gas phase  

Microsoft Academic Search

Gas-phase reactivity of a positively charged aromatic ?,?-biradical (N-methyl-6,8-didehydroquinolinium) was examined toward six aliphatic amino acids and 15 dipeptides by using Fourier transform\\u000a ion cyclotron resonance mass spectrometry (FT-ICR) and laser-induced acoustic desorption (LIAD). While previous studies have\\u000a revealed that H-atom and NH2 abstractions dominate the reactions of related monoradicals with aliphatic amino acids and small peptides, several additional,\\u000a unprecedented

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

2010-01-01

176

Bioactive peptides released from Saccharomyces cerevisiae under accelerated autolysis in a wine model system.  

PubMed

The ACE inhibitory activity (IACE) and the oxygen radical absorbance capacity (ORAC-FL) values of yeast peptides isolated from a model wine during accelerated autolysis of Saccharomyces cerevisiae have been studied. Samples were taken at 6, 24, 48, 121, and 144 h of autolysis. Peptide concentration increased throughout autolysis process. Peptides were fractionated into 2 fractions: F1, constituted by hydrophilic peptides, and F2, containing hydrophobic peptides. Both IACE activity and ORAC-FL values increased during 121 h of autolysis, then decreased afterward. Peptide fraction F2 was the main fraction involved in IACE activity and ORAC-FL. PMID:17995652

Alcaide-Hidalgo, J M; Pueyo, E; Polo, M C; Martínez-Rodríguez, A J

2007-09-01

177

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

Microsoft Academic Search

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

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

2001-01-01

178

Crystal Structure of a Model Spider Silk Peptide  

NASA Astrophysics Data System (ADS)

Crystallization study on a novel model silk peptide has been carried out using optical microscopy, AFM, TEM and electron diffraction. The sequence of the peptide, (E)5(GDVGGAGATGGS)2(E)5, is based on the GXYGGZ motif in the less repetitive amorphous blocks of Nephila clavipes spider dragline silk. When the peptide was crystallized out of aqueous solution, spherulites as well as dendritic crystals on the order of several to tens of microns in diameter were observed under polarizing optical microscope, depending on drying speed, volume of the droplet and concentration. The same crystals were collected and sonicated in methanol, a non-solvent, to yield individual crystals that were later examined in the electron microscope. Regular-shaped lamellar crystals of micron size were observed in the TEM. The lamellar thickness as determined by Pt/Pd shadowing and AFM is 50 Å. Selected area electron diffraction showed single crystal diffraction patterns indicating a possible orthorhombic unit cell of 9.91 x 5.57 x 20.40 Å.

Chen, Shujun; Gido, Samuel; Valluzzi, Regina; Kaplan, David

2001-03-01

179

Gas-Phase Spectroscopy of Biomolecular Building Blocks  

NASA Astrophysics Data System (ADS)

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

de Vries, Mattanjah S.; Hobza, Pavel

2007-05-01

180

Gas-Phase Aldol Condensation Over Tin on Silica Catalysts.  

National Technical Information Service (NTIS)

Contents: Aldol condensation; Catalyst preparation and composition; Catalyst performance; Kinetics; On the nature of the active site for the aldol condensation over tin on silica catalysts; Gas-phase aldol condensation of n-butanal over tin on silica cata...

J. Venselaar

1980-01-01

181

Development and validation of a portable gas phase standard ...  

Treesearch

MOCCS was validated using three different comparisons: (1) TOC of high ... (2) a gas-phase benzene standard was generated using a permeation source and ... agreement (<4% relative difference), and (3) total carbon measurement of 4 ...

182

Low-pressure Ion Mobility-Time-of-Flight Mass Spectrometry for Metalated Peptide Ion Structural Characterization: Tyrosine -containing Tripeptides and Homologous Septapeptides  

Microsoft Academic Search

In this report, we describe the use of ion mobility (IM) measurements as a structural probe of model metalated peptides, which may aid understanding of the gas-phase structures of metal- bearing peptide\\/protein ions. An important component of this work is the computational methodology used to determine candidate structures which agree with the experimental data. Example systems include the tyrosine-containing tripeptides,

J. Garrett Slaton; Holly A. Sawyer; David H. Russell

183

CHEMKIN2. General Gas-Phase Chemical Kinetics  

Microsoft Academic Search

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,

Rupley

1992-01-01

184

The gas phase oxidation of elemental mercury by ozone  

Microsoft Academic Search

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

B. Hall

1995-01-01

185

Gas-phase selective etching of native oxide  

Microsoft Academic Search

Gas-phase selective etching of native oxide film formed on a silicon surface is an essential requirement for ULSI process technologies. Ultraclear anhydrous hydrogen fluoride (AHF) gas and a corrosion-free system were developed for this etching process. The reaction mechanism of silicon oxide film with moistureless HF was investigated, and selective etching conditions were developed. The gas-phase selective etching of native

NOBUHIRO MIKI; HIROHISA KIKUYAMA; ICHIROH KAWANABE; MASAYUKI MIYASHITA; TADAHIRO OHMI

1990-01-01

186

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

Microsoft Academic Search

The impact of two recent gas-phase chemical kinetic mechanisms (CB05 and RACM2) on the formation of secondary inorganic and organic aerosols is compared for simulations of PM2.5 over Europe between 15 July and 15 August 2001. The host chemistry transport model is Polair3D of the Polyphemus air-quality platform. Particulate matter is modeled with a sectional aerosol model (SIREAM), which is

Y. Kim; K. Sartelet; C. Seigneur

2011-01-01

187

Gas phase effects on laser ignition of XM39  

NASA Astrophysics Data System (ADS)

A CO2 laser was used to investigate the effects of gas phase reactions during radiant heating of XM39 in a closed bomb at low loading density. Times to detect emission of pressurization in N2 or O2 are about the same. At flux levels (cal/(sq cm)-s) between 61 and 112, there is a minimum partial oxygen pressure required for flamespreading. At lower partial pressures, the difference between effects of O2 and N2 on the XM39 response to laser radiation is small. At higher partial pressures, the presence of O2 leads to increased pressurization rates. At one atm this minimum occurs at approximately .2 atms. Results in N2 indicate that the minimum value is lower at higher initial pressures. Predictions of a heterogeneous radiant ignition model were inconsistent with ignition delays derived from pressure measurements. The validity of the model for ignition in closed bombs may be questionable, but part of the problem may be attributed to difficulties in estimating the rate constant of the exothermic heterogeneous reaction needed for the model calculations.

Cohen, Art; Beyer, Richard; Kotlar, A.; Newberry, J.

1993-11-01

188

Question 7: Modelling Minimal `Lipid-Peptide' Cells  

NASA Astrophysics Data System (ADS)

This contribution is aimed to give support to ‘bottom-up’ approaches to the minimal or early cell research project. Even if, from this perspective, the most simple living cell still seems very far away, the analysis of less complex, infrabiological cellular systems (some of which could be relatively soon implemented in the lab) probably holds the key, or one of the fundamental keys, to the problem of origins of life. On these lines, we propose a simulation model to study the transition from proto-metabolic ‘lipid’ cells to ‘lipid-peptide’ cells, as a critical step in which self-reproducing vesicles could develop into more functionalized supramolecular systems

Ruiz-Mirazo, Kepa; Mavelli, Fabio

2007-10-01

189

Gas-phase Acidities of Aspartic Acid, Glutamic Acid, and their Amino Acid Amides.  

SciTech Connect

Gas-phase acidities (GA or ?Gacid) for the two most acidic common amino acids, aspartic acid and glutamic acid, have been determined for the first time. Because of the amide linkage’s importance in peptides and as an aid in studying side chain versus main chain deprotonation, aspartic acid amide and glutamic acid amide were also studied. Experimental GA values were measured by proton transfer reactions in an electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer. Calculated GAs were obtained by density functional and molecular orbital theory approaches. The best agreement with experiment was found at the G3MP2 level; the MP2/CBS and B3LYP/aug-cc-pVDZ results are 3–4 kcal/mol more acidic than the G3MP2 results. Experiment shows that aspartic acid is more acidic than glutamic acid by ca. 3 kcal/mol whereas the G3MP2 results show a smaller acidity difference of 0.2 kcal/mol. Similarly, aspartic acid amide is experimentally observed to be ca. 2 kcal/mol more acidic than glutamic acid amide whereas the G3MP2 results show a correspondingly smaller energy difference of 0.7 kcal/mol. The computational results clearly show that the anions are all ring-like structures with strong hydrogen bonds between the OH or NH2 groups and the CO2? group from which the proton is removed. The two amino acids are main-chain deprotonated. In addition, use of the COSMO model for the prediction of the free energy differences in aqueous solution gave values in excellent agreement with the most recent experimental values for pKa. Glutamic acid is predicted to be more acidic than aspartic acid in aqueous solution due to differential solvation effects.

Li, Zhong; Matus, Myrna H.; Velazquez, Hector A.; Dixon, David A.; Cassady, Carolyn J.

2007-02-14

190

How cations change peptide structure.  

PubMed

Specific interactions between cations and proteins have a strong impact on peptide and protein structure. Herein, we shed light on the nature of the underlying interactions, especially regarding effects on the polyamide backbone structure. This was done by comparing the conformational ensembles of model peptides in isolation and in the presence of either Li(+) or Na(+) by using state-of-the-art density-functional theory (including van der Waals effects) and gas-phase infrared spectroscopy. These monovalent cations have a drastic effect on the local backbone conformation of turn-forming peptides, by disruption of the hydrogen-bonding networks, thus resulting in severe distortion of the backbone conformations. In fact, Li(+) and Na(+) can even have different conformational effects on the same peptide. We also assess the predictive power of current approximate density functionals for peptide-cation systems and compare to results with those of established protein force fields as well as high-level quantum chemistry calculations (CCSD(T)). PMID:23853047

Baldauf, Carsten; Pagel, Kevin; Warnke, Stephan; von Helden, Gert; Koksch, Beate; Blum, Volker; Scheffler, Matthias

2013-07-12

191

Molecular View of Water Dynamics near Model Peptides  

PubMed Central

Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for lowconcentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent ? and a longer structural relaxation time ? than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.

Russo, Daniela; Murarka, Rajesh K.; Copley, John R. D.; Head-Gordon, Teresa

2009-01-01

192

Gas-phase conformational and energetic properties of deprotonated dinucleotides  

NASA Astrophysics Data System (ADS)

Ion mobility experiments and molecular modeling calculations were used to investigate the gas-phase conformations and folding energetics of 16 deprotonated dinucleotides. [M H]^- ions were formed by MALDI and their collision cross-sections measured in helium using ion mobility based techniques. Cross-sections of theoretical structures, generated by molecular mechanics/dynamics calculations, were compared to the experimental values for conformational identification of the dinucleotides. Temperature dependent measurements and kinetic theory were also used to obtain energetic and dynamic data concerning the folding properties of the dinucleotides. Three distinct families of conformations, with significantly different collision cross-sections, were identified: a “stacked” family in which the two nucleobases stack; an “H-bonded” family in which the two nucleobases stay in the same plane and are hydrogen-bonded to each other; and an “open” family in which the two nucleobases are separated from each other. At temperatures geq 300 K these conformers rapidly interconvert in most systems, but they can be separated and individually observed in the lower temperature (80 200 K) experiments. The types and relative amounts of each conformer observed, and the temperature at which they can be separated, are base and sequence dependent. Theoretical modeling of the temperature-dependent data was used to determine isomerization barrier heights between the various conformers and yielded values between 0.8 12.9 kcal/mol, depending on the dinucleotide.

Gidden, J.; Bowers, M. T.

2002-09-01

193

Atomic and molecular physics in the gas phase.  

PubMed

The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This circumstance has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years, there has been a great deal of progress in our understanding of these interactions, much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections, and lead to knowledge of the regions of energy deposition where molecular and phase effects are important-knowledge that guides development in appropriate theory. In this report, studies of the doubly differential cross sections, which are crucial to the development of stochastic energy deposition calculations and track structure simulation, are reviewed. We discuss areas of understanding and address directions for future work. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged-particle interactions with atomic and molecular targets. PMID:1811483

Toburen, L H

1991-01-01

194

Gas-Phase Reactions of Halogen Species of Atmospheric Importance.  

NASA Astrophysics Data System (ADS)

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

Heard, Anne C.

195

Comparison of Different Gas-Phase Mechanisms and Aerosol Modules for Simulating Particulate Matter Formation  

Microsoft Academic Search

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 ?2.5 ?m) particulate matter (PM2.5) formation is studied. The major sources of uncertainty in the chemistry of SOA formation are

Youngseob Kim; Florian Couvidat; Karine Sartelet; Christian Seigneur

2011-01-01

196

Gas-phase radiation-chemical formation of dioxins from chlorinated phenols  

Microsoft Academic Search

The gas-phase radiation-chemical formation of dioxins from chlorinated phenols in the electron-beam removal of toxic impurities\\u000a from industrial gases is considered. A kinetic model of the process is proposed. Conditions under which the efficiency of\\u000a removal of the above compounds from gases significantly decreases were determined with the use of this model. The results\\u000a of a numerical simulation are compared

G. Ya. Gerasimov

2007-01-01

197

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

Microsoft Academic Search

The impact of two recent gas-phase chemical kinetic mechanisms (CB05 and RACM2) on the formation of secondary inorganic and organic aerosols is compared for simulations of PM2.5 over Europe between 15 July and 15 August 2001. The host chemistry transport model is Polair3D of the Polyphemus air-quality platform. Particulate matter is modeled with SIREAM, which is coupled to the thermodynamic

Y. Kim; K. Sartelet; C. Seigneur

2010-01-01

198

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

PubMed

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

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

2013-03-01

199

Estimation of gas phase mixing in packed beds  

SciTech Connect

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

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

2008-04-15

200

Kinetic theory of steady chemical nucleation in the gas phase  

NASA Astrophysics Data System (ADS)

We develop a kinetic theory of nucleation involving chemical reactions in the gas phase. For the basis of deriving the chemical nucleation rate, chemical kinetic considerations are presented on the steady current density and the effective rate constants of the overall reaction, which is a sum of a sequential elementary reactions. We formulate the steady rate of chemical nucleation in a multi-component vapor, in which nucleation occurs via the chemical reactions yielding a condensate having a stoichiometric composition. An exact expression of the steady nucleation rate is given together with its approximate formulas for practical applications. The present formulation is not concerned with any particular cluster model. The supersaturation ratio for a many-component vapor is defined so as to be a natural extension of that for a one-component vapor. It is shown that the transition probabilities due to growth and decay of the clusters are of the same form as the growth and evaporation rates in a one-component vapor.

Yamamoto, T.; Chigai, T.; Watanabe, S.; Kozasa, T.

2001-12-01

201

Binding of inositol stereoisomers to model amyloidogenic peptides.  

PubMed

The self-aggregation of proteins into amyloid fibrils is a pathological hallmark of numerous incurable diseases such as Alzheimer's disease. scyllo-Inositol is a stereochemistry-dependent in vitro inhibitor of amyloid formation. As the first step to elucidate its mechanism of action, we present molecular dynamics simulations of scyllo-inositol and its inactive stereoisomer, chiro-inositol, with simple peptide models, alanine dipeptide (ADP) and (Gly-Ala)(4). We characterize molecular interactions and compute equilibrium binding constants between inositol and ADP as well as, successively, monomers, amorphous aggregates, and fibril-like ?-sheet aggregates of (Gly-Ala)(4). Inositol interacts weakly with all peptide systems considered, with millimolar to molar affinities, and displaces the conformational equilibria of ADP but not of the (Gly-Ala)(4) systems. However, scyllo- and chiro-inositol adopt different binding modes on the surface of ?-sheet aggregates. These results suggest that inositol does not inhibit amyloid formation by breaking up preformed aggregates but rather by binding to the surface of prefibrillar aggregates. PMID:22091989

Li, Grace; Rauscher, Sarah; Baud, Stéphanie; Pomès, Régis

2011-12-09

202

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

SciTech Connect

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

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

2009-02-01

203

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

PubMed

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

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

2012-12-13

204

Mass spectrometry analysis of hepcidin peptides in experimental mouse models.  

PubMed

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

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

2011-03-08

205

Subunit architecture of multiprotein assemblies determined using restraints from gas-phase measurements.  

PubMed

Protein interaction networks are becoming an increasingly important area of research within structural genomics. Here we present an ion mobility-mass spectrometry approach capable of distinguishing the overall subunit architecture of protein complexes. The approach relies on the simultaneous measurement in the gas phase of the mass and size of intact assemblies and subcomplexes. These data are then used as restraints to generate topological models of protein complexes. To test and develop our method, we have chosen two well-characterized homo-dodecameric protein complexes: ornithine carbamoyl transferase and glutamine synthetase. By forming subcomplexes related to the comparative strength of the subunit interfaces, acquiring ion mobility data, and subsequent modeling, we show that these "building blocks" retain their native interactions and do not undergo major rearrangement in either solution or gas phases. We apply this approach to study two subcomplexes of the human eukaryotic initiation factor 3, for which there is no high-resolution structure. PMID:19748344

Pukala, Tara L; Ruotolo, Brandon T; Zhou, Min; Politis, Argyris; Stefanescu, Raluca; Leary, Julie A; Robinson, Carol V

2009-09-01

206

Gas-phase dissociation pathways of a tetrameric protein complex  

NASA Astrophysics Data System (ADS)

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

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

2003-12-01

207

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

NASA Astrophysics Data System (ADS)

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

Mikolaitis, David; Griffen, Patrick

2006-11-01

208

Gas-phase chemical reactions activated by an e-beam  

Microsoft Academic Search

A gas mixture containing silicon tetrachloride, hydrogen and argon was selected as a model system to study gas-phase reactions activated by electron beam (e-beam). The process of the e-beam activated conversion of silicon tetrachloride into trichlorosilane is realized. In the optimal case, the yield of the process reaches 70%. Laser-induced breakdown spectroscopy was used for the study of kinetic phenomena

M. F Reznitchenko

2001-01-01

209

Gas phase infrared spectra and corresponding DFT calculations of ?, ?-diphenylpolyenes  

NASA Astrophysics Data System (ADS)

We present gas phase Fourier Transform Infrared (FTIR) spectra of the homologue series of ?, ?-diphenylpolyenes consisting of trans- and cis-stilbene, diphenylbutadiene (DPB) and diphenylhexatriene (DPH) obtained by a fast thermal heating technique that enables vaporization without decomposition. Infrared marker bands for the cis-isomers of the polyenes have been identified by density functional calculations at the B3LYP/TZVP level of theory. The all trans isomers of DPB and DPH do not interconvert to the cis-isomers in the gas phase at 200 °C.

Biemann, Lars; Braun, Michaela; Kleinermanns, Karl

2010-01-01

210

Gas phase radiative effects in diffusion flames  

NASA Astrophysics Data System (ADS)

Several radiation models are evaluated for a stagnation point diffusion flame of a solid fuel in terms of accuracy and computational time. Narrowband, wideband, spectral line weighted sum of gray gases (SLWSGG), and gray gas models are included in the comparison. Radiative heat flux predictions by the nongray narrowband, wideband, and SLWSGG models are found to be in good agreement with each other, whereas the gray gas models are found to be inaccurate. The narrowband model, the most complex among the models evaluated, is then applied first to a solid fuel and second to a pure gaseous diffusion flame. A polymethylmethacrylate (PMMA) diffusion flame in a stagnation point geometry is solved with the narrowband model with COsb2, Hsb2O, and MMA vapor included in participating species. A detailed account of the emission and absorption from these species as well as the radiative heat fluxes are given as a function of the stretch rate. It is found that at low stretch rate the importance of radiation is increased due to an increase in the optical thickness, and a decrease in the conductive heat flux. Results show that COsb2 is the biggest emitter and absorber in the flame, MMA vapor is the second and Hsb2O is the least important. A pure gaseous flame in an opposed jet configuration is solved with the narrowband radiation model with CO as the fuel, and Osb2 as the oxidizer. Detailed. chemical kinetics and transport are incorporated into the combustion model with the use of the CHEMKIN and TRANSPORT software packages. The governing equations are solved with a modified version of the OPPDIF code. Dry and wet CO flames as well as COsb2 dilution are studied. Comparison of the results with and without the consideration of radiation reveals that the radiation is important for the whole flammable range of dry CO flames and for the low stretch rates of wet flames. Without the consideration of radiation the temperature and the species mole fractions (especially of minor species) predictions are different in comparison to the results with the inclusion of the radiation in the model. A flammability map with added Hsb2O fraction and stretch rate as coordinates is drawn. The flammability map contains a blow off extinction boundary at high stretch rate and a quenching extinction boundary at low stretch rate. With increasing Hsb2O addition the quenching boundary shifts to lower stretch rates and the blow off boundary shifts to higher stretch rates, hence the range of flammable stretch rates increases. COsb2 dilution of the fuel (CO) jet is found to decrease the flame temperature. A flammability map with COsb2 mole fraction in the fuel jet and the stretch rate as coordinates is also drawn. With increasing COsb2 dilution the range of flammable stretch rate decreases. For the dry CO-Osb2 case, when COsb2 dilution exceeds 17%, the system is nonflammable for any stretch rate. The most flammable stretch rate is around 2 ssp{-1}.

Bedir, Hasan

211

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

SciTech Connect

The liquid-gas phase transition in hot asymmetric nuclear matter is investigated within the 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.

Sharma, Bharat K.; Pal, Subrata [Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005 (India)

2010-06-15

212

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides  

PubMed Central

We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of ?-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV)4 are used to examine peptide aggregation in different environments, in water, and at the water–octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling ?-strands.

2012-01-01

213

HomoSAR: Bridging comparative protein modeling with quantitative structural activity relationship to design new peptides.  

PubMed

Peptides play significant roles in the biological world. To optimize activity for a specific therapeutic target, peptide library synthesis is inevitable; which is a time consuming and expensive. Computational approaches provide a promising way to simply elucidate the structural basis in the design of new peptides. Earlier, we proposed a novel methodology termed HomoSAR to gain insight into the structure activity relationships underlying peptides. Based on an integrated approach, HomoSAR uses the principles of homology modeling in conjunction with the quantitative structural activity relationship formalism to predict and design new peptide sequences with the optimum activity. In the present study, we establish that the HomoSAR methodology can be universally applied to all classes of peptides irrespective of sequence length by studying HomoSAR on three peptide datasets viz., angiotensin-converting enzyme inhibitory peptides, CAMEL-s antibiotic peptides, and hAmphiphysin-1 SH3 domain binding peptides, using a set of descriptors related to the hydrophobic, steric, and electronic properties of the 20 natural amino acids. Models generated for all three datasets have statistically significant correlation coefficients (r(2) ) and predictive r2 (rpred?2) and cross validated coefficient ( qLOO?2). The daintiness of this technique lies in its simplicity and ability to extract all the information contained in the peptides to elucidate the underlying structure activity relationships. The difficulties of correlating both sequence diversity and variation in length of the peptides with their biological activity can be addressed. The study has been able to identify the preferred or detrimental nature of amino acids at specific positions in the peptide sequences. © 2013 Wiley Periodicals, Inc. PMID:24105965

Borkar, Mahesh R; Pissurlenkar, Raghuvir R S; Coutinho, Evans C

2013-09-18

214

Surface and gas phase temperatures of a tungsten coil atomizer  

NASA Astrophysics Data System (ADS)

The electrothermal atomization of elements is critically affected by the volatility of the analyte and its compounds, the matrix constituents, the atomizer material and the surface and gas phase temperatures. There are scarce temperature data about the tungsten coil atomizer (TCA). This paper involves measurements of surface and gas phase temperatures of a TCA (Osram 150 W). Three strategies were adopted to assess the surface temperature: electric current measurements in each applied voltage to calculate resistivity and correlation of this latter parameter with temperature; melting points of organic and inorganic compounds in the 120-800 °C range, and optical pyrometer measurements in the 1000-3000 °C range. The first two methods led to at least estimate values and more accurate results were attained with the optical pyrometer. The gas phase temperature was estimated based on the two-line absorption method using tin as thermometric element. The data showed a pronounced difference between surface and gas phase temperatures that can reach values higher than 1000 °C depending on the applied voltage and observation height. Data are discussed considering thermochemical processes in a double layer tungsten coiled filament.

Queiroz, Zilvanir F.; Oliveira, Pedro V.; Nóbrega, Joaquim A.; Silva, C?´ntia S.; Rufini, Iolanda A.; de Sousa, Samuel Simião; Krug, Francisco J.

2002-11-01

215

Apparatus for the gas phase combustion of liquid fuels  

Microsoft Academic Search

An arrangement to produce high efficiency gas phase combustion of liquid fuels is described. A liquid fuel, such as conventional heating oil, is pumped through a heat exchanger immersed in a liquid bath whose temperature is maintained at a level which is sufficiently high to cause the fuel to gassify but low enough to preclude undesirable chemical decomposition. The liquid

G. A. Roffe; H. A. Trucco

1977-01-01

216

Apparatus for the premixed gas phase combustion of liquid fuels  

Microsoft Academic Search

This invention relates to improvements in the art of liquid fuel combustion and, more particularly, concerns a method and apparatus for the controlled gasification of liquid fuels, the thorough premixing of the then gasified fuel with air and the subsequent gas-phase combustion of the mixture to produce a flame substantially free of soot, carbon monoxide, nitric oxide and unburned fuel.

G. A. Roffe; H. A. Trucco

1981-01-01

217

Gas-phase silicon micromachining with xenon difluoride  

Microsoft Academic Search

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

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

1995-01-01

218

Gas-phase purification of single-wall carbon nanotubes  

Microsoft Academic Search

A gas-phase purification method for raw nanotube material has been developed which incorporates a chlorine, water, and hydrogen chloride gas mixture to remove unwanted carbon. The evolved gases can be easily monitored by infrared spectroscopy to follow the cleaning process. The quality of the final material was verified by SEM (scanning electron microscopy), TGA (thermogravimetric analysis), and UV-vis (ultraviolet and

John L. Zimmerman; Robert Kelley Bradley; Chad B. Huffman; Robert H. Hauge; John L. Margrave

2000-01-01

219

Enzymatic dehalogenation of gas phase substrates with haloalkane dehalogenase.  

PubMed

Haloalkane dehalogenase is an enzyme capable of catalyzing the conversion of short-chained (C(2)-C(8)) aliphatic halogenated hydrocarbons to a corresponding primary alcohol. Because of its broad substrate specificity for mono-, di-, and trisubstituted halogenated hydrocarbons and cofactor independence, haloalkane dehalogenases are attractive biocatalysts for gas-phase bioremediation of pollutant halogenated vapor emissions. A solid preparation of haloalkane dehalogenase from Rhodococcus rhodochrous was used to catalyze the dehalogenation reaction of 1-chlorobutane or 1,3-dichloropropane delivered in the gas phase. For optimal gas-phase dehalogenase activity, a relative humidity of 100%, a(w) = 1, was desired. With a 50% reduction in the vapor-phase hydration level, an 80% decrease in enzymatic activity was observed. The enzyme kinetics for the gas-phase substrates obeyed an Arrhenius-"like" behavior and the solid haloalkane dehalogenase preparation was more thermally stable than its water-soluble equivalent. Triethylamine was added to the gaseous reaction environment in efforts to increase the rate of reaction. A tenfold increase in the dehalogenase activity for the vapor-phase substrates was observed with the addition of triethylamine. Triethylamine altered the electrostatic environment of haloalkane dehalogenase via a basic shift in local pH, thereby minimizing the effect of the pH-reducing reaction product on enzyme activity. Both organic phase and solid-state buffers were used to confirm the activating role of the altered ionization state. PMID:10861403

Dravis, B C; LeJeune, K E; Hetro, A D; Russell, A J

2000-08-01

220

The application of monoliths for gas phase catalytic reactions  

Microsoft Academic Search

A general introductory review of the fundamental principles of monoliths as supports for catalytic gas phase reactions is presented. Monoliths are used because of low pressure drop and high mechanical strength required for the harsh conditions encountered in environmental applications. The chemical and physical properties of monoliths and the basics for mass transfer calculations and pressure drop are presented. Existing

Ronald M. Heck; Suresh Gulati; Robert J. Farrauto

2001-01-01

221

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)

1992-01-24

222

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. CHEMKIN was designed as an easily transportable program for use on CDC, Cray, and DEC VAX systems. 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.

Kee, R.J. [Sandia National Labs., Livermore, CA (United States); Warnatz, J. [Institut fuer Angewandte Physikalische Chemie, Universitaet Heidleberg, Heidleberg (Germany)

1980-03-01

223

CHEMKIN2. General Gas-Phase Chemical Kinetics  

Microsoft Academic Search

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. CHEMKIN was designed as an easily transportable program for use on CDC, Cray, and DEC VAX systems. It consists of two major

R. J. Kee; J. Warnatz

1980-01-01

224

X-Ray Absorption Spectroscopy of Gas Phase Metal Clusters.  

National Technical Information Service (NTIS)

The production and control of vapor phase metal clusters in sizes ranging from one to thousands of atoms is discussed. Electron yield detection has a very high sensitivity to species in the gas phases. These events suggested the possibility of a combined ...

E. C. Marques D. S. Olson D. R. Sandstron F. W. Lytle R. B. Greegor

1986-01-01

225

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

1981-01-01

226

GAS PHASE CHEMISTRY OF SULFONATE ANIONS: BASICITIES AND FRAGMENTATION REACTIONS  

Microsoft Academic Search

The gas phase relative acidities of 15 sulfonic acids, RSO3H, have been determine via Cooks' kinetic method. The following acidity scale was established (starting with the weakest acid): methane sulfonic acid < ethane sulfonic acid < methoxy sulfonic acid < sulfuric acid < m-aminobenzene sulfonic acid - p-aminobenzene sulfonic acids < p-toluene sulfonic acid < benzene sulfonic acid < o-aminobenzene

Jacob D. Smith; Richard A. J. Ohair; Todd D. Williams

1996-01-01

227

New Spectroscopic Methods in Gas-Phase Chemical Kinetics  

Microsoft Academic Search

The possibilities provided by the application of advances in laser technology to the solution of problems in gas-phase chemical kinetics have been analysed. The basic principles of various laser methods for producing and recording active chemical species have been described. Examples of the use of lasers to study the reactions of radicals and excited species, in the diagnostics of complex

Oleg M. Sarkisov; S. G. Cheskis

1985-01-01

228

Evaluated Chemical Kinetic Rate Constants for Various Gas Phase Reactions  

Microsoft Academic Search

The available information, up to mid-1972, for the rate constants of a series of gas phase chemical reactions has been evaluated critically. For each reaction, relevant thermodynamic data are presented and values for the equilibrium constant expressed in mathematical form. Kinetic data are presented in tabular and graphical form together with a discussion of the pertinent details. Recommended rate constant

Keith Schofield

1973-01-01

229

Condensed phase decomposition and gas phase combustion of hydrazinium nitroformate  

Microsoft Academic Search

This paper presents the results of a series of experiments on the condensed phase decomposition and the gas phase combustion of hydrazinium nitroformate (HNF). The experiments include SEM analysis of quenched samples that showed evidence of the formation of a foam layer. FTIR spectrometry and mass spectrometry provide details on species formation during decomposition and combustion. The analysis of the

O. E. Dragomir; M. J. Tummers; E. H. van Veen; A. E. D. M. van der Heijden; D. J. E. M. Roekaerts

2009-01-01

230

Kinetic theory of steady chemical nucleation in the gas phase  

Microsoft Academic Search

We develop a kinetic theory of nucleation involving chemical reactions in the gas phase. For the basis of deriving the chemical nucleation rate, chemical kinetic considerations are presented on the steady current density and the effective rate constants of the overall reaction, which is a sum of a sequential elementary reactions. We formulate the steady rate of chemical nucleation in

T. Yamamoto; T. Chigai; S. Watanabe; T. Kozasa

2001-01-01

231

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

Microsoft Academic Search

Detailed chemical kinetic modeling based on computational quantum chemistry has been quite successful in making quantitative predictions about some systems, particularly the combustion of small hydrocarbons and certain areas of atmospheric chemistry. The gas phase chemistry of many processes in high-temperature inorganic systems, from materials synthesis to propulsion to waste incineration, could in principle be modeled with equal or greater

Mark T. Swihart

2005-01-01

232

The Gas-Phase Deuterium Fractionation of Formaldehyde  

NASA Astrophysics Data System (ADS)

The dominant mechanism for the deuteration of formaldehyde in the gas phase of low-temperature interstellar cloud cores occurs via reaction with the deuterating ions H2D+, HD+2, and D+3. Until now, it has been assumed that deuteration leads to an ion that, on recombination with electrons, can produce a deuterated neutral species with a statistical branching fraction. Quantum chemical calculations reported here, however, show an entirely different picture, in which the deuteration of formaldehyde leads to the molecular ion H2COD+, where the deuterium binds only on the oxygen side of the molecule. The structure is quite stable, while an alternative structure, H2DCO+, cannot be produced in a straightforward manner. Dissociative recombination of H2COD+ to reproduce a formaldehyde structure then removes the deuteration if the dissociation is direct, i.e., it occurs without change of structure. There are several possible indirect mechanisms by which dissociative recombination can lead to HDCO, however. For example, if the direct products are HCOD+H, it is possible that subsequent isomerization to HDCO can occur, although this involved process is unlikely. Another possibility is isomerization during the actual dissociation of the H2COD intermediate. Models of deuterium fractionation in which dissociative recombination is predominantly direct are presented, and it is found that the deuterium fractionation of formaldehyde to form both HDCO and D2CO can still occur via other mechanisms, although with less efficiency than previously obtained. If the dissociative recombination is half indirect, however, then we can recover the previously calculated efficiency.

Osamura, Yoshihiro; Roberts, Helen; Herbst, Eric

2005-03-01

233

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

SciTech Connect

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

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

2005-10-01

234

A Molecular Model of Alzheimer Amyloid beta Peptide Fibril Formation  

Microsoft Academic Search

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

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

1999-01-01

235

Polar angle as a determinant of amphipathic alpha-helix-lipid interactions: a model peptide study.  

PubMed Central

Various physicochemical properties play important roles in the membrane activities of amphipathic antimicrobial peptides. To examine the effects of the polar angle, two model peptides, thetap100 and thetap180, with polar angles of 100 degrees and 180 degrees, respectively, were designed, and their interactions with membranes were investigated in detail. These peptides have almost identical physicochemical properties except for polar angle. Like naturally occurring peptides, these peptides selectively bind to acidic membranes, assuming amphipathic alpha-helices, and formed peptide-lipid supramolecular complex pores accompanied by lipid flip-flop and peptide translocation. Despite its somewhat lower membrane affinity, thetap100 exhibited higher membrane permeabilization activity, a greater flip-flop rate, as well as more antimicrobial activity due to a higher pore formation rate compared with thetap180. Consistent with these results, the peptide translocation rate of thetap100 was higher. Furthermore, the number of peptides constituting thetap100 pores was less than that of thetap180, and thetap100 pores involved more lipid molecules, as reflected by its cation selectivity. The polar angle was found to be an important parameter determining peptide-lipid interactions.

Uematsu, N; Matsuzaki, K

2000-01-01

236

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.

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

2012-01-01

237

Gas Phase Theoretical Kinetics for Astrochemistry  

NASA Astrophysics Data System (ADS)

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

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

2012-05-01

238

Gas phase kinetic and optical emission spectroscopy studies in plasma-enhanced hot filament catalytic CVD production of carbon nanotubes  

NASA Astrophysics Data System (ADS)

Optical emission spectroscopy (OES) is used as the main experimental tool for comparison with simulations of the plasma and gas phase composition during plasma-enhanced hot filament catalytic chemical vapor deposition (PE HF CCVD) growth of carbon nanotubes (CNTs). Calculated concentration of more than 45 species in model of the CVD reactor is acquired by Chemkin™ software. Study of different conditions is performed and a close relationship can be found between the nature and the growth rate of carbon nanostructures and the concentration of the active gas phase species. Moreover it is shown that significant changes in the density and morphology of the CNTs grown in the presence of NH 3 could be mainly explained by the gas phase formation of CN and HCN.

Guláš, M.; Le Normand, F.; Veis, P.

2009-03-01

239

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

PubMed

The mycobactericidal properties of macrophages include the delivery of bacteria to a hydrolytic lysosome enriched in bactericidal ubiquitin-derived peptides (Ub-peptides). To improve our understanding of interactions of ubiquitin-derived peptides with mycobacteria, we further characterized the structure and function of bactericidal Ub-peptide Ub2. We found that Ub2 adopts a ?-sheet conformation in the context of sodium dodecyl sulfate micelles and phospholipid (1:1 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine) 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 is localized 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

2012-11-30

240

Rapid Selection of Cyclic Peptides that Reduce ?-Synuclein Toxicity in Yeast and Animal Models  

PubMed Central

Phage display has demonstrated the utility of cyclic peptides as general protein ligands, but cannot access proteins inside eukaryotic cells. Expanding a novel chemical genetics tool, we describe the first expressed library of head-to-tail cyclic peptides in yeast (Saccharomyces cerevisiae). We applied the library to selections in a yeast model of ?-synuclein toxicity that recapitulates much of the cellular pathology of Parkinson’s disease. From a pool of five million transformants, we isolated two related cyclic peptide constructs which specifically reduce the toxicity of human ?-synuclein. These expressed cyclic peptide constructs also prevent dopaminergic neuron loss in an established Caenorhabditis elegans Parkinson’s model. This work highlights the speed and efficiency of using libraries of expressed cyclic peptides for forward chemical genetics in cellular models of human disease.

Kritzer, Joshua A.; Hamamichi, Shusei; McCaffery, J. Michael; Santagata, Sandro; Naumann, Todd A.; Caldwell, Kim A.; Caldwell, Guy A.; Lindquist, Susan

2009-01-01

241

Rapid selection of cyclic peptides that reduce alpha-synuclein toxicity in yeast and animal models.  

PubMed

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 of head-to-tail cyclic peptides in yeast (Saccharomyces cerevisiae). We applied the library to selections in a yeast model of alpha-synuclein toxicity that recapitulates much of the cellular pathology of Parkinson's disease. From a pool of 5 million transformants, we isolated two related cyclic peptide constructs that specifically reduced the toxicity of human alpha-synuclein. These expressed cyclic peptide constructs also prevented dopaminergic neuron loss in an established Caenorhabditis elegans Parkinson's model. This work highlights the speed and efficiency of using libraries of expressed cyclic peptides for forward chemical genetics in cellular models of human disease. PMID:19597508

Kritzer, Joshua A; Hamamichi, Shusei; McCaffery, J Michael; Santagata, Sandro; Naumann, Todd A; Caldwell, Kim A; Caldwell, Guy A; Lindquist, Susan

2009-07-13

242

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

SciTech Connect

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

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

2012-07-20

243

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.

244

Rapid selection of cyclic peptides that reduce ?-synuclein toxicity in yeast and animal models  

Microsoft Academic Search

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 of head-to-tail cyclic peptides in yeast (Saccharomyces cerevisiae). We applied the library to selections in a yeast model of ?-synuclein toxicity that recapitulates much of the cellular pathology

Joshua A Kritzer; Shusei Hamamichi; J Michael McCaffery; Sandro Santagata; Todd A Naumann; Kim A Caldwell; Guy A Caldwell; Susan Lindquist

2009-01-01

245

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

PubMed

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

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

2012-03-01

246

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

Microsoft Academic Search

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

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

2002-01-01

247

Modeling of ion-pairing effect in peptide reversed-phase chromatography.  

PubMed

The modeling of counterion and organic modifier concentration effects in peptide APIs reversed-phase preparative chromatography is discussed in this manuscript. A stoichiometric retention model based on the counterion binding to the charged functional groups of the peptide is proposed. The model parameters were evaluated using a rather large set of retention data measured in mobile phases with various counterions and acetonitrile concentrations. The model parameters were experimentally validated by a new counterion binding measurement technique. The n(max) model parameter value was found to be equal to the peptide net charge, whereas the K model parameter value was found to be specific to the counterion type (i.e. AcO(-)peptide saturation capacity was also investigated. It was shown that, at low acetonitrile concentration, the peptide saturation capacity was constant for all investigated counterion types and concentrations. On the other hand, at intermediate acetonitrile concentration, the peptide saturation capacity was significantly lower and with a tendency to increase with the counterion concentration. On the whole, the developed model provides a reliable a reliable tool for the design and development of peptide purification processes at the preparative and industrial scale. PMID:22748374

Gétaz, David; Hariharan, Subrahmaniam B; Butté, Alessandro; Morbidelli, Massimo

2012-06-12

248

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

2009-01-01

249

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

PubMed

Collisional growth and ionization is commonplace for gas phase nanoparticles (i.e., in aerosols). Nanoparticle collisions in atmospheric pressure environments occur in the mass transfer transition regime, and further attractive singular contact potentials (which arise when modeling nanoparticles as condensed matter and for which the potential energy approaches -? when two entities contact) often have a non-negligible influence on collision processes. For these reasons collision rate calculations for nanoparticles in the gas phase are not straightforward. We use mean first passage time calculations to develop a simple relationship to determine the collision rate in the gas phase, accounting for the influences of both the transition regime and singular contact potentials (specifically the non-retarded van der Waals and image potentials). In the presented analysis, methods to determine the degree of enhancement in collision rate due to attractive singular potentials in the continuum (diffusive) regime, ?(C), and the degree of enhancement in the free molecular (ballistic) regime, ?(FM), are first reviewed. Accounting for these enhancement factors, with mean first passage time calculations it is found that the collision rate for gas phase nanoparticles with other gas phase entities can be determined from a relationship between the dimensionless collision rate coefficient, H, and the diffusive Knudsen number, Kn(D), i.e., the ratio of the mean collision persistence distance to the collision length scale. This coincides with the H(Kn(D)) relationship found to appropriately describe collisions between entities interacting via a hard-sphere potential, but with ?(C) and ?(FM) incorporated into the definitions of both H and Kn(D), respectively. The H(Kn(D)) relationship is compared to the predictions of flux matching theory, used prevalently in prior work for collision rate calculation, and through this comparison it is found that at high potential energy to thermal energy ratios, flux matching theory predictions underestimate the true collision rate. Finally, a series of experimental measurements of nanoparticle-nanoparticle collision rates are compared to the determined H(Kn(D)) expression, considering that nanoparticles interact via non-retarded van der Waals potentials. Very good agreement is found with collision rates inferred from experiments, with almost all measured values from four separate studies within 25% of model predictions. PMID:22897282

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

2012-08-14

250

Gas-phase salt bridge interactions between glutamic acid and arginine.  

PubMed

The gas-phase side chain-side chain (SC-SC) interaction and possible proton transfer between glutamic acid (Glu) and arginine (Arg) residues are studied under low-temperature conditions in an overall neutral peptide. Conformation-specific IR spectra, obtained with the free electron laser FELIX, in combination with density functional theory (DFT) calculations, provide insight into the occurrence of intramolecular proton transfer and detailed information on the conformational preferences of the peptides Z-Glu-Alan-Arg-NHMe (n = 0,1,3). Low-energy structures are obtained using molecular dynamics simulations via the simulated annealing approach, resulting in three types of SC-SC interactions, in particular two types of pair-wise interactions and one bifurcated interaction. These low-energy structures are optimized and frequency calculations are performed using the B3LYP functional, for structural analysis, and the M05-2x functional, for relative energies, employing the 6-311+G(d,p) basis set. Comparison of experimental and computed spectra suggests that only a single conformation was present for each of the three peptides. Despite the increasing spacing between the Glu and Arg residues, the peptides have several types of interactions in common, in particular specific SC-SC and dispersion interactions between the Arg side chain and the phenyl ring of the Z-cap. Comparison with previous experiments on Ac-Glu-Ala-Phe-Ala-Arg-NHMe as well as molecular dynamics simulations further suggest that the pairwise interaction observed here is indeed energetically most favorable for short peptide sequences. PMID:23999680

Jaeqx, Sander; Oomens, Jos; Rijs, Anouk M

2013-09-03

251

PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes  

PubMed Central

One of the most adaptive immune responses is triggered by specific T-cell receptors (TCR) binding to peptide-major histocompatibility complexes (pMHC). Despite the availability of many prediction servers to identify peptides binding to MHC, these servers are often lacking in peptide–TCR interactions and detailed atomic interacting models. PAComplex is the first web server investigating both pMHC and peptide-TCR interfaces to infer peptide antigens and homologous peptide antigens of a query. This server first identifies significantly similar TCR–pMHC templates (joint Z-value???4.0) of the query by using antibody–antigen and protein–protein interacting scoring matrices for peptide-TCR and pMHC interfaces, respectively. PAComplex then identifies the homologous peptide antigens of these hit templates from complete pathogen genome databases (?108 peptide candidates from 864?628 protein sequences of 389 pathogens) and experimental peptide databases (80?057 peptides in 2287 species). Finally, the server outputs peptide antigens and homologous peptide antigens of the query and displays detailed interacting models (e.g. hydrogen bonds and steric interactions in two interfaces) of hitTCR-pMHC templates. Experimental results demonstrate that the proposed server can achieve high prediction accuracy and offer potential peptide antigens across pathogens. We believe that the server is able to provide valuable insights for the peptide vaccine and MHC restriction. The PAComplex sever is available at http://PAcomplex.life.nctu.edu.tw.

Liu, I-Hsin; Lo, Yu-Shu; Yang, Jinn-Moon

2011-01-01

252

Gas Phase Chiral Separations By Ion Mobility Spectrometry  

PubMed Central

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

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

2013-01-01

253

Gas phase acidities of N-substituted amine-boranes.  

PubMed

Complexation energies and acidities of 19 primary, secondary and tertiary amine-boranes were investigated using MP2/6-311+G(d,p) and B3LYP/6-311+G(d,p) methods. Gas phase acidities for free amines were also calculated. Acidity values for studied complexes range from 327.3 to 349.1 kcal mol(-1) and the most acidic are the ones with direct connection between deprotonation center and a ?-system. Results obtained by both computational methods are in good agreement with each other and with known experimental data. Addition of BH3 increases the acidity of amines by 30 to 50 kcal mol(-1). This enhancement effect was compared to the respective effect witnessed in phosphine-boranes and traced back to changes of charge delocalization on nitrogen. A question about the structural stability of several deprotonated amine-borane anions in the gas phase was also raised. PMID:24085539

Adamson, Aiko; Guillemin, Jean-Claude; Burk, Peeter

2013-10-02

254

Gas-phase Fragmentation of Deprotonated p-Hydroxyphenacyl Derivatives  

PubMed Central

Electrospray ionization of methanolic solutions of p-hydroxyphenacyl derivatives HO-C6H4-C(O)-CH2-X (X = leaving group) provides abundant signals for the deprotonated species which are assigned to the corresponding phenolate anions ?O-C6H4-C(O)-CH2-X. Upon collisional activation in the gas phase, these anions inter alia undergo loss of a neutral “C8H6O2” species concomitant with formation of the corresponding anions X?. The energies required for the loss of neutral roughly correlate with the gas phase acidities of the conjugate acids (HX). Extensive theoretical studies performed for X = CF3COO in order to reveal the energetically most favorable pathway for the formation of neutral “C8H6O2” suggest three different routes of similar energy demands, involving a spirocyclopropanone, epoxide formation, and a diradical, respectively.

Remes, Marek; Roithova, Jana; Schroder, Detlef; Cope, Elizabeth D.; Perera, Chamani; Senadheera, Sanjeewa N.; Stensrud, Kenneth; Ma, Chi-cheng; Givens, Richard S.

2011-01-01

255

Birch reduction of chlorobenzene in gas-phase hydrated electrons  

NASA Astrophysics Data System (ADS)

Reactions of gas-phase hydrated electrons (H2O)n-, n = 30-65, with chlorobenzene are investigated by Fourier transform ion cyclotron resonance mass spectrometry. The clusters lose water molecules via collision and black-body radiation induced dissociation. In addition, chemical reactions with chlorobenzene lead to formation of Cl-(H2O)n and OH-(H2O)n. While the former product is well-known from pulsed radiolysis studies in the bulk, the latter is observed for the first time in gas-phase clusters. It is indicative of a Birch reduction of the aromatic ring, leading to formation of a chloro-cyclohexadienyl radical C6H6Cl.

Cao, Yali; Höckendorf, Robert F.; Beyer, Martin K.

2008-11-01

256

Gas phase chemical detection with an integrated chemical analysis system  

SciTech Connect

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

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

2000-04-12

257

Molecular Tagging Velocimetry (MTV) measurements in gas phase flows  

Microsoft Academic Search

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

B. Stier; M. M. Koochesfahani

1999-01-01

258

Gas-phase degradation of organic compounds in the troposphere  

Microsoft Academic Search

The present status of knowledge of the gas-phase reactions of selected classes of volatile non-methane organic compounds (NMOCs) (alkanes, alkenes, aromatic hydrocarbons, oxygen-containing NMOCs and nitrogen-containing NMOCs) and their degradation products in the troposphere is briefly discussed. In the troposphere, NMOCs can undergo photolysis, reaction with the hydroxyl (OH) radical during daylight hours, reaction with the nitrate (NO3) radical (primarily

Roger Atkinson

1998-01-01

259

Gas Phase Xenon131 Quadrupolar Splitting at High Magnetic Fields  

Microsoft Academic Search

At very high magnetic fields strengths (14 Tesla and higher) the xenon-131 gas phase NMR spectrum shows a well resolved quadrupolar splitting. Quadrupolar coupling between a non-spherical (S>1\\/2) nuclei and an electric field gradient will occur when the electrical isotropy of the surrounding electron cloud is disturbed. The experimental results suggest that the origin of the observed splitting in the

Thomas Meersmann

1998-01-01

260

Gas phase fractionation method using porous ceramic membrane  

DOEpatents

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

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

1996-01-01

261

Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids  

Microsoft Academic Search

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

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

2011-01-01

262

Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids  

Microsoft Academic Search

Nitro-fatty acids are electrophilic signaling mediators formed in increased amounts during inflammation by nitric oxide and\\u000a nitrite-dependent redox reactions. A more rigorous characterization of endogenously-generated species requires additional\\u000a understanding of their gas-phase induced fragmentation. Thus, collision induced dissociation (CID) of nitroalkane and nitroalkene\\u000a groups in fatty acids were studied in the negative ion mode to provide mass spectrometric tools for

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

263

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.

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

2008-01-01

264

A toy model of prebiotic peptide evolution: the possible role of relative amino acid abundances.  

PubMed

This paper presents a mathematical-computational toy model based on the assumed dynamic principles of prebiotic peptide evolution. Starting from a pool of amino acid monomers, the model describes in a generalized manner the generation of peptides and their sequential information. The model integrates the intrinsic and dynamic key elements of the initiation of biopolymerization, such as the relative amino acid abundances and polarities, as well as the oligomer reversibility, i.e. fragmentation and recombination, and peptide self-replication. Our modeling results suggest that the relative amino acid abundances, as indicated by Miller-Urey type electric discharge experiments, played a principal role in the early sequential information of peptide profiles. Moreover, the computed profiles display an astonishing similarity to peptide profiles observed in so-called biological common ancestors found in the following three microorganisms; E. coli, M. jannaschii, and S. cereviasiae. The prebiotic peptide fingerprint was obtained by the so-called polarity index method that was earlier reported as a tool for the identification of cationic amphipathic antibacterial short peptides. PMID:23741717

Polanco, Carlos; Buhse, Thomas; Samaniego, José Lino; Castañón González, Jorge Alberto

2013-06-06

265

A Bayesian hierarchical model for identifying epitopes in peptide microarray data.  

PubMed

Peptide Microarray Immunoassay (PMI for brevity) is a novel technology that enables researchers to map a large number of proteomic measurements at a peptide level, providing information regarding the relationship between antibody response and clinical sensitivity. PMI studies aim at recognizing antigen-specific antibodies from serum samples and at detecting epitope regions of the protein antigen. PMI data present new challenges for statistical analysis mainly due to the structural dependence among peptides. A PMI is made of a complete library of consecutive peptides. They are synthesized by systematically shifting a window of a fixed number of amino acids through the finite sequence of amino acids of the antigen protein as ordered in the primary structure of the protein. This implies that consecutive peptides have a certain number of amino acids in common and hence are structurally dependent. We propose a new flexible Bayesian hierarchical model framework, which allows one to detect recognized peptides and bound epitope regions in a single framework, taking into account the structural dependence between peptides through a suitable latent Markov structure. The proposed model is illustrated using PMI data from a recent study about egg allergy. A simulation study shows that the proposed model is more powerful and robust in terms of epitope detection than simpler models overlooking some of the dependence structure. PMID:21856651

Arima, Serena; Lin, Jing; Pecora, Valentina; Tardella, Luca

2011-08-18

266

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

EPA Science Inventory

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

267

Charge state of lysozyme molecules in the gas phase produced by IR-laser ablation of droplet beam.  

PubMed

Molecules exhibit their intrinsic properties in their isolated forms. Investigations of isolated large biomolecules require an understanding of the detailed mechanisms for their emergence in the gas phase because these properties may depend on the isolation process. In this study, we apply droplet-beam laser-ablation mass spectrometry to isolate protein molecules in the gas phase by IR-laser ablation of aqueous protein solutions, and we discuss the isolation mechanism. Multiply charged hydrated lysozyme clusters were produced by irradiation of the IR laser onto a droplet beam of aqueous lysozyme solutions with various pH values prepared by addition of sodium hydroxide to the solution. The ions produced in the gas phase show significantly low abundance and have a lower number of charges on them than those in the aqueous solutions, which we explained using a nanodroplet model. This study gives quantitative support for the nanodroplet model, which will serve as a fundamental basis for further studies of biomolecules in the gas phase. PMID:23234475

Kohno, Jun-ya; Nabeta, Kyohei; Sasaki, Nobuteru

2012-12-28

268

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

Microsoft Academic Search

A comprehensive mathematical model incorporating multicomponent molecular diffusion, complex chemistry, and heterogeneous processes was developed to investigate a variety of chemically and physical processes rather than complex flow geometry. The goal here is not only to calculate chemical species profiles, temperature profiles, and mass flow rates, but also to obtain sensitivity information. The time-dependent, one-dimensional partial differential equations resulting from

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

1992-01-01

269

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

PubMed Central

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

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

1996-01-01

270

Liquid-gas phase transition in nuclear matter in the mean-field approximation  

NASA Astrophysics Data System (ADS)

The liquid gas phase transition in nuclear systems is a unique phenomenon, at the frontier of nuclear, many-body and statistical physics. We use self-consistent mean-field calculations to quantify the properties of the transition in symmetric nuclear matter. We explore the available parameter space of critical properties by analyzing the mean-field dependence of the phase transition. The latent heat of the transition is computed and we find that it exhibits a model independent temperature dependence due to basic physical principles.

Rios, A.; Carbone, A.; Polls, A.; Vidaña, I.

2011-09-01

271

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

SciTech Connect

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

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

2008-12-15

272

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.

1993-12-31

273

Solution NMR studies of peptide-lipid interactions in model membranes.  

PubMed

Many important processes in life take place in or around the cell membranes. Lipids have different properties regarding their membrane-forming capacities, their mobility, shape, size and surface charge, and all of these factors influence the way that proteins and peptides interact with the membrane. In order for us to correctly understand these interactions, we need to be able to study all aspects of the interplay between lipids and peptides and proteins. Solution-state NMR offers a somewhat unique possibility to investigate structure, dynamics and location of proteins and peptides in bilayers. This review focuses on solution NMR as a tool for investigating peptide-lipid interaction, and special attention is given to the various membrane mimetics that are used to model the membrane. Examples from the field of cell-penetrating peptides and their lipid interactions will be given. The importance of studying lipid and peptide dynamics, which reflect on the effect that peptides have on bilayers, is highlighted, and in this respect, also the need for realistic membrane models. PMID:22583052

Mäler, Lena

2012-05-14

274

Nuclear liquid-gas phase transition with finite range force  

NASA Astrophysics Data System (ADS)

The possibilities of the occurrence of liquid-gas phase transition in nuclear matter and finite nuclei are investigated in the framework of temperature-dependent Hartree-Fock theory employing the finite-range Brink-Boeker effective interaction. The equation of state at subnuclear density is obtained. It is found that for infinite nuclear matter critical temperature for the phase transition is substantially reduced because of the finite-range nature of the force as compared to those obtained using zero-range forces. When finite-size effect and Coulomb force are taken into account, critical temperature is found to be around 8 MeV.

Satpathy, L.; Mishra, M.; Nayak, R.

1989-01-01

275

Gas Phase Chemical Detection with an Integrated Chemical Analysis System  

SciTech Connect

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

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

1999-07-08

276

Modelling relationship between angiotensin-(I)-converting enzyme inhibition and the bitter taste of peptides  

Microsoft Academic Search

Relationships between angiotensin-(I)-converting enzyme inhibition and the bitter taste of peptides were studied. In cases where ACE inhibition or bitter taste had not been experimentally determined, their activity was estimated using several different peptide quantitative structure–activity relationship (QSAR) models. Significant correlations between increased ACE inhibition and bitterness were found for dipeptides using both observed and QSAR-predicted values. The relationship between

Are Hugo Pripp; Ylva Ardö

2007-01-01

277

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

278

Improvement of Anselme's adhesion model for evaluating human osteoblast response to peptide-grafted titanium surfaces.  

PubMed

Investigations on the relationships between the properties of biomaterial surfaces and cell adhesion/proliferation processes have recently gained increasing interest. To describe the behaviour of cells adhering and proliferating over different types of (and/or differently treated) substrates, some mathematical models have been also suggested in literature; these models consider both the dependence of cell adhesion/proliferation over time, and the influence of substrate morphology in allowing (or even hampering) cell attachment. Major developments in the biochemical functionalization of the materials used for the production of endosseous devices have been achieved; the ability of the so-called "biomimetic" surfaces to promote cell adhesion, thus favoring the osseointegration process, is already well acknowledged. The aim of this study was to formulate a mathematical model for osteoblast adhesion, mediated by an adhesion peptide (sequence 351-359 mapped on the Human Vitronectin Protein) covalently grafted to a titanium-based surface. To assure a highly homogenous orientation of the peptide to cells, the "specific functionalization" strategy was properly designed. Enzymatic detachment assays allowed comparing osteoblast behaviour over three differently treated titanium substrates (i.e., oxidized, silanized, and peptide-grafted), thus determining how and how much the bioactive peptide can improve the strength of cell adhesion. The results confirmed the capacity of the peptide to increase cell adhesion and adhesion strength; moreover, the role of the peptide was described by a mathematical equation characterizing cells behaviour. PMID:17656172

Bagno, Andrea; Piovan, Alessandro; Dettin, Monica; Brun, Paola; Gambaretto, Roberta; Palù, Giorgio; Di Bello, Carlo; Castagliuolo, Ignazio

2007-06-22

279

A model for the controlled assembly of semiconductor peptides  

NASA Astrophysics Data System (ADS)

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

Kim, Se Hye; Parquette, Jon R.

2012-10-01

280

Interaction of Alzheimer's Amyloid Beta Peptide with Model Membranes  

NASA Astrophysics Data System (ADS)

Deposits of amyloid beta (A-beta) peptides in the brain are hallmark features found in patients with Alzheimer's disease. Using a combination of synchrotron X-ray reflectivity, grazing incidence X-ray diffraction and fluorescence microscopy, we have examined interactions between amyloid beta peptides and lipids of various charges. A-beta shows little interaction with zwitterionic films, but inserts equally well into cationic and anionic ones and disrupts their lipid ordering to a similar extent. Yet enhanced A-beta ordering is found only for anionic lipids. This can be understood in terms of the different electrostatic environments provided by oppositely charged lipids. A templating effect by anionic lipids may accelerate oligomerization and point to the role of damaged cell membranes for the initiation of A-beta aggregation.

Lee, Ka Yee C.

2004-03-01

281

Toluene gas phase biofiltration by Paecilomyces lilacinus and isolation and identification of a hydrophobin protein produced thereof.  

PubMed

Paecilomyces lilacinus consumed toluene as the sole carbon source in a gas-phase biofilter packed with perlite obtaining an average elimination capacity of 50 g m(-3) h(-1), a removal efficiency of 53%, and a final biomass of 31.6 mg biomass g dry support(-1). Hydrophobin proteins from the mycelium produced in the biofilter were purified by formic acid extraction and precipitated by electrobubbling, and the molecular weight was found to be 10.6 +/- 0.3 kDa. The peptide mass fingerprinting analysis of the purified hydrophobin by matrix-assisted laser desorption/ionization time-of-flight resulted in the identification of two peptides that presented high homology with sequences of class I hydrophobin proteins from other ascomycetous fungi when compared against the National Center for Biotechnology Information database. The yield of hydrophobin (PLHYD) from P. lilacinus was 1.1 mg PLHYD g biomass(-1). These proteins modified the hydrophobicity of Teflon by lowering the contact angle from 130.1 (+/-2) degrees to 57.0 (+/-5) degrees supporting hot sodium dodecyl sulfate washing. This work is the first report about biodegradation of toluene by the nematophagous fungus P. lilacinus in a gas-phase biofilter and the identification of its hydrophobin protein. PMID:18443779

Vigueras, Gabriel; Shirai, Keiko; Martins de Souza, Daniel; Martins, Daniel; Franco, Telma Teixeira; Fleuri, Luciana Francisco; Revah, Sergio

2008-04-29

282

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

SciTech Connect

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

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

1995-08-01

283

Modeling protein-Peptide recognition based on classical quantitative structure-affinity relationship approach: implication for proteome-wide inference of Peptide-mediated interactions.  

PubMed

Peptide-mediated interactions are crucial to a variety of functions in the living cell and are estimated to be involved in up to 40 % of all cellular processes. Fast and reliable inference of such interactions is fundamentally important for our understanding and, then, reconstruction of complete virtual interactomics involved in a specific cell, tissue or organism. In the current study, we performed structure-level characterization, modeling and prediction of protein-peptide recognition specificity and stability in a high-throughput manner. To achieve this, the classical chemometrics methodology quantitative structure-activity relationship (QSAR), which is traditionally applied to small-molecule entities such as drug compounds and environmental chemicals, was employed to statistically correlate structure features with binding affinities for a panel of structure-solved, affinity-known protein-peptide complexes compiled from the PDB database and literatures. In the standard QSAR procedure, various structural descriptors including physicochemical, geometrical and constitutional parameters that characterize diverse aspects of protein-peptide interaction property were derived from the biomacromolecular complex structure architecture, and these descriptors were then correlated with experimentally measured affinities by using the partial least squares (PLS) regression and Gaussian process (GP) in conjunction with genetic algorithm (GA) variable selection. The nonlinear GA/GP method was found to perform much well as compared to linear GA/PLS modeling, suggesting that the protein-peptide interaction system is highly complicated that may involve strong noise and interactive effect. The optimal GA/GP model revealed that the interface size and solvent effect play a critical role in protein-peptide binding, and other properties such as peptide length and flexibility also contribute significantly to the binding. A further test on 2,018 human amphiphysin SH3 domain-binding peptides demonstrated that the purposed QSAR modeling procedure is very fast and effective, which can thus be readily used to perform proteome-wide inference of peptide-mediated interactions. PMID:24150505

Zhou, Yang; Ni, Zhong; Chen, Keping; Liu, Haijun; Chen, Liang; Lian, Chaoqun; Yan, Lirong

2013-10-01

284

The gas-phase alcoholysis of protonated homoleptic alkoxysilanes.  

PubMed

Tetra-alkoxysilanes are common and useful reagents in sol-gel processes and understanding their reactivity is important in the design of new materials. The mechanism of gas-phase reactions that mimic alcoholyis of Si(OMe)(4) (usually known as TMOS) under acidic conditions have been studied by Fourier transform ion cyclotron resonance techniques and density functional calculations at the B3LYP/6-311+G(d,p) level. The proton affinity of TMOS has been estimated at 836.4 kJ mol(-1) and protonation of TMOS gives rise to an ionic species that is best represented as trimethoxysilyl cations associated with a methanol molecule. Protonated TMOS undergoes rapid and sequential substitution of the methoxy groups in the gas-phase upon reaction with alcohols. The calculated energy profile of the reaction indicates that the substitution reaction through an S(N)2 type mechanism may be more favorable than frontal attack at silicon. Furthermore, the sequential substitution reactions are promoted by a mechanism that involves proton shuttle from the most favorable protonation site to the oxygen of the departing group mediated by the neutral reagent molecule. PMID:20530843

Rainone, Raquel; Malaspina, Thaciana; Xavier, Luciano A; Riveros, José M

2010-01-01

285

Gas phase reaction of sulfur trioxide with water vapor  

SciTech Connect

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

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

1994-12-31

286

Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids  

PubMed Central

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 NO2? anion or neutral loss of HNO2. The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional ? or ? unsaturation occurred through a multiple step cyclization reaction process, leading to 5 and 6 member ring heterocyclic products and carbon chain fragmentation. Cyclization products were not obtained during nitroalkane fragmentation, highlighting the role of double bond ? electrons during NO2? rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of 13C and 15N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples.

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

2012-01-01

287

Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids  

NASA Astrophysics Data System (ADS)

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

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

2011-09-01

288

Preconceptual design of the gas-phase decontamination demonstration cart  

SciTech Connect

Removal of uranium deposits from the interior surfaces of gaseous diffusion equipment will be a major portion of the overall multibillion dollar effort to decontaminate and decommission the gaseous diffusion plants. Long-term low-temperature (LTLT) gas-phase decontamination is being developed at the K-25 Site as an in situ decontamination process that is expected to significantly lower the decontamination costs, reduce worker exposure to radioactive materials, and reduce safeguard concerns. This report documents the preconceptual design of the process equipment that is necessary to conduct a full-scale demonstration of the LTLT method in accordance with the process steps listed above. The process equipment and method proposed in this report are not intended to represent a full-scale production campaign design and operation, since the gas evacuation, gas charging, and off-gas handling systems that would be cost effective in a production campaign are not cost effective for a first-time demonstration. However, the design presented here is expected to be applicable to special decontamination projects beyond the demonstration, which could include the Deposit Recovery Program. The equipment will therefore be sized to a 200 ft size 1 converter (plus a substantial conservative design margin), which is the largest item of interest for gas phase decontamination in the Deposit Recovery Program. The decontamination equipment will allow recovery of the UF{sub 6}, which is generated from the reaction of ClF{sub 3} with the uranium deposits, by use of NaF traps.

Munday, E.B.

1993-12-01

289

Gas-phase fragmentation analysis of nitro-fatty acids.  

PubMed

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

2011-07-13

290

Quantitative modeling of peptide binding to TAP using support vector machine.  

PubMed

The transport of peptides to the endoplasmic reticulum by the transporter associated with antigen processing (TAP) is a necessary step towards determining CD8 T cell epitopes. In this work, we have studied the predictive performance of support vector machine models trained on single residue positions and residue combinations drawn from a large dataset consisting of 613 nonamer peptides of known affinity to TAP. Predictive performance of these TAP affinity models was evaluated under 10-fold cross-validation experiments and measured using Pearson's correlation coefficients (R(p)). Our results show that every peptide position (P1-P9) contributes to TAP binding (minimum R(p) of 0.26 +/- 0.11 was achieved by a model trained on the P6 residue), although the largest contributions to binding correspond to the C-terminal end (R(p) = 0.68 +/- 0.06) and the P1 (R(p) = 0.51 +/- 0.09) and P2 (0.57 +/- 0.08) residues of the peptide. Training the models on additional peptide residues generally improved their predictive performance and a maximum correlation (R(p) = 0.89 +/- 0.03) was achieved by a model trained on the full-length sequences or a residue selection consisting of the first 5 N- and last 3 C-terminal residues of the peptides included in the training set. A system for predicting the binding affinity of peptides to TAP using the methods described here is readily available for free public use at http://imed.med.ucm.es/Tools/tapreg/. PMID:19705485

Diez-Rivero, Carmen M; Chenlo, Bernardo; Zuluaga, Pilar; Reche, Pedro A

2010-01-01

291

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

SciTech Connect

Gas phase chromatography using The Heavy Element Volatility Instrument (HEVI) and the On Line Gas Apparatus (OLGA III) was used to determine volatilities of ZrBr{sub 4}, HfBr{sub 4}, RfBr{sub 4}, NbBr{sub 5}, TaOBr{sub 3}, HaCl{sub 5}, WBr{sub 6}, FrBr, and BiBr{sub 3}. Short-lived isotopes of Zr, Hf, Rf, Nb, Ta, Ha, W, and Bi were produced via compound nucleus reactions at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory and transported to the experimental apparatus using a He gas transport system. The isotopes were halogenated, separated from the other reaction products, and their volatilities determined by isothermal gas phase chromatography. Adsorption Enthalpy ({Delta}H{sub a}) values for these compounds were calculated using a Monte Carlo simulation program modeling the gas phase chromatography column. All bromides showed lower volatility than molecules of similar molecular structures formed as chlorides, but followed similar trends by central element. Tantalum was observed to form the oxybromide, analogous to the formation of the oxychloride under the same conditions. For the group 4 elements, the following order in volatility and {Delta}H{sub a} was observed: RfBr{sub 4} > ZrBr{sub 4} > HfBr{sub 4}. The {Delta}H{sub a} values determined for the group 4, 5, and 6 halides are in general agreement with other experimental data and theoretical predictions. Preliminary experiments were performed on Me-bromides. A new measurement of the half-life of {sup 261}Rf was performed. {sup 261}Rf was produced via the {sup 248}Cm({sup 18}O, 5n) reaction and observed with a half-life of 74{sub -6}{sup +7} seconds, in excellent agreement with the previous measurement of 78{sub -6}{sup +11} seconds. We recommend a new half-life of 75{+-}7 seconds for {sup 261}Rf based on these two measurements. Preliminary studies in transforming HEVI from an isothermal (constant temperature) gas phase chromatography instrument to a thermochromatographic (variable temperature) instrument have been completed. Thermochromatography is a technique that can be used to study the volatility and {Delta}H{sub a} of longer-lived isotopes off-line, Future work will include a comparison between the two techniques and the use of thermochromatography to study isotopes in a wider range of half-lives and molecular structures.

Sylwester, Eric Robert

1998-10-01

292

Inactivating peptide of the Shaker B potassium channel: conformational preferences inferred from studies on simple model systems.  

PubMed Central

Previous studies on the interaction between the inactivating peptide of the Shaker B K+ channel (ShB peptide, H2N-MAAVAGLYGLGEDRQHRKKQ) and anionic phospholipid vesicles, used as model targets, have shown that the ShB peptide: (i) binds to the vesicle surface with high affinity; (ii) readily adopts a strongly hydrogen-bonded beta-structure; and (iii) becomes inserted into the hydrophobic bilayer. We now report fluorescence studies showing that the vesicle-inserted ShB peptide is in a monomeric form and, therefore, the observed beta-structure must be intramolecularly hydrogen-bonded to produce a beta-hairpin conformation. Also, additional freeze-fracture and accessibility-to-trypsin studies, which aimed to estimate how deeply and in which orientation the folded monomeric peptide inserts into the model target, have allowed us to build structural models for the target-inserted peptide. In such models, the peptide has been folded near G6 to configure a long beta-hairpin modelled to produce an internal cancellation of net charges in the stretch comprising amino acids 1-16. As to the positively charged C-terminal portion of the ShB peptide (RKKQ), this has been modelled to be in parallel with the anionic membrane surface to facilitate electrostatic interactions. Since the negatively charged surface and the hydrophobic domains in the model vesicle target may partly imitate those present at the inactivation 'entrance' in the channel protein [Kukuljan, M., Labarca, P. and Latorre, R. (1995) Am. J. Physiol. Cell Physiol. 268, C535-C556], we believe that the structural models postulated here for the vesicle-inserted peptide could help to understand how the ShB peptide associates with the channel during inactivation and why mutations at specific sites in the ShB peptide sequence, such as that in the ShB-L7E peptide, result in non-inactivating peptide variants.

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

1998-01-01

293

Formation and Dissociation of Phosphorylated Peptide Radical Cations  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

294

Recent Advances in Computational Modeling of ?-Helical Membrane-Active Peptides.  

PubMed

Membrane-active peptides (MAPs) represent a broad variety of molecules, and biological functions of most are directly associated with their ability to interact with membranes. Taking into account the effect of MAPs on living cells they can be nominally divided into three major groups - fusion (FPs), antimicrobial/cytolytic (AMPs/CPs) and cell-penetrating (CPPs) peptides. Although spatial structure of different MAPs varies to a great extent, linear ?-helical peptides represent the most studied class. These peptides possess relatively simple structural organization and share a set of similar molecular features, which make them very attractive to both experimental and computational studies. Here, we review different molecular modeling methods in prospective of their applications to study of ?-helical MAPs. The most sophisticated of them, such as molecular dynamics simulations, give atomistic information about molecular interactions driving peptide binding to the water-lipid interface, cooperative mechanisms of membrane destabilization and thermodynamics of these processes. Significant progress has been achieved in this field during the last few years, resulting in a possibility to observe computationally MAPs action in realistic peptide-to-lipid ratios and over the microsecond timescale. Other relatively simple but powerful approaches allow assessment of important characteristics of MAPs such as ?-helical propensity, amphiphilicity, total hydrophobicity, and spatial distribution of charge and hydrophobic/hydrophilic properties, etc. Altogether, computational methods provide efficient basis for rational design of MAPs with predefined properties and a spectrum of biological activities. PMID:23131190

Polyansky, Anton A; Chugunov, Anton O; Vassilevski, Alexander A; Grishin, Eugene V; Efremov, Roman G; Shemyakin, M M; Ovchinnikov, Yu A

2012-11-01

295

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

PubMed Central

The energetics and partition of two hybrid peptides of cecropin A and melittin (CA(1–8)M(1–18) and CA(1–7)M(2–9)) with liposomes of different composition were studied by time-resolved fluorescence spectroscopy, isothermal titration calorimetry, and surface plasmon resonance. The study was carried out with large unilamellar vesicles of three different lipid compositions: 1,2-dimyristoil-sn-glycero-3-phosphocholine (DMPC), 1,2-dimyristoyl-sn-glycero-3-phospho-rac-(1-glycerol) (DMPG), and a 3:1 binary mixture of DMPC/DMPG in a wide range of peptide/lipid ratios. The results are compatible with a model involving a strong electrostatic surface interaction between the peptides and the negatively charged liposomes, giving rise to aggregation and precipitation. A correlation is observed in the calorimetric experiments between the observed events and charge neutralization for negatively charged and mixed membranes. In the case of zwitterionic membranes, a very interesting case study was obtained with the smaller peptide, CA(1–7)M(2–9). The calorimetric results obtained for this peptide in a large range of peptide/lipid ratios can be interpreted on the basis of an initial and progressive surface coverage until a threshold concentration, where the orientation changes from parallel to perpendicular to the membrane, followed by pore formation and eventually membrane disruption. The importance of negatively charged lipids on the discrimination between bacterial and eukaryotic membranes is emphasized.

Bastos, Margarida; Bai, Guangyue; Gomes, Paula; Andreu, David; Goormaghtigh, Erik; Prieto, Manuel

2008-01-01

296

Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model  

PubMed Central

The increasing rate in antibiotic-resistant bacterial strains has become an imperative health issue. Thus, pharmaceutical industries have focussed their efforts to find new potent, non-toxic compounds to treat bacterial infections. Antimicrobial peptides (AMPs) are promising candidates in the fight against antibiotic-resistant pathogens due to their low toxicity, broad range of activity and unspecific mechanism of action. In this context, bioinformatics' strategies can inspire the design of new peptide leads with enhanced activity. Here, we describe an artificial neural network approach, based on the AMP's physicochemical characteristics, that is able not only to identify active peptides but also to assess its antimicrobial potency. The physicochemical properties considered are directly derived from the peptide sequence and comprise a complete set of parameters that accurately describe AMPs. Most interesting, the results obtained dovetail with a model for the AMP's mechanism of action that takes into account new concepts such as peptide aggregation. Moreover, this classification system displays high accuracy and is well correlated with the experimentally reported data. All together, these results suggest that the physicochemical properties of AMPs determine its action. In addition, we conclude that sequence derived parameters are enough to characterize antimicrobial peptides.

Torrent, Marc; Andreu, David; Nogues, Victoria M.; Boix, Ester

2011-01-01

297

Modeling the structure of bound peptide ligands to major histocompatibility complex  

PubMed Central

In this article, we present a new technique for the rapid and precise docking of peptides to MHC class I and class II receptors. Our docking procedure consists of three steps: (1) peptide residues near the ends of the binding groove are docked by using an efficient pseudo-Brownian rigid body docking procedure followed by (2) loop closure of the intervening backbone structure by satisfaction of spatial constraints, and subsequently, (3) the refinement of the entire backbone and ligand interacting side chains and receptor side chains experiencing atomic clash at the MHC receptor–peptide interface. The method was tested by remodeling of 40 nonredundant complexes of at least 3.00 Å resolution for which three-dimensional structural information is available and independently for docking peptides derived from 15 nonredundant complexes into a single template structure. In the first test, 33 out of 40 MHC class I and class II peptides and in the second test, 11 out of 15 MHC–peptide complexes were modeled with a C? RMSD < 1.00 Å.

Tong, Joo Chuan; Tan, Tin Wee; Ranganathan, Shoba

2004-01-01

298

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.

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

2010-01-01

299

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

NASA Astrophysics Data System (ADS)

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

Hays, Gerry

1997-10-01

300

Weak intermolecular interactions in gas-phase nuclear magnetic resonance.  

PubMed

Gas-phase nuclear magnetic resonance (NMR) spectra demonstrating the effect of weak intermolecular forces on the NMR shielding constants of the interacting species are reported. We analyse the interaction of the molecular hydrogen isotopomers with He, Ne, and Ar, and the interaction in the He-CO(2) dimer. The same effects are studied for all these systems in the ab initio calculations. The comparison of the experimental and computed shielding constants is shown to depend strongly on the treatment of the bulk susceptibility effects, which determine in practice the pressure dependence of the experimental values. Best agreement of the results is obtained when the bulk susceptibility correction in rare gas solvents is evaluated from the analysis of the He-rare gas interactions, and when the shielding of deuterium in D(2)-rare gas systems is considered. PMID:21895188

Garbacz, Piotr; Piszczatowski, Konrad; Jackowski, Karol; Moszynski, Robert; Jaszu?ski, Micha?

2011-08-28

301

The intrinsic (gas-phase) acidities of bridgehead alcohols  

NASA Astrophysics Data System (ADS)

The gas-phase acidities of 1-adamantanol and perfluoro1-adamantanol were determined by means of Fourier transform ion cyclotron resonance spectrometry (FT-ICR). The acidity of perfluoro1-adamantanol seems to be the highest ever reported for an alcohol. A computational study of these species and their anions at both the MP2/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) levels was performed. Also studied were the tertiary alcohols (including their perfluorinated forms) derived from norbornane, bicyclo[2.2E2]octane and cubane. It was found that: (i) the intrinsic acidity of non-fluorinated bridgehead alcohols increases with the strain of the hydrocarbon framework and, (ii) perfluorination of these compounds strongly increases their acidity and, likely, significantly modifies their internal strain.

Herrero, Rebeca; Dávalos, Juan Z.; Abboud, José-Luis M.; Alkorta, I.; Koppel, I.; Koppel, I. A.; Sonoda, T.; Mishima, M.

2007-11-01

302

Molecular gas phase counterparts to solid state grain mantles features  

NASA Astrophysics Data System (ADS)

We present ISO-SWS observations of the dense part surrounding the protostellar object RAFGL7009S. In this study, we concentrate on simple molecules detected in the gas and ice state (H_2O, CO_2 and CH_4) with the SWS(AOT06). Estimates are derived for their corresponding gas-to-solid ratios and lead to fractions around 0.2 for both H_2$O and CH_4 and almost an order of magnitude lower for CO_2. The gas phase temperature for these species in the gas is dominated by a rather cold component (~50 K). We discuss briefly the possible implications for the chemistry in this region.

Dartois, E.; D'Hendecourt, L.; Boulanger, F.; Puget, J. L.; Jourdain de Muizon, M.; Breitfellner, M.; Habing, H. J.

303

Ceramic microreactors for heterogeneously catalysed gas-phase reactions.  

PubMed

The high surface to volume ratio of microchannel components offers many advantages in micro chemical engineering. It is obvious, however, that the reactor material and corrosion phenomena play an important role when applying these components. For chemical reactions at very high temperatures or/and with corrosive reactants involved, microchannel components made of metals or polymers are not suited. Hence, a modular microreactor system made of alumina was developed and fabricated using a rapid prototyping process chain. With exchangeable inserts the system can be adapted to the requirements of various reactions. Two heterogeneously catalysed gas-phase reactions (oxidative coupling of methane, isoprene selective oxidation to citraconic anhydride) were investigated to check the suitability of the system at temperatures of up to 1000 degrees C. Apart from the high thermal and chemical resistance, the lack of any blind activity was found to be another advantage of ceramic components. PMID:15269808

Knitter, Regina; Liauw, Marcel A

2004-05-03

304

Gas-phase syntheses for interstellar carboxylic and amino acids  

NASA Astrophysics Data System (ADS)

We report experimental results that demonstrate gas-phase, ionic syntheses of glycine and ?-alanine, as well as acetic and propanoic acid, from smaller molecules found in space; in doing so, we infer the formation of these acids in the interstellar environment. We show that ionized glycine and ?-alanine are produced in the reactions of hydroxylamine ions, NH2OH+, with acetic and propanoic acid respectively. Even more promising in the context of interstellar synthesis are our results that demonstrate the corresponding production of the protonated amino acids from analogous reactions with protonated hydroxylamine. The striking specificity of these syntheses for the ?-isomer of alanine suggests that the amino acids of CI (Carbonaceous Ivona) chondrite meteorites are products of interstellar chemistry and supports the hypothesis that these meteorites are of cometary origin.

Blagojevic, Voislav; Petrie, Simon; Bohme, Diethard K.

2003-02-01

305

Gas-phase spectroscopy of biomolecular ions: Porphyrins and metalloporphyrins  

NASA Astrophysics Data System (ADS)

The electronic structure of a biochromophore (i.e., light absorber) is strongly perturbed by its environment, e.g., water or amino acid residues within protein pockets. To reveal the intrinsic electronic properties, it is therefore necessary to study isolated molecules in vacuo. Many biochromophores are ionic in their natural environment, which renders experiments complicated as it is not possible to produce enough absorbing species for traditional light transmission spectroscopy. In Aarhus we have developed state-of-the-art apparatus to record gas-phase absorption spectra. Some recent results for porphyrin and metalloporphyrin ions are presented, including both electronic ground state ions and electronically excited ions. Fragmentation channels are found from quickly switching the ring voltages after photoexcitation to store particular daughter ions.

Brøndsted Nielsen, Steen

2012-11-01

306

Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase  

NASA Astrophysics Data System (ADS)

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

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

2007-03-01

307

Synthesis and Gas Phase Thermochemistry of Germanium-Containing Compounds  

SciTech Connect

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

Nathan Robert Classen

2002-12-31

308

Structures of platinum oxide clusters in the gas phase.  

PubMed

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

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

2012-08-28

309

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer.  

PubMed

Benchmark calculations of proton affinities and gas-phase basicities of molecules most relevant to biological phosphoryl transfer reactions are presented and compared with available experimental results. The accuracy of proton affinity and gas-phase basicity results obtained from several multi-level model chemistries (CBS-QB3, G3B3, and G3MP2B3) and density-functional quantum models (PBE0, B1B95, and B3LYP) are assessed and compared. From these data, a set of empirical bond enthalpy, entropy, and free energy corrections are introduced that considerably improve the accuracy and predictive capability of the methods. These corrections are applied to the prediction of proton affinity and gas-phase basicity values of important biological phosphates and phosphoranes for which experimental data does not currently exist. Comparison is made with results from semiempirical quantum models that are commonly employed in hybrid quantum mechanical/molecular mechanical simulations. Data suggest that the design of improved semiempirical quantum models with increased accuracy for relative proton affinity values is necessary to obtain quantitative accuracy for phosphoryl transfer reactions in solution, enzymes, and ribozymes. PMID:16186912

Range, Kevin; Riccardi, Demian; Cui, Qiang; Elstner, Marcus; York, Darrin M

2005-07-07

310

Printing nanoparticles from the liquid and gas phases using nanoxerography  

NASA Astrophysics Data System (ADS)

This paper reports on the directed self-assembly of nanoparticles onto charged surface areas with a resolution of 200 nm from the liquid phase and 100 nm from the gas phase. The charged areas required for this type of nanoxerographic printing were fabricated using a parallel method that employs a flexible, electrically conductive, electrode to charge a thin-film electret. As electrodes, we used metal-coated polymeric stamps and 10 µm thick doped silicon wafers carrying a pattern in topography. Each electrode was brought in contact with a thin-film electret on an n-doped silicon substrate. The charge pattern was transferred into the thin-film electret by applying a voltage pulse between the conductive electrode and the silicon substrate. Areas as large as 1 cm2 were patterned with charge with 100 nm scale resolution in 10 s. These charge patterns attract nanoparticles. A liquid-phase assembly process where electrostatic forces compete with disordering forces due to ultrasonication has been developed to assemble nanoparticles onto charged based receptors in 10 s from a liquid suspension. A gas-phase assembly process was developed that uses a transparent particle assembly module to direct particles towards the charged surface while monitoring the total charge of assembled particles. Nanoparticles were generated using a tube furnace by evaporation and condensation at the outlet. The electrostatically directed assembly of 10-100 nm sized metal (gold, silver) and 30 nm sized carbon particles was accomplished with a resolution 500-1000 times greater than the resolution of existing xerographic printers.

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

2003-10-01

311

Feasibility of gas-phase decontamination of gaseous diffusion equipment  

SciTech Connect

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

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

1993-02-01

312

Artificial signal peptide prediction by a hidden markov model to improve protein secretion via Lactococcus lactis bacteria  

PubMed Central

A hidden Markov model (HMM) has been utilized to predict and generate artificial secretory signal peptide sequences. The strength of signal peptides of proteins from different subcellular locations via Lactococcus lactis bacteria correlated with their HMM bit scores in the model. The results show that the HMM bit score +12 are determined as the threshold for discriminating secreteory signal sequences from the others. The model is used to generate artificial signal peptides with different bit scores for secretory proteins. The signal peptide with the maximum bit score strongly directs proteins secretion.

Razmara, Jafar; Deris, Safaai B; Illias, Rosli Bin Md; Parvizpour, Sepideh

2013-01-01

313

An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC  

Microsoft Academic Search

The proposed model is based on the measurement of the retention times of 346 tryptic peptides in the 560- to 4,000-Da mass range, derived from a mixture of 17 protein digests. These peptides were measured in HPLC-MALDI MS runs, with peptide identities confirmed by MS\\/MS. The model relies on summation of the retention coefficients of the individual amino acids, as

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

314

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.

1999-05-01

315

Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination.  

PubMed

In this work, synthetic peptides were used to determine the fragmentation behavior of ubiquitinated peptides and to find ions diagnostic for peptide ubiquitination. The ubiquitin-calmodulin peptide1 was chosen as the model peptide for naturally occurring ubiquitinated proteins cleaved with endoproteinase gluC. In addition, the fragmentation behavior of model ubiquitinated peptides produced by tryptic digestion was also of great interest since the standard protocols for proteomics-based protein identification use trypsin as the protease. Attachment of ubiquitin to a target protein results in a branched structure, but only ions from the ubiquitin side chain (and the lysine to which it is attached) can be used as diagnostic ions, since fragment ions that contain other amino acids from the parent protein will vary in mass. Characteristic b-type fragment ions from the gluC cleavage of the ubiquitin side chain (designated as b ions) were found which involve only the ubiquitin tail (b2, b3, b4, b5 and b6 ions at m/z 189.06, 302.12, 439.18, 552.30 and 651.30, respectively). Maximum production of these ions occurred at a collision energy of 45 eV in a Q-TOF instrument. Although a non-ubiquitinated peptide may produce isobaric fragment ions, it is unlikely that it can produce these ions in combination. With liquid chromatography/tandem mass spectrometry (LC/MS/MS) experiments, ubiquitinated peptides can readily be determined by surveying the reconstructed or extracted ion chromatograms of the diagnostic fragment ions for common peaks. Characteristic ions resulting from tryptic cleavage of the side chain were found in cleavage products with a missed cleavage, resulting in a LRGG- tag instead of a GG- tag. For the LRGG-tagged peptide, diagnostic MS/MS fragment ions (at m/z 270.17 and 384.21) from the ubiquitin tail (b2 and b4, respectively) were found, along with an internal fragment ion (LRGGK-28) at m/z 484.30. These ions should prove useful in precursor-ion scanning experiments for identifying peptides modified by attachment of ubiquitin, and for locating the site of ubiquitin attachment. PMID:15655800

Warren, Maria R Esteban; Parker, Carol E; Mocanu, Viorel; Klapper, David; Borchers, Christoph H

2005-01-01

316

Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models  

PubMed Central

Background The binding between peptide epitopes and major histocompatibility complex proteins (MHCs) is an important event in the cellular immune response. Accurate prediction of the binding between short peptides and the MHC molecules has long been a principal challenge for immunoinformatics. Recently, the modeling of MHC-peptide binding has come to emphasize quantitative predictions: instead of categorizing peptides as "binders" or "non-binders" or as "strong binders" and "weak binders", recent methods seek to make predictions about precise binding affinities. Results We developed a quantitative support vector machine regression (SVR) approach, called SVRMHC, to model peptide-MHC binding affinities. As a non-linear method, SVRMHC was able to generate models that out-performed existing linear models, such as the "additive method". By adopting a new "11-factor encoding" scheme, SVRMHC takes into account similarities in the physicochemical properties of the amino acids constituting the input peptides. When applied to MHC-peptide binding data for three mouse class I MHC alleles, the SVRMHC models produced more accurate predictions than those produced previously. Furthermore, comparisons based on Receiver Operating Characteristic (ROC) analysis indicated that SVRMHC was able to out-perform several prominent methods in identifying strongly binding peptides. Conclusion As a method with demonstrated performance in the quantitative modeling of MHC-peptide binding and in identifying strong binders, SVRMHC is a promising immunoinformatics tool with not inconsiderable future potential.

Liu, Wen; Meng, Xiangshan; Xu, Qiqi; Flower, Darren R; Li, Tongbin

2006-01-01

317

Selective and sensitive chromogenic detection of cyanide and HCN in solution and in gas phase.  

PubMed

Two triphenylmethane based chemodosimeters for selective and chromogenic sensing of cyanide anions in aqueous environments and of hydrogen cyanide in gas phase were prepared and studied. PMID:23680816

Gotor, Raúl; Costero, Ana M; Gil, Salvador; Parra, Margarita; Martínez-Máñez, Ramón; Sancenón, Félix; Gaviña, Pablo

2013-05-17

318

Binding of a C-end rule peptide to neuropilin-1 receptor: A molecular modeling approach  

PubMed Central

Neuropilin-1 (NRP-1) is a receptor that plays an essential role in angiogenesis, vascular permeability and nervous system development. Previous studies have shown that peptides with an N-terminal Arg, especially peptides with the four residue consensus sequence R/K/XXR/K bind to NRP-1 cell surfaces. Peptides containing such consensus sequences promote binding and internalization into cells, while blocking the C-terminal Arg (or Lys) prevents the internalization. In this study we use molecular dynamics simulations to model the structural properties of the NRP-1 complex with a prototypic CendR peptide, RPAR. Our simulations show that RPAR binds NRP-1 through specific interactions of the RPAR C-terminus: three hydrogen bonds and a salt bridge anchor the ligand in the receptor pocket. The modeling results were used as the starting point for a systematic computational study of new RPAR analogs based on chemical modifications of its natural amino acids. Comparison of the structural properties of the new peptide - receptor complexes with the original organization suggest that some of the analogs can increase the binding affinity while reducing the natural sensitivity of RXXR to endogenous proteases.

Haspel, Nurit; Zanuy, David; Nussinov, Ruth; Teesalu, Tambet; Ruoslahti, Erkki; Aleman, Carlos

2011-01-01

319

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

NASA Astrophysics Data System (ADS)

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

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

1997-11-01

320

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

PubMed Central

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

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

2011-01-01

321

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

NASA Astrophysics Data System (ADS)

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

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

2011-09-01

322

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

PubMed

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

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

2010-11-01

323

Charge transfer in metal-atom-containing molecules in the gas phase  

NASA Astrophysics Data System (ADS)

The presence of charge transfer (CT) is ubiquitous in metal-atom-containing molecules in the gas phase. The states of interest range from ground states to the lower excited states, given the generally low ionisation potentials of metal atoms. This review is written from an experimentalist's perspective, to describe the specifics of CT states in stable molecules containing a metal atom or of transient CT states in dynamical processes. The large body of experimental evidence allows the description of such states in an empirical or semi-empirical manner, including partial point charges and polarised electron clouds on the ions. These simple models are compared with more quantitative models, allowing the development of sophisticated descriptions. The simple perspective deriving from experimental evidence is justified, when it is possible via accurate quantum calculations and allows building a rather complete framework for the ionic bond or CT-induced dynamics.

Shafizadeh, Niloufar; Soep, Benoit; Mestdagh, Jean Michel; Breckenridge, W. H.

324

A theoretical model for the association of amphiphilic transmembrane peptides in lipid bilayers  

Microsoft Academic Search

A theoretical model is proposed for the association of trans-bilayer peptides in lipid bilayers. The model is based on a\\u000a lattice model for the pure lipid bilayer, which accounts accurately for the most important conformational states of the lipids\\u000a and their mutual interactions and statistics. Within the lattice formulation the bilayer is formed by two independent monolayers,\\u000a each represented by

Maria Maddalena Sperotto

1997-01-01

325

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

PubMed Central

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

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

2010-01-01

326

Enhancement of gas-phase diffusion in the presence of liquid  

NASA Astrophysics Data System (ADS)

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

Webb, S.; Angert, A.

2003-04-01

327

Quantification of chemical peptide reactivity for screening contact allergens: a classification tree model approach.  

PubMed

In the interest of reducing animal use, in vitro alternatives for skin sensitization testing are under development. One unifying characteristic of chemical allergens is the requirement that they react with proteins for the effective induction of skin sensitization. The majority of chemical allergens are electrophilic and react with nucleophilic amino acids. To determine whether and to what extent reactivity correlates with skin sensitization potential, 82 chemicals comprising allergens of different potencies and nonallergenic chemicals were evaluated for their ability to react with reduced glutathione (GSH) or with two synthetic peptides containing either a single cysteine or lysine. Following a 15-min reaction time with GSH, or a 24-h reaction time with the two synthetic peptides, the samples were analyzed by high-performance liquid chromatography. UV detection was used to monitor the depletion of GSH or the peptides. The peptide reactivity data were compared with existing local lymph node assay data using recursive partitioning methodology to build a classification tree that allowed a ranking of reactivity as minimal, low, moderate, and high. Generally, nonallergens and weak allergens demonstrated minimal to low peptide reactivity, whereas moderate to extremely potent allergens displayed moderate to high peptide reactivity. Classifying minimal reactivity as nonsensitizers and low, moderate, and high reactivity as sensitizers, it was determined that a model based on cysteine and lysine gave a prediction accuracy of 89%. The results of these investigations reveal that measurement of peptide reactivity has considerable potential utility as a screening approach for skin sensitization testing, and thereby for reducing reliance on animal-based test methods. PMID:17400584

Gerberick, G Frank; Vassallo, Jeffrey D; Foertsch, Leslie M; Price, Brad B; Chaney, Joel G; Lepoittevin, Jean-Pierre

2007-03-30

328

Retardation of dissolved oxygen due to a trapped gas phase in porous media  

SciTech Connect

Information on the transport of dissolved gases in ground water is needed to design ways to increase dissolved gas concentrations in ground water for use in in situ bioremediation (e.g., O{sub 2} and CH{sub 4}) and to determine if dissolved gases are conservative tracers of ground-water flow (e.g., He). A theoretical model was developed to describe the effect of small quantities of trapped gas bubbles on the transport of dissolved gases in otherwise saturated porous media. Dissolved gas transport in porous media can be retarded by gas partitioning between the mobile aqueous phase and a stationary trapped gas phase. The model assumes equilibrium partitioning where the retardation factor is defined as R = 1 + H{prime} (V{sub g}/V{sub w}) where H{prime} is the dimensionless Henry`s Law constant for the dissolved gas, and V{sub g} and V{sub w} are the volumes of the trapped gas and water phases, respectively. At 15 C and with V{sub g}/V{sub w} = 0.05, the predicted retardation factors for He, O{sub 2}, and CH{sub 4} are 5.8, 2.4, and 2.3, respectively. The validity of the model was tested for dissolved oxygen in small-scale column experiments over a range of trapped gas volumes. Retardation factors of dissolved oxygen increased from 1 to 6.6 as V{sub g}/V{sub w} increased from 0 to 0.123 and are in general agreement with model predictions except for the larger values of V{sub g}/V{sub w}. The theoretical and experimental results suggest that gas partitioning between the aqueous phase and a trapped gas phase can greatly influence rates of dissolved gas transport in ground water.

Fry, V.A.; Istok, J.D.; Semprini, L. [Oregon State Univ., Corvallis, OR (United States). Dept. of Civil Engineering; O`Reilly, K.T.; Buscheck, T.E. [Chevron Research and Technology Co., Richmond, CA (United States)

1995-05-01

329

On the design of zinc-finger models with cyclic peptides bearing a linear tail.  

PubMed

Cyclic peptides with a linear tail (CPLT) have been successfully used to model two zinc fingers (ZFs) adopting the treble-clef- and loosened zinc-ribbon folds. In this article, we examine the factors that may influence the design of such ZF models: mutations in the sequence, size of the cycle, and size of the tail. For this purpose, several peptides derived from the CPLT-based models of the treble-clef- and loosened zinc-ribbon ZF were synthesized and studied. CPLT-based models appear to be robust toward mutations, accommodate various cycle sizes, and are sensible to the size of the linking region of the tail located between the cycle and the coordinating amino acids. Based on these criteria, we describe the design of a new CPLT-based model for the zinc-ribbon ZFs, LZR , and compare it to a linear analogue, LZR(lin) . The model complex Zn?LZR is able to fold correctly around the metal ion contrary to Zn?LZR(lin) , suggesting that CPLT-based models are more likely to yield structurally meaningful models of ZF sites than linear peptide models. Finally, we draw some rules that could allow the design of new CPLT-based metallopeptides with a controlled fold. PMID:23436718

Jacques, Aurélie; Mettra, Bastien; Lebrun, Vincent; Latour, Jean-Marc; Sénèque, Olivier

2013-02-21

330

MINLP Models for the Synthesis of Optimal Peptide Tags and Downstream Protein Processing  

Microsoft Academic Search

The development of systematic methods for the synthesis of downstream protein processing operations has seen growing interest in recent years, as purification is often the most complex and costly stage in biochemical production plants. The objective of the work presented here is to develop mathematical models based on mixed integer optimization techniques, which integrate the selection of optimal peptide purification

Evangelos Simeonidis; Jose M. Pinto; M. Elena Lienqueo; Sophia Tsoka; Lazaros G. Papageorgiou

2005-01-01

331

Peptide neuroregulators: the opioid system as a model.  

PubMed Central

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

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

1985-01-01

332

Effect of the aminoacid composition of model ?-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation.  

PubMed

The interaction of a model Lys flanked ?-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown that these peptides cause disordering of the lipid bilayer in the gel state but only small changes have been monitored in a liquid-crystalline state. The peptides affect ordering of the surrounding lipids depending on the helix stability which is determined by amino acid side chains - their volume, shape, etc. We have shown that the helix does not keep the linear shape in all simulations but often bends or breaks. During some simulations with a very small difference between hydrophobic length of peptide and membrane thickness the peptide exhibits negligible tilt. At the same time changes in peptide conformations during simulations resulted in appearance of superhelix. PMID:22893120

Melicher?ík, Milan; Holúbeková, Alžbeta; Hianik, Tibor; Urban, Ján

2012-08-15

333

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.

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

2011-01-01

334

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.

2007-12-01

335

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

336

Gas-phase nuclear magnetic resonance studies of conformational kinetics  

NASA Astrophysics Data System (ADS)

The gas-phase conformational exchange kinetics of several amide and thioamide systems have been examined. The most fundamental amide system, formamide, has been studied extensively. The internal rotation rate constants for gaseous formamide are temperature and pressure dependent. The temperature dependent unimolecular high-pressure limit activation parameters are consistent with E? = 16.6(0.3) kcal mol-1 and A ? = 1.60(1.02) × 1013 sec-1 . The pressure dependent rate constants for formamide internal rotation are found to follow statistical RRKM kinetics. In addition, experimental and computational conformational analyses have been performed for solvated formamide systems. The internal rotation activation barriers are found to increase with increasing polarity of the solvent. The experimental values are compared to values calculated according to SC - IPCM and IPCM methodologies. The conformational exchange and equilibria in gas-phase asymmetrically substituted amides and thioamides have also been studied. The internal rotation activation barriers and conformational equilibria are found to be primarily influenced by the nature of the carbonyl substituent on the carbonyl or thiocarbonyl carbon in amides and thioamides. The conformational equilibria and activation energies are significantly different for the thioamides relative to their oxoamide analogs. Solvation significantly affects both the activation and conformational energies for all systems. The phase dependence of the values is attributed to solvent internal pressure effects and solvent stabilizing interactions. The Berry pseudorotation process in gaseous SF4 has been examined. Rate constants determined from exchange broadened 19F NMR spectra are temperature and pressure dependent. The temperature dependence of the unimolecular rate constants are consistent with E? = 11.9(0.2) kcal mol-1, A? = 3.56(1.09) × 1012 sec-1, ?G? = 12.2(0.2) kcal mol-1, ?H? = 11.3(0.4) kcal mol-1, and ?S? = -3.3(0.4) cal mol-1 K-1. The experimental values are compared to theoretical predictions using HF, MP2, DFT, MP4, and G2 methods. The pressure dependent rate constants agree well with RRKM predictions. Finally, the degenerate migration of the trimethylsilyl group in gaseous 5-trimethylsilylcyclopentadiene is studied. The temperature dependent rate constants for this process are consistent with ?G? = 15.7(0.1) kcal mol-1, ?H? = 15.4(0.2) kcal mol-1, and ?S? = -1.1(0.1) cal mol-1 K-1. The kinetic parameters are slightly higher than previously reported values for the neat liquid.

Taha, Angela Najah

337

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.

Weber, Arthur L.; Pizzarello, Sandra

2006-01-01

338

Effects of osmolytes on the helical conformation of model peptide: Molecular dynamics simulation  

NASA Astrophysics Data System (ADS)

Co-solvents such as glycerol and sorbitol are small organic molecules solvated in the cellular solutions that can have profound effects on the protein structures. Here, the molecular dynamics simulations and comparative structural analysis of magainin, as a peptide model, in pure water, 2,2,2-trifluoroethanol/water, glycerol/water, and sorbitol/water are reported. Our results show that the peptide NMR structure is largely maintained its native structure in osmolytes-water mixtures. The simulation data indicates that the stabilizing effect of glycerol and sorbitol is induced by preferential accumulation of glycerol and sorbitol molecules around the nonpolar and aromatic residues. Thus, the presence of glycerol and sorbitol molecules decreases the interactions of water molecules with the hydrophobic residues of the peptide, and the alpha helical structure is stabilized.

Mehrnejad, Faramarz; Ghahremanpour, Mohammad Mehdi; Khadem-Maaref, Mahmoud; Doustdar, Farahnoosh

2011-01-01

339

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

PubMed

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

2006-08-11

340

Acetylcholine receptor-alpha-bungarotoxin interactions: determination of the region-to-region contacts by peptide-peptide interactions and molecular modeling of the receptor cavity.  

PubMed Central

In previous studies from this laboratory, the binding regions of alpha-neurotoxins on human and Torpedo acetylcholine (AcCho) receptors (AcChoRs) and the binding regions for the receptor on the toxin were characterized with synthetic peptides of the respective molecules. In the present work, peptides representing the active regions of one molecule are each allowed to bind to each of the active-region peptides of the other molecule. Thus, the interaction of three alpha-bungarotoxin (alpha-BTX) synthetic loop peptides with four synthetic peptides representing the toxin-binding regions on human AcChoR permitted the determination of the region-region interactions between alpha-BTX and the human receptor. Based on the known three-dimensional structure of the toxin, the active peptides of the receptor were then assembled to their appropriate toxin-contact regions by computer model building and energy minimization. This allowed the three-dimensional construction of the toxin-binding cavity on human AcChoR. The cavity appears to be conical, 30.5 A in depth, involving several receptor regions that make contact with the alpha-BTX loop regions. One AcChoR region (within residues 125-136) involved in the binding to alpha-BTX also resides in a known AcCho-binding site, thus demonstrating in three dimensions a critical site involved in both AcCho activation and alpha-BTX blocking. The validity of this approach was first established for three of four peptides corresponding to regions on the beta chain of human hemoglobin involved in binding to the alpha chain. Thus, studying the interaction between peptides representing the binding regions of two protein molecules may provide an approach in molecular recognition by which the binding site on one protein can be described if the three-dimensional structure of the other protein is known.

Ruan, K H; Spurlino, J; Quiocho, F A; Atassi, M Z

1990-01-01

341

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

PubMed Central

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

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

2011-01-01

342

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

Microsoft Academic Search

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

Matthew Celnik; Robert Patterson; Markus Kraft; Wolfgang Wagner

2007-01-01

343

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

Microsoft Academic Search

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

PAUL CLAVIN; DAVID LAZIMI

1992-01-01

344

Partitioning of phthalates among the gas phase, airborne particles and settled dust in indoor environments  

Microsoft Academic Search

A critical evaluation of human exposure to phthalate esters in indoor environments requires the determination of their distribution among the gas phase, airborne particles and settled dust. If sorption from the gas phase is the dominant mechanism whereby a given phthalate is associated with both airborne particles and settled dust, there should be a predictable relationship between its particle and

Charles J. Weschler; Tunga Salthammer; Hermann Fromme

2008-01-01

345

Gas phase and catalytic ignition of methane and ethane in air over platinum  

Microsoft Academic Search

The ignition of gas phase combustion by heated catalytically active surface involves dynamic coupling of transport processes and chemical kinetics. Researchers have observed that surfaces with high catalytic activity require higher surface temperatures to ignite gas phase combustion, compared to nonactive surfaces, and that this difference is greatest for a stoichiometric mixture. In this paper an analysis of the ignition

Timothy A. Griffin; Lisa D. Pfefferle

1990-01-01

346

Determination of gas phase adsorption isotherms—a simple constant volume method  

Microsoft Academic Search

Single and ternary solute gas phase adsorption isotherms were conducted in this study to evaluate the effectiveness of a simple constant volume method, which was utilized by using Tedlar gas sampling bags as a constant volume batch reactor. For this purpose, gas phase adsorption of toluene, methyl ethyl ketone (MEK), and methyl isobutyl ketone (MIBK) on two types of activated

Daekeun Kim; Zhangli Cai; George A. Sorial

2006-01-01

347

Kinetics and growth mechanism of gallium arsenide crystals in gas-phase epitaxy  

Microsoft Academic Search

In conclusion, we note that gallium arsenide itself is the material with which the physicochemical and crystallophysical fundamentals of gas-phase epitaxy are presently being developed. It is hoped that the basic principles or crystal growth in gas-phase systems discovered in gallium arsenide will prove sufficiently general to be applied to other analogous systems.

L. G. Lavrent'eva

1980-01-01

348

Pt(111) reconstruction induced by enhanced Pt gas-phase chemical potential  

Microsoft Academic Search

Large terraces of the Pt(111) surface are shown to reconstruct in the presence of a Pt gas- phase environment down to 400 K. The lifting of the reconstruction in the absence of the Pt gas-phase is kinetically hindered up to 700 K. The main features of the reconstruction network as seen by the scanning tunneling microscope correspond to those inferred

Michael Bott; Michael Hohage; Thomas Michely; George Comsa

1993-01-01

349

Gas-phase coupling of reactive surfaces by oscillating reactant clouds  

Microsoft Academic Search

The collective, global behavior of a heterogeneous catalytic system depends on the effective communication of local reactivity variations to distant points in the system. One particularly efficient mode of communication occurs via partial pressure fluctuations in the gas-phase above the reactive surface. Although gas-phase communication has been implicated in a number of heterogeneous systems, the details of this coupling mechanism

Daniel Bilbao; Jochen Lauterbach

2010-01-01

350

Borate Ions in the Gas Phase, Fast-Atom Bombardment of Condensed-Phase Borates.  

National Technical Information Service (NTIS)

The intractable properties of crystalline and vitreous, condensed-phase boron-oxygen compounds have always hindered the generation and analysis of gas-phase boron-oxygen species. Recently, structures of gas-phase boron oxide cations, generated by fast-ato...

R. J. Doyle

1988-01-01

351

DETERMINATION OF GAS-PHASE DIMETHYL SULFATE AND MONOMETHYL HYDROGEN SULFATE  

EPA Science Inventory

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

352

Frequency metrology of a photomixing source for gas phase spectroscopy  

NASA Astrophysics Data System (ADS)

The availability of frequency combs has opened new possibilities for the measurement of optical frequencies. Photomixing is an attractive solution for high resolution THz spectroscopy of gases due to the narrow spectral resolution and ability to access the 100 GHz to 3.5 THz range. One limitation of present photomixing spectrometers is the accuracy with which the THz frequency is established. Measurement of the centre frequency gas phase molecular transitions requires an accuracy better than 100 kHz in order to allow spectroscopic constants to be determined. Standard optical techniques like those employed in wavelength meters can only provide accuracies in the order of 50 MHz. We have used a turnkey fibre based frequency comb and a standard photomixing configuration to realize a THz synthesizer with an accuracy of around 50kHz. Two ECDLs used to pump the photomixer are phase locked onto the frequency comb and provide a tuning range of 10 MHz. In order to extend the tuning range an additional phase locked ECLD has been added to obtain a range in excess of 100 MHz. The absorption profiles of many Doppler limited transitions of carbonyl sulphide and formaldehyde have been measured to validate this instrument.

Hindle, Francis; Mouret, Gael; Yang, Chun; Cuisset, Arnaud; Bocquet, Robin; Lours, Michel; Rovera, Daniele

2010-08-01

353

Transuranic actinide reactions with simple gas-phase molecules.  

SciTech Connect

The intent of this research is to conduct an experimental study of f-element chemistry fo r the purpose of identifying reaction trends and mechanisms of the early actinide metals with simple gas phase molecules . Previous research has elucidated some of the fundamenta l chemistry of the 4f elements,1-5 however, more complex chemistry is expected for the 5f serie s due to the inclusion of the 5f electrons in the valence shell . The matrix isolation approach, which is well-suited to the experimental study of transient species, will be used for sample collection, and IR/NIR/VIS spectroscopy will be employed to interrogate deposited matrices . The strength of this method lies in the use of isotopes of reactants, which permits the identification of guest molecules in a noble gas matrix by observation of vibrational frequenc y shifts and patterns upon isotopic substitution . Using this technique at the University of Virginia, the first noble gas-actinide bond has recently been identified, a weak U-Ar bond on the CUO molecule.6 Uranium has similarly been observed to bond to krypton and xenon, whereas thoriu m and the lanthanides have not exhibited this activity . It is expected that plutonium will be even more reactive in this respect . We will extend the body of actinide experimental evidence t o include the transuranic elements neptunium, plutonium, and americium reacted with isotopes o f oxygen, nitrogen, hydrogen, carbon monoxide, and carbon dioxide .

Willson, S. P. (Stephen P.); Veirs, D. K. (Douglas Kirk); Baiardo, J. P. (Joseph P.)

2003-01-01

354

Gas phase chromatography of halides of elements 104 and 105  

SciTech Connect

On-line isothermal gas phase chromatography was used to study halides of {sup 261}104 (T{sub {1/2}} = 65 s) and {sup 262,263}105 (T{sub {1/2}} = 34 s and 27 s) produced an atom-at-a time via the reactions {sup 248}Cm({sup 18}O, 5n) and {sup 249}Bk({sup 18}O, 5n, 4n), respectively. Using HBr and HCl gas as halogenating agents, we were able to produce volatile bromides and chlorides of the above mentioned elements and study their behavior compared to their lighter homologs in Groups 4 or 5 of the periodic table. Element 104 formed more volatile bromides than its homolog Hf. In contrast, element 105 bromides were found to be less volatile than the bromides of the group 5 elements Nb and Ta. Both 104 and Hf chlorides were observed to be more volatile than their respective bromides. 31 refs., 8 figs.

Tuerler, A.; Gregorich, K.E.; Czerwinski, K.R.; Hannink, N.J.; Henderson, R.A.; Hoffman, D.C.; Kacher, C.D.; Kadkhodayan, B.; Kreek, S.A.; Lee, D.M.; Leyba, J.D.; Nurmia, M.J. (Lawrence Berkeley Lab., CA (United States)); Gaeggeler, H.W.; Jost, D.T.; Kovacs, J.; Scherer, U.W.; Vermeulen, D.; Weber, A. (Paul Scherrer Inst. (PSI), Villigen (Switzerland)); Barth, H.; Gober, M.K.; Kratz, J.V. (Philipps-Univ., Marburg

1991-04-01

355

Gas-phase ion-molecule reactions in organophosphorus esters  

PubMed

Self-condensation ion-molecule reactions of trimethyl phosphite, triethyl phosphite, dimethyl phosphonate, trimethyl phosphate and 2, 2-dichlorovinyl dimethyl phosphate (dichlorvos) were investigated by ion trap mass spectrometry and Fourier transform ion cyclotron resonance mass spectrometry. Reaction paths for the main processes observed were elucidated by parent ion selection and for reaction times up to 500 ms. In parallel, high-resolution measurements were performed in order to determine the composition of the principal ions. Among the compounds under examination, trimethyl phosphite and triethyl phosphite mainly give [M + H](+) and [M + (RO)(2)P](+) (R = CH(3), C(2)H(5)) adduct ions, whereas trimethyl phosphate and dimethyl phosphonate display [2M + H](+) ions, as the only abundant products, formed by reaction of [M + H](+) and M. 2,2-Dichlorovinyl dimethyl phosphate mostly shows fragmentation processes. The reaction patterns of the compounds examined were related to their different structural features. Gas-phase basicities of the phosphoryl compounds were also determined or re-examined. Copyright 1999 John Wiley & Sons, Ltd. PMID:10587624

Gal; Herreros; Maria; Operti; Pettigiani; Rabezzana; Vaglio

1999-12-01

356

Isomeric alkyl cation/arene complexes in the gas phase.  

PubMed

The kinetics and the stereochemistry of the protonation-induced unimolecular isomerization of (S)-(+)-1-D(1)-3-(p-tolyl)butane have been investigated in the gas phase in the 100-160 degrees C range. The process leads to the almost exclusive formation of the relevant meta isomer with complete racemization and partial 1,2-H shift in the migrating sec-butyl group. These results, together with the relevant activation parameters, point to the occurrence of low-energy, tightly bound isomeric sec-butyl cation/toluene complexes of defined structure and stability along the isomerization coordinate. The existence and the eta(1)-type structure of these low-energy intermediate species are confirmed by ab initio calculations on closely related systems at the MP2(full)/6-311++G**//HF/6-31+G** level of theory. Their role in the relevant energy surface clearly emerges from the comparison of the present results with those concerning sec-butylation of toluene carried out under comparable experimental conditions. PMID:12740856

Filippi, Antonello; Roselli, Graziella; Renzi, Gabriele; Grandinetti, Felice; Speranza, Maurizio

2003-05-01

357

Gas-phase chemistry of alkylcarbonate anions and radicals  

NASA Astrophysics Data System (ADS)

Alkylcarbonate anions and radicals ROCOO-/ (R = H, CH3, C2H5, i-C3H7, and t-C4H9) are investigated in the gas phase by means of mass spectrometry and ab initio calculations. Structural parameters and energies are obtained at the MP2/6-311++G(3df,3pd)//MP2/6-311++G(d,p) level of theoryE Standard enthalpies of formation for the anions and radicals are determined via atomization energies and isodesmic reactions using the CBS-Q method. Further, alkylcarbonate anions are probed by metastable ion and collisional activation experiments, and the chemistry of the neutral radicals is investigated by charge-reversal and neutralization-reionization mass spectrometry. Although decarboxylation dominates the unimolecular reactivity of the species for both charge states, some other interesting features are observed, particularly for the anions, such as the formation of the CO3- radical anion or the presence of ionic fragments formed via hydrogen atom transfer.

Soldi-Lose, Héloïse; Schröder, Detlef; Schwarz, Helmut

2008-02-01

358

Uptake of gas-phase formaldehyde by aqueous acid surfaces  

SciTech Connect

The uptake of gas-phase formaldehyde, CH{sub 2}O, by aqueous sulfuric and nitric acid droplets has been measured as a function of temperature, acid concentration, and gas-droplet contact time. The results are interpreted in terms of the mass accommodation coefficient for formaldehyde on aqueous surfaces, the Henry`s law constant for formaldehyde in aqueous acid solutions, and the liquid-phase formation kinetics of methylenediol, CH{sub 2}(OH){sub 2}, and protonated formaldehyde, CH{sub 3}O{sup +}. Time-dependent uptake studies under mildly acid solutions where CH{sub 2}(OH){sub 2} and CH{sub 3}O{sup +} formation is slow reveal the existence of a chemisorbed surface complex for CH{sub 2}O at the gas-liquid interface. Uptake studies on nitric acid and mixed sulfuric acid/nitric acid solutions show slightly enhanced uptake relative to sulfuric acid only solutions. This observation has been attributed to variation of formaldehyde solubility (expressed as Setchenow coefficients) and CH{sub 3}O{sup +} equilibrium constant in nitric and sulfuric acid solutions. The implications of these measurements for the aqueous acid chemistry of formaldehyde and its role in atmospheric chemistry are discussed. 46 refs., 7 figs., 2 tabs.

Jayne, J.T.; Worsnop, D.R.; Kolb, C.E. [Aerodyne Research, Inc., Billerica, MA (United States); Swartz, E.; Davidovits, P. [Boston College, Chestnut Hill, MA (United States)

1996-05-09

359

Conformational analysis of octopamine and synephrine in the gas phase.  

PubMed

Four and six conformers of the neurotransmitters octopamine and synephrine, respectively, have been identified in the gas phase using a laser ablation device in combination with a molecular-beam Fourier transform microwave spectrometer operating in the 4-10 GHz frequency range. The identification of all of the conformers was based on a comparison of the experimental rotational and (14)N quadrupole coupling constants with those predicted by ab initio calculations, as well as the relative values of their electric dipole moment components. The conformational preferences have been rationalized in terms of the various intramolecular forces operating in the different conformers of the studied molecules. All observed species are characterized by an intramolecular hydrogen bond of the type O-H···N established in the side chain of the neurotransmitters, which adopts an extended disposition in their most stable forms. For conformers with a folded side chain, an extra N-H···? hydrogen-bond-type interaction is established between the amino group and the ? system of the aromatic ring. PMID:23675821

Cabezas, Carlos; Simão, Alcides; Bermúdez, Celina; Varela, Marcelino; Peña, Isabel; Mata, Santiago; Fausto, Rui; Alonso, José Luis

2013-05-30

360

Liquid chromatographic arsenic speciation with gas-phase chemiluminescence detection.  

PubMed

We present a newly developed gas-phase chemiluminescence (CL) detection method for the separation and quantification of inorganic and organic arsenic species. Arsenite, arsenate, dimethylarsinic acid (DMA), and monomethylarsonic acid (MMA) were separated by anion exchange using carbonate-bicarbonate and NaOH eluents with step-gradient elution. The separated species were passed through a UV photooxidation reactor which decomposed the organic species and converted them to inorganic As(V). Subsequent on-line hydride generation with acid and sodium borohydride produces AsH3 and H2, which are separated from the liquid in a gas-liquid separator. The produced AsH3, driven by H2, reacts with ozone in a small reflective cell located atop a photomultiplier tube, resulting in intense CL. In the present form, the limits of detection (LODs, signal-to-noise = 3), based on peak height, for arsenite, arsenate, MMA, and DMA are 0.4, 0.2, 0.5, and 0.3 microg/L, respectively, for a 100 microL injected sample. This analyzer demonstrates the robustness of the CL detection system for arsenic and provides an affordable alternative to atomic spectrometry for use as a detector after chromatographic speciation. We found no significant practical interferences. PMID:17949013

Idowu, Ademola D; Dasgupta, Purnendu K

2007-10-19

361

Identification of the dimethylamine-trimethylamine complex in the gas phase.  

PubMed

We have identified the dimethylamine-trimethylamine complex (DMA-TMA) at room temperature in the gas phase. The Fourier transform infrared (FTIR) spectrum of DMA-TMA in the NH-stretching fundamental region was obtained by spectral subtraction of spectra of each monomer. Explicitly correlated coupled cluster calculations were used to determine the minimum energy structure and interaction energy of DMA-TMA. Frequencies and intensities of NH-stretching transitions were also calculated at this level of theory with an anharmonic oscillator local mode model. The fundamental NH-stretching intensity in DMA-TMA is calculated to be approximately 700 times larger than that of the DMA monomer. The measured and calculated intensity is used to determine a room temperature equilibrium constant of DMA-TMA of 1.7 × 10(-3) atm(-1) at 298 K. PMID:22583285

Du, Lin; Lane, Joseph R; Kjaergaard, Henrik G

2012-05-14

362

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

2013-04-01

363

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

364

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

SciTech Connect

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

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

2009-03-31

365

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

SciTech Connect

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

Hunter, D.

2009-03-16

366

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

SciTech Connect

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

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

2006-05-15

367

Gas-phase hydrogen\\/deuterium exchange of 5?- and 3?-mononucleotides in a quadrupole ion trap: Exploring the role of conformation and system energy  

Microsoft Academic Search

Gas-phase hydrogen\\/deuterium (H\\/D) exchange reactions for deprotonated 2?-deoxy-5?-monophosphate and 2?-deoxy-3?-monophosphate\\u000a nucleotides with D2O were performed in a quadrupole ion trap mass spectrometer. To augment these experiments, molecular modeling was also conducted\\u000a to identify likely deprotonation sites and potential gas-phase conformations of the anions. A majority of the 5?-monophosphates\\u000a exchanged extensively with several of the compounds completely incorporating deuterium in place

Joseph E. Chipuk; Jennifer S. Brodbelt

2007-01-01

368

Tilt and Rotation Angles of a Transmembrane Model Peptide as Studied by Fluorescence Spectroscopy  

PubMed Central

Abstract In this study the membrane orientation of a tryptophan-flanked model peptide, WALP23, was determined by using peptides that were labeled at different positions along the sequence with the environmentally sensitive fluorescent label BADAN. The fluorescence properties, reflecting the local polarity, were used to determine the tilt and rotation angles of the peptide based on an ideal ?-helix model. For WALP23 inserted in dioleoylphosphatidylcholine (DOPC), an estimated tilt angle of the helix with respect to the bilayer normal of 24° ± 5° was obtained. When the peptides were inserted into bilayers with different acyl chain lengths or containing different concentrations of cholesterol, small changes in tilt angle were observed as response to hydrophobic mismatch, whereas the rotation angle appeared to be independent of lipid composition. In all cases, the tilt angles were significantly larger than those previously determined from 2H NMR experiments, supporting recent suggestions that the relatively long timescale of 2H NMR measurements may result in an underestimation of tilt angles due to partial motional averaging. It is concluded that although the fluorescence technique has a rather low resolution and limited accuracy, it can be used to resolve the discrepancies observed between previous 2H NMR experiments and molecular-dynamics simulations.

Holt, Andrea; Koehorst, Rob B.M.; Rutters-Meijneke, Tania; Gelb, Michael H.; Rijkers, Dirk T.S.; Hemminga, Marcus A.; Killian, J. Antoinette

2009-01-01

369

Entropic control of the relative stability of triple-helical collagen peptide models.  

PubMed

Herein, we show that current methodologies in atomistic simulations can yield reliable standard free energy values in aqueous solution for the transition from the dissociated monomeric form to the triple-helix state of collagen model peptides. The calculations are performed on a prototypical highly stable triple-helical peptide, [(Pro-Hyp-Gly)10]3 (POG10), and on the so-called T3-785 triple-helix mimicking a fragment from the type III human collagen, which is more thermally labile. On the basis of extensive MD simulations in explicit solvent followed by molecular-mechanical and electrostatic Poisson-Boltzmann calculations complemented with an accurate estimation of the nonpolar contributions to solvation, the computed free energy change for the aggregation processes of the POG10 and T3-785 peptides leading to their triple-helices is -6.6 and -6.1 kcal/mol, respectively. For POG10, this value is in agreement with differential scanning calorimetric data. However, it is shown that conformational entropy, which is estimated by means of an expansion of mutual information functions, preferentially destabilizes the triple-helical state of T3-785 by around 4.6 kcal/mol, thus explaining its lower thermal stability. Altogether, our computational results allow us to ascertain, for the first time, the actual thermodynamic forces controlling the absolute and relative stability of collagen model peptides. PMID:18973364

Suárez, Ernesto; Díaz, Natalia; Suárez, Dimas

2008-11-27

370

Algorithmically designed peptides ameliorate behavioral defects in animal model of ADHD by an allosteric mechanism.  

PubMed

This study exemplifies the use of three ADHD-relevant methodological innovations. (1) The use of novel, patented, computational peptide design techniques to generate peptides targeting the extra-cellular and para-transmembrane amino acid loops of the putatively ADHD-involved, D(2) dopamine receptor, D(2)DAR; (2) experimental evidence that these peptides in L-amino acid/ortho ordered or D-amino acid/reverse ordered (retro-inverso), D(2)DAR, hydrophobic eigenmode matched forms, evoked positive allosteric and indirect agonist influences on in vitro stably receptor transfected CHO and LtK cells and on in vivo, brain mediated activity; (3) a representative 15 residue all-D-amino acid, D(2) mode matched peptide, given parenterally, was found to "repair" a key aberrant ADHD behavioral characteristic in a standard animal model of ADHD, the Spontaneously Hypertensive Rat, SHR, relative to its progenitor species control, the Wistar-Kyoto rat, WKY. The representative, retro-inverso peptide, all-D-LLYKNKPRYPKRNRE, reversed SHR's relative deficiency in sensory motor gating (pre-pulse inhibition, PPI) while leaving SHR's nonselective attention (rearings), impulsive behavior (time in center), and activity level (timed total motor behavior) unchanged. Amphetamine also reversed SHRs sensory gating defect, but with significant increases in nonselective attention, impulsivity and hyperactivity. These preliminary results suggest the possibility of a new, "softer" pharmacological approach to ADHD: hydrophobic mode matched peptide allosteric augmentation of the activity of indigenous dopamine with respect to D(2)DAR mediated function, in place of stimulant drug-induced presynaptic dopamine release or impairment of dopamine uptake. PMID:16423408

Kinkead, Becky; Selz, Karen A; Owens, Michael J; Mandell, Arnold J

2006-01-19

371

Topology of the trans-membrane peptide WALP23 in model membranes under negative mismatch conditions.  

PubMed

The organization and orientation of membrane-inserted helices is important for better understanding the mode of action of membrane-active peptides and of protein-membrane interactions. Here we report on the application of ESEEM (electron spin-echo envelope modulation) and DEER (double electron-electron resonance) techniques to probe the orientation and oligomeric state of an ?-helical trans-membrane model peptide, WALP23, under conditions of negative mismatch between the hydrophobic cores of the model membrane and the peptide. Using ESEEM, we measured weak dipolar interactions between spin-labeled WALP23 and (2)H nuclei of either the solvent (D2O) or of lipids specifically deuterated at the choline group. The ESEEM data obtained from the deuterated lipids were fitted using a model that provided the spin label average distance from a layer of (2)H nuclei in the hydrophilic region of the membrane and the density of the (2)H nuclei in the layer. DEER was used to probe oligomerization through the dipolar interaction between two spin-labels on different peptides. We observed that the center of WALP23 does not coincide with the bilayer midplane and its N-terminus is more buried than the C-terminus. In addition, the ESEEM data fitting yielded a (2)H layer density that was much lower than expected. The DEER experiments revealed the presence of oligomers, the presence of which was attributable to the negative mismatch and the electrostatic dipole of the peptide. A discussion of a possible arrangement of the individual helices in the oligomers that is consistent with the ESEEM and DEER data is presented. PMID:23311473

Matalon, Erez; Kaminker, Ilia; Zimmermann, Herbert; Eisenstein, Miriam; Shai, Yechiel; Goldfarb, Daniella

2013-02-14

372

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

NASA Astrophysics Data System (ADS)

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

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

2006-06-01

373

Fragmentation Mechanisms of Oxidized Peptides Elucidated by SID, RRKM Modeling and Molecular Dynamics  

SciTech Connect

The gas phase fragmentation reactions of singly charged angiotensin II (AngII, DRVYIHPF) and the ozonolysis products AngII+O (DRVY*IHPF), AngII+3O (DRVYIH*PF), and AngII+4O (DRVY*IH*PF) were studied using SID FT-ICR mass spectrometry and molecular dynamics. Oxidation of Tyr (AngII+O) leads to an additional low-energy charge-remote selective fragmentation channel resulting in the b4 fragment ion. Modification of His leads to a series of new selective dissociation channels. For AngII+3O and AngII+4O, the formation of [MH+3O]+-45 and [MH+3O]+-71 are driven by charge-remote processes while it is suggested that the b5 and [MH+3O]+-88 fragments are a result of charge-directed reactions. Energy-resolved SID experiments and RRKM modeling were able to provide insight into the energetics of the lowest energy fragmentation channel for each of the parent ions. Destabilization of the ozonolysis products was found to be strictly due to entropic effects. Mechanistic details for each of the new dissociation pathways were determined by relating the SID FT-ICR MS results to parent ion conformations samples using molecular dynamics.

Spraggins, Jeffrey M.; Lloyd, Julie A.; Johnston, Murray V.; Laskin, Julia; Ridge, Douglas P.

2009-09-08

374

Simple off-lattice model to study the folding and aggregation of peptides  

NASA Astrophysics Data System (ADS)

We present a numerical study of a new protein model. This off-lattice model takes into account both the hydrogen bonds and the amino-acid interactions. It reproduces the folding of a small protein (peptide): morphological analysis of the conformations at low temperature shows two well-known substructures ?-helix and ?-sheet depending on the chosen sequence. The folding pathway in the scope of this model is studied through a free-energy analysis. We then study the aggregation of proteins. Proteins in the aggregate are mainly bound via hydrogen bonds. Performing a free-energy analysis we show that the addition of a peptide to such an aggregate is not favourable. We qualitatively reproduce the abnormal aggregation of proteins in prion diseases.

Combe, Nicolas; Frenkel, Daan

375

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

PubMed

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

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

1991-02-15

376

Carbon-deuterium vibrational probes of peptide conformation: Alanine dipeptide and glycine dipeptide  

NASA Astrophysics Data System (ADS)

The utility of ?-carbon deuterium-labeled bonds (C?-D) as infrared reporters of local peptide conformation was investigated for two model dipeptide compounds: C?-D labeled alanine dipeptide (Adp-d1) and C?-D2 labeled glycine dipeptide (Gdp-d2). These model compounds adopt structures that are analogous to the motifs found in larger peptides and proteins. For both Adp-d1 and Gdp-d2, we systematically mapped the entire conformational landscape in the gas phase by optimizing the geometry of the molecule with the values of ? and ?, the two dihedral angles that are typically used to characterize the backbone structure of peptides and proteins, held fixed on a uniform grid with 7.5° spacing. Since the conformations were not generally stationary states in the gas phase, we then calculated anharmonic C?-D and C?-D2 stretch transition frequencies for each structure. For Adp-d1 the C?-D stretch frequency exhibited a maximum variability of 39.4 cm-1 between the six stable structures identified in the gas phase. The C?-D2 frequencies of Gdp-d2 show an even more substantial difference between its three stable conformations: there is a 40.7 cm-1 maximum difference in the symmetric C?-D2 stretch frequencies and an 81.3 cm-1 maximum difference in the asymmetric C?-D2 stretch frequencies. Moreover, the splitting between the symmetric and asymmetric C?-D2 stretch frequencies of Gdp-d2 is remarkably sensitive to its conformation.

Miller, C. S.; Ploetz, E. A.; Cremeens, M. E.; Corcelli, S. A.

2009-03-01

377

A 'universal' B3LYP-based method for gas-phase molecular properties: bond dissociation enthalpy, ionization potential, electron and proton affinity and gas-phase acidity  

NASA Astrophysics Data System (ADS)

The paper describes a density functional theory methodology using the B3LYP functional, with small correction terms introduced for open shell doublet states and closed-shell anions. The procedure is based on a B3LYP/6-31G(d) geometry optimization and frequency determination, followed by (RO)B3LYP/6-311 + G(2d,2p) single point energy calculations. Using a correction term of +8.368 kJ mol-1 for (doublet) radicals and + 4.184 kJ mol-1 for (closed shell) anions, close agreement is obtained with experiment (i.e. within 10 kJ mol-1) for a series of molecular properties. These include bond dissociation enthalpies for X-H, where X = functional groups containing C, N, O, F, S, and X-Y, where X and Y are binary combinations of the same five heavy atoms plus Si and Cl, ionization potentials, electron and proton affinities, and gas-phase acidities. Using locally dense basis sets the approach can be extended to bond dissociation enthalpy calculations of large molecules with only a small increase in error. Using the same approach and popular solvation models allows a good starting point for reaction properties in solution. The approach is termed 'niversal' because by applying these corrections there is no need to change functionals and/or basis sets to obtain accurate results for different molecular properties, unlike some of the work reported previously.

Wright, J. S.; Rowley, C. N.; Chepelev, L. L.

378

Gas-phase interactions of organotin compounds with glycine.  

PubMed

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

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

2013-07-01

379

Infrared spectroscopy of ionized corannulene in the gas phase  

NASA Astrophysics Data System (ADS)

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

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

2011-02-01

380

Infrared spectra of dimethylphenanthrenes in the gas phase.  

PubMed

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

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

2011-07-28

381

Effect of HCl addition on gas-phase and surface reactions during homoepitaxial growth of SiC at low temperatures  

NASA Astrophysics Data System (ADS)

A complex influence of HCl addition on gas-phase and surface reactions during the low-temperature halo-carbon homoepitaxial growth of 4H-SiC was investigated. The addition of HCl was employed to reduce the undesirable effects of homogeneous gas-phase nucleation leading to formation of silicon clusters in the gas phase. It was established that dissociation of silicon clusters by HCl is efficient even at untraditionally low homoepitaxial growth temperature below 1300 °C. The information about the spatial distribution of this dissociation process along the gas flow direction was obtained. It was established that the influence of HCl is more complicated than the simple model suggesting that the enhanced dissociation of silicon clusters in the gas phase leads to an additional supply of silicon species for the epitaxial growth. While the growth rate does significantly increase at least for some HCl flow rates, complex changes in the effective silicon-to-carbon ratio in the growth zone of the reactor indicate that the supply of carbon species may also be enhanced at least at low HCl flow rates. This fact supports the hypothesis that the gas-phase clusters may contain a significant amount of carbon in addition to silicon. Also, the magnitude of the growth rate enhancement was found to be less significant than what was expected from the apparent degree of the cluster dissociation. Evidence of a new mechanism for precursors' depletion are provided. Pronounced changes in the pattern of the polycrystalline deposits at the upstream portion of the hot zone of the reactor were caused by the HCl addition. Premature dissociation of the gas-phase clusters and release of silicon may cause depletion of silicon by vigorous polycrystalline deposition. Depending on the kinetics of the process, the carbon species may also get depleted by the polycrystalline deposition mechanism. This mechanism partially reduces the benefits of the HCl addition unless its influence is minimized.

Melnychuk, G.; Lin, H. D.; Kotamraju, S. P.; Koshka, Y.

2008-09-01

382

Photodissociation of Non-Covalent Peptide-Crown Ether Complexes  

PubMed Central

Highly chromogenic 18-crown-6-dipyrrolylquinoxaline coordinates primary amines of peptides, forming non-covalent complexes that can be transferred to the gas phase by electrospray ionization. The appended chromogenic crown ether facilitates efficient energy transfer to the peptide upon ultraviolet irradiation in the gas phase, resulting in diagnostic peptide fragmentation. Collisional activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) of these non-covalent complexes results only in their disassembly with the charge retained on either the peptide or crown ether, yielding no sequence ions. Upon UV photon absorption the intermolecular energy transfer is facilitated by the fast activation time scale of UVPD (< 10 ns) and by the collectively strong hydrogen bonding between the crown ether and peptide, thus allowing effective transfer of energy to the peptide moiety prior to disruption of the intermolecular hydrogen bonds.

Wilson, Jeffrey J.; Kirkovits, Gregory J.; Sessler, Jonathan L.; Brodbelt, Jennifer S.

2008-01-01

383

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

PubMed Central

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

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

2013-01-01

384

Thermodynamic model of secondary structure for alpha-helical peptides and proteins.  

PubMed

A thermodynamic model describing formation of alpha-helices by peptides and proteins in the absence of specific tertiary interactions has been developed. The model combines free energy terms defining alpha-helix stability in aqueous solution and terms describing immersion of every helix or fragment of coil into a micelle or a nonpolar droplet created by the rest of protein to calculate averaged or lowest energy partitioning of the peptide chain into helical and coil fragments. The alpha-helix energy in water was calculated with parameters derived from peptide substitution and protein engineering data and using estimates of nonpolar contact areas between side chains. The energy of nonspecific hydrophobic interactions was estimated considering each alpha-helix or fragment of coil as freely floating in the spherical micelle or droplet, and using water/cyclohexane (for micelles) or adjustable (for proteins) side-chain transfer energies. The model was verified for 96 and 36 peptides studied by 1H-nmr spectroscopy in aqueous solution and in the presence of micelles, respectively ([set 1] and [set 2]) and for 30 mostly alpha-helical globular proteins ([set 3]). For peptides, the experimental helix locations were identified from the published medium-range nuclear Overhauser effects detected by 1H-nmr spectroscopy. For sets 1, 2, and 3, respectively, 93, 100, and 97% of helices were identified with average errors in calculation of helix boundaries of 1.3, 2.0, and 4.1 residues per helix and an average percentage of correctly calculated helix-coil states of 93, 89, and 81%, respectively. Analysis of adjustable parameters of the model (the entropy and enthalpy of the helix-coil transition, the transfer energy of the helix backbone, and parameters of the bound coil), determined by minimization of the average helix boundary deviation for each set of peptides or proteins, demonstrates that, unlike micelles, the interior of the effective protein droplet has solubility characteristics different from that for cyclohexane, does not bind fragments of coil, and lacks interfacial area. PMID:9235002

Lomize, A L; Mosberg, H I

1997-08-01

385

Surftherm: A program to analyze thermochemical and kinetic data in gas-phase and surface chemical reaction mechanisms.  

National Technical Information Service (NTIS)

This report documents the Surftherm program that analyzes transport coefficient, thermochemical- and kinetic rate information in complex gas-phase and surface chemical reaction mechanisms. The program is designed for use with the Chemkin (gas-phase chemis...

M. E. Coltrin H. K. Moffat

1994-01-01

386

Tentative Method for the Calibration of Nitric Oxide, Nitrogen Dioxide, and Ozone Analyzers by Gas Phase Titration.  

National Technical Information Service (NTIS)

A detailed procedural description of a technique for the dynamic calibration of ambient air monitors for ozone, nitric oxide, and nitrogen dioxide is presented. A gas phase titration technique utilizing the rapid gas phase reaction between nitric oxide an...

K. A. Rehme B. E. Martin J. A. Hodgeson

1974-01-01

387

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

2005-01-01

388

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

Microsoft Academic Search

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

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

2011-01-01

389

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

Microsoft Academic Search

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

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

2011-01-01

390

The photochemical reaction of excited acetophenone and benzaldehyde in the gas phase  

NASA Astrophysics Data System (ADS)

The photochemistry of acetophenone and benzaldehyde with hydrogen donors has been studied in the gas phase. The quenching rate constants of the triplet acetophenone and benzaldehyde can be well correlated with the ionization potentials of hydrogen donors. The results suggested that the charge-transfer interaction plays an important role in the gas-phase reaction as in the case of condensed phase reaction. The slopes of Rehm-Weller plot are more stiff in the gas-phase reaction than condensed phase reaction, which indicates higher degree of charge transfer. Secondary amines were consistently better quencher of carbonyl triplet than tertiary amines, and steric effects are probably to be of importance.

Matsushita, Yoshihisa; Yamaguchi, Yoshitaka; Hikida, Takumi

1996-12-01

391

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.

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

2012-01-01

392

Calcium-containing diatomic dications in the gas phase.  

PubMed

Sputtering (ion surface bombardment) of various calcium-containing powder samples with an energetic (17 keV), high-current (16)O(-) beam has produced the diatomic dications of CaSi(2+), CaP(2+), CaF(2+), CaH(2+), CaCl(2+), CaBr(2+) and CaI(2+). These molecular gas-phase species have been identified in positive ion mass spectra at half-integer m/z values; their ion flight times through a magnetic-sector mass spectrometer were roughly 10(-5) s. Most of them appear to be novel molecular ions; the stability of the latter four (CaH(2+), CaCl(2+), CaBr(2+) and CaI(2+)) had been demonstrated in previous theoretical studies, whereas only CaF(2+) and CaBr(2+) had been observed before. Here we combine the results of our experimental search with a detailed theoretical study of the remaining three systems CaSi(2+), CaP(2+) and CaF(2+). All electronic states correlating with the first dissociation channel are characterized using high level ab initio electronic structure calculations. In their ground states, we find CaSi(2+) to be a long-lived metastable molecule, whereas CaF(2+) and CaP(2+) are thermodynamically stable, with respective equilibrium internuclear distances of 6.253, 4.740, and 5.731 a(0). CaSi(2+) has a well depth of 7116 (0.88) cm(-1) (eV) and a dissociation asymptote 7956 (0.99) cm(-1) (eV) below the ground state minimum. The dissociation energy of CaF(2+) is estimated to be 3404 (0.42) cm(-1) (eV), whereas for CaP(2+) we found 2547 (0.32) cm(-1) (eV), and a barrier height of 8118 (1.01) cm(-1) (eV). Their adiabatic double ionisation energies are 22.87, 16.91, and 17.32 eV, respectively, for the F, Si, and P containing dications. PMID:21603705

Alves, Tiago Vinicius; Hermoso, Willian; Franzreb, Klaus; Ornellas, Fernando R

2011-05-20

393

Gas phase chemistry of bis(pentamethylcyclopentadienyl)samarium  

SciTech Connect

The gas phase chemistry of bis(pentamethylcyclopentadienyl)samarium, (C{sub 5}Me{sub 5}){sub 2}Sm, was studied by Fourier transform ion cyclotron resonance mass spectrometry (FTICR/MS). Positive electron impact (EI) spectra showed the formation of (C{sub 5}Me{sub 5}){sub 2} Sm{sup +}, (C{sub 5}Me{sub 5})Sm{sup +}, and Sm{sup +}. All three ions reacted with (C{sub 5}Me{sub 5}){sub 2}Sm by charge transfer, as verified by double-resonance techniques, and (C{sub 5}Me{sub 5})Sm{sup +} also formed the (C{sub 5}Me{sub 5}){sub 3}Sm{sub 2}{sup +} ion in a condensation reaction with neutral (C{sub 5}Me{sub 5}){sub 2}Sm. The laser desorption/ionization (LDI) spectra showed, in addition to (C{sub 5}Me{sub 5}){sub 2}Sm{sup +}, (C{sub 5}Me{sub 5})Sm{sup +}, and Sm{sup +}, the formation of (C{sub 5}Me{sub 4}H)Sm{sup +} and (C{sub 5}Me{sub 4}CH{sub 2})Sm{sup +}. The latter species most probably involves a tetramethylfulvenide ligand. Access to all of the ionic species cited here could also be obtained by reacting laser-desorbed Sm{sup +} ions with pentamethylcyclopentadiene, C{sub 5}Me{sub 5}H. (C{sub 5}Me{sub 4}CH{sub 2})Sm{sup +}, (C{sub 5}Me{sub 4}H)Sm{sup +}, and (C{sub 5}Me{sub 5})Sm{sup +} were formed as primary products, and the metallocene ion (C{sub 5}Me{sub 5}){sub 2}Sm{sup +} resulted from the rapid addition of C{sub 5}Me{sub 5}H to (C{sub 5}Me{sub 4}CH{sub 2})Sm{sup +}. 34 refs., 4 figs.

Marcalo, J.; Matos, A.P. de [Instituto Technologico e Nuclear, Sacavem (Portugal); Evans, W. [Univ. of California, Irvine, CA (United States)

1996-01-09

394

Gas phase RNA and DNA ions 2. Conformational dependence of the gas-phase H\\/D exchange of nucleotide-5?-monophosphates  

Microsoft Academic Search

The conformational dependence of the gas-phase hydrogen\\/deuterium (H\\/D) exchange of nucleotide-5-monophosphate anions with\\u000a the H\\/D exchange reagent D2S is reported here. The electrospray-generated [M ? H]? anions of adenosine-5?-monophosphate, adenosine-5?-carboxylic acid, ribitol-5-phosphate, and 2-deoxy-ribitol-5-phosphate\\u000a were reacted with D2S in the gas phase. Their reactivity (adenosine-5?-monophosphate exchanged 2 of 5 labile hydrogens, adenosine-5?-carboxylic\\u000a acid exchanged 1 of 4, ribitol-5-phosphate exchanged 2

Michael A. Freitas; Alan G. Marshall

2001-01-01

395

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

NASA Astrophysics Data System (ADS)

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

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

2009-09-01

396

A human cellular model for studying the regulation of glucagon-like peptide-1 secretion.  

PubMed

GLP-1 (glucagon-like peptide-1) is a potent insulin secretagogue released from L cells in the intestine. The regulation of GLP-1 secretion has been described both in vivo and in vitro in several animal species, but data from human cellular models are lacking. For this purpose, factors and cell-signaling pathways regulating GLP-1 secretion were investigated in the NCI-H716 human intestinal cell line. After differentiation, these cells homogeneously produced 16.8 pmol GLP-1/mg protein with a basal release of 4.2% during a 2-h incubation period. Nutrients, such as palmitic acid, oleic acid, and meat hydrolysate, stimulated GLP-1 secretion in a dose-dependent manner, as did the cholinergic agonist carbachol and the neuromediator gastrin-releasing peptide. Along with stimulating GLP-1 release, gastrin-releasing peptide, like ionomycin, increased intracellular calcium levels. Activators of PKA and PKC were able to increase GLP-1 secretion in NCI-H716 cells. However, neither PKA activators nor meat hydrolysate increased proglucagon mRNA levels. These findings indicate that the NCI-H716 cell line constitutes a unique model to study the cellular mechanism of GLP-1 secretion in humans and suggest potential interspecies divergence in the regulation of proglucagon gene expression in enteroendocrine cells. PMID:11564718

Reimer, R A; Darimont, C; Gremlich, S; Nicolas-Métral, V; Rüegg, U T; Macé, K

2001-10-01

397

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

NASA Astrophysics Data System (ADS)

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

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

2011-09-01

398

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.

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

2010-01-01

399

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

EPA Science Inventory

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

400

Ambient temperature gas phase electrochemical nitrogen reduction to ammonia at ruthenium\\/solid polymer electrolyte interface  

Microsoft Academic Search

The direct gas phase electrochemical reduction of nitrogen to ammonia is reported at ruthenium\\/solid polymer electrolyte interface using cells of the general configuration N2, Ru\\/Nafion417\\/Pt, Ar(90%), H2(10%).

Ronald L. Cook; Anthony F. Sammells

1988-01-01

401

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

SciTech Connect

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

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

2000-05-01

402

Ultrafast electronic relaxation of excited state vitamin B 12 in the gas phase  

NASA Astrophysics Data System (ADS)

The time evolution of electronically excited vitamin B 12 (cyanocobalamin) has been observed for the first time in the gas phase. It reveals an ultrafast decay to a state corresponding to metal excitation. This decay is interpreted as resulting from a ring to metal electron transfer. This opens the observation of the excited state of other complex biomimetic systems in the gas phase, the key to the characterisation of their complex evolution through excited electronic states.

Shafizadeh, Niloufar; Poisson, Lionel; Soep, Beno?ˆt

2008-06-01

403

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

Microsoft Academic Search

This paper describes the use of electrospray ionization-Fourier transform ion cyclotron mass spectrometry (ESI-FTICR-MS) to study the relative stabilities of noncovalent complexes of carbonic anhydrase II (CAII, EC 4.2.1.1) and benzenesulfonamide inhibitors in the gas phase. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) was used to determine the energetics of dissociation of these CAII-sulfonamide complexes in the gas phase. When two

Jinming Gao; Jeffrey Carbeck; Q. Paula Lei; Richard D. Smith; George M. Whitesides

1999-01-01

404

The gas-phase reaction of ClONO 2 with hydrogen chloride  

Microsoft Academic Search

The gas-phase reaction of ClONO2 with HCl was investigated using two large-volume environmental chambers with analysis by in situ long pathlength Fourier transform infrared absorption spectroscopy. In these chambers the reaction was observed to proceed, at least in part, by heterogenous routes, and an upper limit to the rate constant for the homogeneous gas-phase reaction of geneous routes, and an

Roger Atkinson; Sara M. Aschmann; Ernesto C. Tuazon; Mark A. Goodman; Arthur M. Winer

1987-01-01