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1

Spectroscopic investigation of H atom transfer in a gas-phase dissociation reaction: McLafferty rearrangement of model gas-phase peptide ions.  

PubMed

Wavelength-selective infrared multiple-photon photodissociation (WS-IRMPD) was used to study isotopically-labeled ions generated by McLafferty rearrangement of nicotinyl-glycine-tert-butyl ester and betaine-glycine-tert-butyl ester. The tert-butyl esters were incubated in a mixture of D(2)O and CH(3)OD to induce solution-phase hydrogen-deuterium exchange and then converted to gas-phase ions using electrospray ionization. McLafferty rearrangement was used to generate the free-acid forms of the respective model peptides through transfer of an H atom and elimination of butene. The specific aim was to use vibrational spectra generated by WS-IRMPD to determine whether the H atom remains at the acid group, or migrates to one or more of the other exchangeable sites. Comparison of the IRMPD results in the region from 1200-1900 cm(-1) to theoretical spectra for different isotopically-labeled isomers clearly shows that the H atom is situated at the C-terminal acid group and migration to amide positions is negligible on the time scale of the experiment. The results of this study suggest that use of the McLafferty rearrangement for peptide esters could be an effective approach for generation of H-atom isotope tracers, in situ, for subsequent investigation of intramolecular proton migration during peptide fragmentation studies. PMID:18500397

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

2008-06-14

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

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

5

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

NASA Astrophysics Data System (ADS)

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

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

2012-02-01

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

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

PubMed

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

McGee, William M; McLuckey, Scott A

2014-01-28

8

Bifurcating fragmentation behavior of gas-phase tryptic peptide dications in collisional activation  

Microsoft Academic Search

Collision-activated dissociation (CAD) of tryptic peptides is a cornerstone of mass spectrometry-based proteomics research.\\u000a Principal component analysis of a database containing 15,000 high-resolution CAD mass spectra of gas-phase tryptic peptide\\u000a dications revealed that they fall into two classes with a good separation between the classes. The main factor determining\\u000a the class identity is the relative abundance of the peptide bond

Mikhail M. Savitski; Maria Fälth; Y. M. Eva Fung; Christopher M. Adams; Roman A. Zubarev

2008-01-01

9

Gas Phase Organophosphate Detection Using Enzymes Encapsulated Within Peptide Nanotubes.  

National Technical Information Service (NTIS)

Previous work to develop biosensors that can be used to detect organophosphorus compounds (OPCs) has successfully demonstrated the potential application of enzymes encapsulated in peptide-nanotubes (PNTs) enhanced with horseradish peroxidase (HRP) to dete...

C. W. Edwards

2014-01-01

10

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

Microsoft Academic Search

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

Roberto Marchese; Rita Grandori; Paolo Carloni; Simone Raugei

2010-01-01

11

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

PubMed

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

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

2014-03-18

12

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

13

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

2013-11-01

14

Gas phase metal cluster model systems for heterogeneous catalysis.  

PubMed

Since the advent of intense cluster sources, physical and chemical properties of isolated metal clusters are an active field of research. In particular, gas phase metal clusters represent ideal model systems to gain molecular level insight into the energetics and kinetics of metal-mediated catalytic reactions. Here we summarize experimental reactivity studies as well as investigations of thermal catalytic reaction cycles on small gas phase metal clusters, mostly in relation to the surprising catalytic activity of nanoscale gold particles. A particular emphasis is put on the importance of conceptual insights gained through the study of gas phase model systems. Based on these concepts future perspectives are formulated in terms of variation and optimization of catalytic materials e.g. by utilization of bimetals and metal oxides. Furthermore, the future potential of bio-inspired catalytic material systems are highlighted and technical developments are discussed. PMID:22669249

Lang, Sandra M; Bernhardt, Thorsten M

2012-07-14

15

Gas-phase ion\\/ion interactions between peptides or proteins and iron ions in a quadrupole ion trap  

Microsoft Academic Search

The gas-phase ion\\/ion reactions of iron ions with oppositely charged peptide and protein ions were studied in a quadrupole ion trap. Both Fe+ and FeCO2? were investigated as possible reactant ions for gas-phase cleavage of peptide and protein ions. Several types of reaction products were observed. Charge exchange lowered the charge states of the proteins. Attachment resulted in a complex

Anne H. Payne; Gary L. Glish

2001-01-01

16

Do amines react with protonated peptides in the gas phase via transacylation reactions to induce peptide bond cleavage?  

PubMed

The proposal that protonated peptides react with NH(3) in the gas phase via transacylation reactions (Tabet et al., Spectros. Int. J. 5: 253 1987) has been investigated by studying the reactions of the fixed charge derivatives [RC(O)NMe(2)CH(2)CO(2)H](+) (R=Me and Ph) with pyridine and triethylamine and the reactions of protonated glycine oligomers and leucine enkenphalin with butylamine. Under the near thermal conditions of the quadrupole ion trap, both the fixed charge derivatives as well as the protonated peptides react with the amines via either proton transfer or proton bound dimer formation. Collision induced dissociation of protonated peptides in the presence of butylamine yields b(n) and y(n) sequence ions as well as [b(n) + BuNH(2)](+) and [y(n) + BuNH(2)](+) ions. MS(3) experiments reveal that a major route to these [b(n) + BuNH(2)](+) and [y(n) + BuNH(2)](+) ions involves ion-molecule reactions between the b(n) and y(n) sequence ions and butylamine. MS(4) experiments, carried out to determine the nature of the [b(n) + BuNH(2)](+) ions, reveal that they correspond to a mixture of hydrogen bonded (i.e. proton bound dimer) and covalent amide bond structures. PMID:10962495

O'Hair, R A; Androutsopoulos, N K; Reid, G E

2000-01-01

17

Ultraviolet action spectroscopy of iodine labeled peptides and proteins in the gas phase.  

PubMed

Structural investigations of large biomolecules in the gas phase are challenging. Herein, it is reported that action spectroscopy taking advantage of facile carbon-iodine bond dissociation can be used to examine the structures of large molecules, including whole proteins. Iodotyrosine serves as the active chromophore, which yields distinctive spectra depending on the solvation of the side chain by the remainder of the molecule. Isolation of the chromophore yields a double featured peak at ~290 nm, which becomes a single peak with increasing solvation. Deprotonation of the side chain also leads to reduced apparent intensity and broadening of the action spectrum. The method can be successfully applied to both negatively and positively charged ions in various charge states, although electron detachment becomes a competitive channel for multiply charged anions. In all other cases, loss of iodine is by far the dominant channel which leads to high sensitivity and simple data analysis. The action spectra for iodotyrosine, the iodinated peptides KGYDAKA, DAYLDAG, and the small protein ubiquitin are reported in various charge states. PMID:22906129

Kirk, Benjamin B; Trevitt, Adam J; Blanksby, Stephen J; Tao, Yuanqi; Moore, Benjamin N; Julian, Ryan R

2013-02-14

18

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

PubMed Central

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

Prentice, Boone M.

2013-01-01

19

Gas-phase intramolecular phosphate shift in phosphotyrosine-containing peptide monoanions.  

PubMed

Phosphotyrosine-containing peptide monoanions [M-H](-) exhibit extensive neutral loss of phosphoric acid (98 Da) upon quadrupole time-of-flight and ion-trap collision-induced dissociation (CID). In contrast, a neutral loss of metaphosphoric acid HPO(3) (80 Da) is negligible from the deprotonated phosphotyrosine peptides. The efficient H(3)PO(4) release is unexpected, given the structure of phosphotyrosine. Our study reveals that the abundant [M-H-98](-) product ions of pTyr-peptides are not a result of consecutive losses of HPO(3) and H(2)O but, rather, are induced by an intramolecular interaction of the phosphotyrosine phosphate with deprotonated peptide functions such as hydroxyl, carboxyl, and to a small extent, amide. As a result, an internal phosphotyrosine phosphate shift occurs, and the obtained phosphorylated functionalities undergo elimination of H(3)PO(4) to give rise to the [M-H-98](-) fragments. The mechanism proposed for the phosphoric acid neutral loss is based on extensive CID studies of Ala-substituted model phosphorylated peptides and oxygen-18 labeling. The proposed mechanistic pathway explains the fact that the pTyr phosphate transfer and the subsequent H(3)PO(4) neutral loss are not observed for multiply charged anions of pTyr-peptides. Monoanions of pSer-containing peptides undergo the intramolecular phosphate shift as well, although its efficiency is much lower compared to the aromatic phosphorylation sites. These observations facilitate correct identification of pSer-, pThr-, and pTyr-peptides in CID studies. This work demonstrates that the established phosphate-specific neutral loss fragmentation rules of protonated pTyr-peptides cannot be applied to the CID spectra of their [M-H](-) ions. PMID:19402683

Edelson-Averbukh, Marina; Shevchenko, Andrej; Pipkorn, Rüdiger; Lehmann, Wolf D

2009-06-01

20

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

NASA Astrophysics Data System (ADS)

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

Mentinova, Marija; McLuckey, Scott A.

2011-05-01

21

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

SciTech Connect

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

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

2008-03-12

22

Methods for Simulating Gas Phase SO2 Oxidation in Atmospheric Models.  

National Technical Information Service (NTIS)

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

J. F. Meagher K. J. Olszyna

1985-01-01

23

Isospin lattice gas model and liquid-gas phase transition in asymmetric nuclear matter  

Microsoft Academic Search

Liquid-gas phase transition in asymmetric nuclear matter is investigated with an isospin lattice gas model. Nuclear matter is considered as a lattice with each lattice site either empty or occupied by a proton or a neutron, with a nearest-neighbor interaction between the nucleons. The Bragg-Williams mean field approximation is employed to evaluate the thermodynamic potential. Our model exhibits liquid-gas phase

S. Ray; J. Shamanna; T. T. S. Kuo

1997-01-01

24

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

25

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

26

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

29

Optimizing a Photochemical Air Quality Model Gas-Phase Chemistry Solver for Parallel Processing.  

National Technical Information Service (NTIS)

In a testbed model based on EPA's Regional Oxidant Model, the Quasi-steady State Approximation (QSSA) gas-phase chemistry solver dominates the computation, which is typical of Eulerian grid cell air quality models. We report results from optimizing the te...

W. Cheung J. O. Young E. W. Davis

1997-01-01

30

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

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

31

probing the gas-phase folding kinetics of peptide ions by IR activated DR-ECD  

Microsoft Academic Search

The effect of infrared (IR) irradiation on the electron capture dissociation (ECD) fragmentation pattern of peptide ions was\\u000a investigated. IR heating increases the internal energy of the precursor ion, which often amplifies secondary fragmentation,\\u000a 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\\u000a due to

Cheng Lin; Jason J. Cournoyer; Peter B. O'Connora

2008-01-01

32

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

PubMed Central

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

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

2010-01-01

33

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

34

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

35

METHODS FOR SIMULATING GAS PHASE SO2 OXIDATION IN ATMOSPHERIC MODELS  

EPA Science Inventory

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

36

Modeling the gas-phase thermochemistry of organosulfur compounds.  

PubMed

Key to understanding the involvement of organosulfur compounds in a variety of radical chemistries, such as atmospheric chemistry, polymerization, pyrolysis, and so forth, is knowledge of their thermochemical properties. For organosulfur compounds and radicals, thermochemical data are, however, much less well documented than for hydrocarbons. The traditional recourse to the Benson group additivity method offers no solace since only a very limited number of group additivity values (GAVs) is available. In this work, CBS-QB3 calculations augmented with 1D hindered rotor corrections for 122 organosulfur compounds and 45 organosulfur radicals were used to derive 93 Benson group additivity values, 18 ring-strain corrections, 2 non-nearest-neighbor interactions, and 3 resonance corrections for standard enthalpies of formation, standard molar entropies, and heat capacities for organosulfur compounds and organosulfur radicals. The reported GAVs are consistent with previously reported GAVs for hydrocarbons and hydrocarbon radicals and include 77 contributions, among which 26 radical contributions, which, to the best of our knowledge, have not been reported before. The GAVs allow one to estimate the standard enthalpies of formation at 298?K, the standard entropies at 298?K, and standard heat capacities in the temperature range 300-1500?K for a large set of organosulfur compounds, that is, thiols, thioketons, polysulfides, alkylsulfides, thials, dithioates, and cyclic sulfur compounds. For a validation set of 26 organosulfur compounds, the mean absolute deviation between experimental and group additively modeled enthalpies of formation amounts to 1.9? kJ? mol(-1). For an additional set of 14 organosulfur compounds, it was shown that the mean absolute deviations between calculated and group additively modeled standard entropies and heat capacities are restricted to 4 and 2?J ?mol(-1) ?K(-1), respectively. As an alternative to Benson GAVs, 26 new hydrogen-bond increments are reported, which can also be useful for the prediction of radical thermochemistry. PMID:21608056

Vandeputte, Aäron G; Sabbe, Maarten K; Reyniers, Marie-Françoise; Marin, Guy B

2011-06-27

37

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

38

Gas-phase deprotonation of the peptide backbone for tripeptides and their methyl esters with hydrogen and methyl side chains.  

PubMed

The gas-phase acidities (GAs) of six tripeptides (GlyGlyGly, GlyAlaGly, AlaGlyAla, AlaAlaAla, AibAibAib, and SarSarSar) and their methyl esters were obtained by proton transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and G3(MP2) molecular orbital theory calculations. All six peptides have GAs in the range 321.0-323.7 kcal/mol. Their deprotonation to produce [M - H](-) occurs at the C-terminal carboxylic acid group. The tripeptides are about 10 kcal/mol more acidic than the amino acids glycine (Gly) and alanine (Ala). This is consistent with the extensive hydrogen bonding that was found in the tripeptide structures. For the methyl esters, deprotonation occurs at the peptide backbone. G3(MP2) calculations show that the most energetically favored site of deprotonation is an amide nitrogen, with the central amide being generally preferred. Nitrogen deprotonation requires 10-20 kcal/mol less energy than deprotonation at a methylene carbon. Only three of the methyl esters (GlyGlyGly-OMe, GlyAlaGly-OMe, and AlaAlaAla-OMe) deprotonate experimentally by electrospray ionization. Experimental GAs for these esters are in the range of 336.7-338.1 kcal/mol, in excellent agreement with the calculated G3(MP2) values. Experimental GAs could not be obtained for the other three methyl esters (AlaGlyAla-OMe, AibAibAib-OMe, and SarSarSar-OMe) because they did not produce sufficient deprotonated molecular ions. Trisarcosine methyl ester, SarSarSar-OMe, cannot be deprotonated at a central amide nitrogen because methyl groups are present at these sites; consequently, it has a high G3(MP2) GA value (less acidic) of 350.6 kcal/mol for deprotonation at the N-terminal nitrogen. For AlaGlyAla-OMe and AibAibAib-OMe, calculations of van der Waals and solvent accessible surfaces reveal that methyl groups are blocking the amide nitrogen sites. Therefore, conformational and steric hindrance effects are limiting the ability of these peptide methyl esters to deprotonate in the mass spectrometer. PMID:23194315

Bokatzian-Johnson, Samantha S; Stover, Michele L; Dixon, David A; Cassady, Carolyn J

2012-12-27

39

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

PubMed

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

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

2014-04-01

40

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

41

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

PubMed

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

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

2012-03-15

42

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

43

Gas-phase reactivity of peptide thiyl (RS•), perthiyl (RSS•), and sulfinyl (RSO•) radical ions formed from atmospheric pressure ion/radical reactions.  

PubMed

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. PMID:23354473

Tan, Lei; Xia, Yu

2013-04-01

44

Adaptive aggregation of peptide model systems.  

PubMed

Jet-cooled infrared spectra of acetylated glycine, alanine, and dialanine esters and their dimers are reported in the amide A and amide I-III regions. They serve as particularly simple peptide aggregation models and are found to prefer a single backbone conformation in the dimer that is different from the most stable monomer backbone conformation. In the case of alanine, evidence for topology-changing chirality discrimination upon dimer formation is found. The jet spectroscopic results are compared to gas phase spectra and quantum chemical calculations. They provide reliable benchmarks for the evaluation of the latter in the field of peptide interactions. PMID:23480425

Lee, Juhyon J; Albrecht, Merwe; Rice, Corey A; Suhm, Martin A; Stamm, Anke; Zimmer, Manuel; Gerhards, Markus

2013-08-15

45

Predicting dermal absorption of gas-phase chemicals: transient model development, evaluation, and application.  

PubMed

A transient model is developed to predict dermal absorption of gas-phase chemicals via direct air-to-skin-to-blood transport under non-steady-state conditions. It differs from published models in that it considers convective mass-transfer resistance in the boundary layer of air adjacent to the skin. Results calculated with this transient model are in good agreement with the limited experimental results that are available for comparison. The sensitivity of the modeled estimates to key parameters is examined. The model is then used to estimate air-to-skin-to-blood absorption of six phthalate esters for scenarios in which (A) a previously unexposed occupant encounters gas-phase phthalates in three different environments over a single 24-h period; (B) the same as 'A', but the pattern is repeated for seven consecutive days. In the 24-h scenario, the transient model predicts more phthalate absorbed into skin and less absorbed into blood than would a steady-state model. In the 7-day scenario, results calculated by the transient and steady-state models converge over a time period that varies between 3 and 4 days for all but the largest phthalate (DEHP). Dermal intake is comparable to or larger than inhalation intake for DEP, DiBP, DnBP, and BBzP in Scenario 'A' and for all six phthalates in Scenario 'B'. PMID:24245588

Gong, M; Zhang, Y; Weschler, C J

2014-06-01

46

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

2011-08-18

47

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

48

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

Microsoft Academic Search

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

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

1993-01-01

49

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

SciTech Connect

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

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

1993-02-01

50

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

PubMed Central

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

Lammich, L.; Petersen, M. Axman; Nielsen, M. Br?ndsted; Andersen, L. H.

2007-01-01

51

High-field fourier transform ion cyclotron resonance mass spectrometry for simultaneous trapping and gas-phase hydrogen\\/deuterium exchange of peptide ions  

Microsoft Academic Search

Gas-phase hydrogen\\/deuterium exchange of D2O with [M+H]+ ions of angiotensin II, angiotensin I, [Sar1]-angiotensin II, bradykinin, des-Arg1-bradykinin, des-Arg9-bradykinin, luteinizing hormone releasing hormone (LH-RH), and substance P has been examined by Fourier transform ion cyclotron\\u000a resonance mass spectrometry at 9.4 tesla. Because the FTICR dynamic range increases quadratically with magnetic field, parent\\u000a ions from a mixture of several peptides may be

Michael A. Freitas; Christopher L. Hendrickson; Mark R. Emmett; Alan G. Marshall

1998-01-01

52

Peptide bond formation in gas-phase ion/molecule reactions of amino acids: a novel proposal for the synthesis of prebiotic oligopeptides.  

PubMed

There is a general fascination with regard to the origin of life on Earth. There is an intriguing possibility that prebiotic precursors of life occurred in the interstellar space and were then transported to the early Earth by comets, asteroids and meteorites. It is probable that some part of the prebiotic molecules may have been generated by gas-phase ion/molecule reactions. Here we show experimentally that gaseous ion/molecule reactions of the amino acids, Glu and Met, may promote the synthesis of protonated dipeptides such as (Glu-Glu)H(+) and (Glu-Met)H(+) and their chemical growth to larger protonated peptides. PMID:10637418

Wincel, H; Fokkens, R H; Nibbering, N M

2000-01-01

53

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

SciTech Connect

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

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

2008-04-15

54

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

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

55

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

NASA Astrophysics Data System (ADS)

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

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

2010-08-01

56

Modeling molecular weight development of gas-phase {alpha}-olefin copolymerization  

SciTech Connect

A comprehensive kinetic model developed for molecular weight calculations of ethylene and {alpha}-olefin copolymerizations in the context of a terminal model accounts for multiple-type active centers of the catalyst, detailed elementary chemical reactions, and catalyst composition. The moments of copolymer chain distributions are defined considering molecular weights of comonomer units so that copolymer molecular weight averages can be directly calculated for those moments. A double Z-transformation is introduced for the derivation of differential equations of the moments. Model simulations are carried out based on ethylene and 1-butene copolymerizations in a gas-phase fluidized-bed reactor. Polydispersity of accumulated copolymer depends on catalyst composition and kinetic characteristics of the catalyst. For a catalyst with specified kinetic characteristics, the polydispersity depends on the mole fraction of each type of active center. For a catalyst with two types of active centers; the maximum polydispersity of copolymer occurs at 50 wt.% of the total copolymer if polydispersities of the copolymers generated at each active site are the same. Polydispersity of accumulated copolymer is sensitive to propagation reactions and chain transfer to hydrogen reactions. Differences in chain transfer to cocatalyst and monomers and in spontaneous deactivation rates for different types of active centers may play minor roles in controlling molecular weight development in the presence of hydrogen. This model can be used for catalyst composition design, simulation of commercial olefin copolymerization processes, and kinetic parameter estimation.

Xie, T.; McAuley, K.B.; Hsu, J.C.C.; Bacon, D.W. [Queen`s Univ., Kingston, Ontario (Canada). Dept. of Chemical Engineering] [Queen`s Univ., Kingston, Ontario (Canada). Dept. of Chemical Engineering

1995-05-01

57

Experimental and modeling study of the selective homogeneous gas phase oxidation of methane to methanol  

SciTech Connect

The partial oxidation of CH{sub 4} to CH{sub 3}OH with air has been. investigated experimentally and theoretically. Experimentally, the homogeneous gas phase reaction was studied at pressures in the range 40 {times} 10{sup 5}--60 {times} 10{sup 5} Pa, temperatures in the range 723--823 K, and O{sub 2} concentrations in the range 2.6--4.4% relative to CH{sub 4}. CH{sub 3}OH selectivities between 35 and 55% were obtained at low conversions, 1.2--2.6%. A kinetic model, based on 61 elementary reactions, was able to reproduce experimental observations, indicating that only moderate selectivities to CH{sub 3}OH (50--65%) are obtainable at low CH{sub 4} conversion (<4%). The model is used to investigate an extended span of temperatures, pressures, and O{sub 2} concentrations in search of favorable conditions for CH{sub 3}OH formation. The model predicts CH{sub 3}OH formation to be favored by high pressure, moderate temperature 673--723 K, and low O{sub 2} concentrations 2--4%. The predicted effects are discussed and illustrated in a mechanistic perspective.

Loedeng, R.; Lindvaag, O.A. [Norwegian Inst. of Technology, Trondheim (Norway). Foundation for Scientific and Industrial Research; Soeraker, P. [Statoil, Trondheim (Norway); Roterud, P.T. [Statoil Bamble, Stathelle (Norway); Onsager, O.T. [Univ. of Trondheim (Norway). Dept. of Industrial Chemistry

1995-04-01

58

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

59

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

NASA Astrophysics Data System (ADS)

We present results of kinetic Monte Carlo simulations of a modified Ziff-Gulari-Barshad model for the reaction CO+O ? CO2 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. EPLEEE81539-375510.1103/PhysRevE.85.031143 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 CO2 production disappears. When the impurities are allowed to desorb, there are regions where the CO2 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.

Buendía, G. M.; Rikvold, P. A.

2013-07-01

60

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

2013-07-01

61

Negatively-charged helices in the gas phase.  

PubMed

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

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

2014-07-15

62

A hybrid formalism of aerosol gas phase interaction for 3-D global models  

NASA Astrophysics Data System (ADS)

Aerosol chemical composition is a relevant factor to the global climate system with respect to both atmospheric chemistry and the aerosol direct and indirect effects. Aerosol chemical composition determines the capacity of aerosol particles to act as cloud condensation nuclei both explicitly via particle size and implicitly via the aerosol hygroscopic property. Due to the primary role of clouds in the climate system and the sensitivity of cloud formation and radiative properties to the cloud droplet number it is necessary to determine with accuracy the chemical composition of the aerosol. Dissolution, although a formally fairly well known process, may be subject to numerically prohibitive properties that result from the chemical interaction of the species engaged. So-far approaches to model the dissolution of inorganics into the aerosol liquid phase in the framework of a 3-D global model were based on an equilibrium, transient or hybrid equilibrium-transient approach. All of these methods present the disadvantage of a priori assumptions with respect to the mechanism and/or are numerically not manageable in the context of a global climate system model. In this paper a new hybrid formalism to aerosol gas phase interaction is presented within the framework of the H2SO4/HNO3/HCl/NH3 system and a modal approach of aerosol size discretisation. The formalism is distinct from prior hybrid approaches in as much as no a priori assumption on the nature of the regime a particular aerosol mode is in is made. Whether a particular mode is set to be in the equilibrium or the transitory regime is continuously determined during each time increment against relevant criteria considering the estimated equilibration time interval and the interdependence of the aerosol modes relative to the partitioning of the dissolving species. Doing this the aerosol composition range of numerical stiffness due to species interaction during transient dissolution is effectively eluded, and the numerical expense of dissolution in the transient regime is reduced through the minimisation of the number of modes in this regime and a larger time step. Containment of the numerical expense of the modes in the equilibrium regime is ensured through the usage of either an analytical equilibrium solver that requires iteration among the equilibrium modes, or a simple numerical solver based on a differential approach that requires iteration among the chemical species. Both equilibrium solvers require iteration over the water content and the activity coefficients. Decision for using either one or the other solver is made upon the consideration of the actual equilibrating mechanism, either chemical interaction or gas phase partial pressure variation, respectively. The formalism should thus ally appropriate process simplification resulting in reasonable computation time to a high degree of real process conformity as it is ensured by a transitory representation of dissolution. The resulting effectiveness and limits of the formalism are illustrated with numerical examples.

Benduhn, F.

2009-04-01

63

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...

64

Vacuum Gas Carburizing with Acetylene - Gas Phase Modeling of a Bench Scale Reactor  

Microsoft Academic Search

Vacuum gas carburizing is an important industrial process used for hardening the steel parts. The addition of carbon to the steel parts is accomplished by the pyrolysis of gaseous hydrocarbons. The gas phase composition is very important in vacuum gas carburizing to control the process. Pyrolysis of gaseous hydrocarbons is a complex process because of large number of reactions which

R. U. Khan; M. Saleem; A. Shafeeq

65

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

66

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

67

Experimental and modeling study of the selective homogeneous gas phase oxidation of methane to methanol  

Microsoft Academic Search

The partial oxidation of CHâ to CHâOH with air has been. investigated experimentally and theoretically. Experimentally, the homogeneous gas phase reaction was studied at pressures in the range 40 à 10⁵--60 à 10⁵ Pa, temperatures in the range 723--823 K, and Oâ concentrations in the range 2.6--4.4% relative to CHâ. CHâOH selectivities between 35 and 55% were obtained at low

R. Loedeng; Odd A. Lindvaag; P. Soeraker; Per T. Roterud; Olav T. Onsager

1995-01-01

68

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

Microsoft Academic Search

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

Robert W. Barber; David R. Emerson

2006-01-01

69

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

PubMed

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

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

2012-01-01

70

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

PubMed Central

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

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

2012-01-01

71

MODELING AEROSOL FORMATION FROM ALPHA-PINENE + NOX IN THE PRESENCE OF NATURAL SUNLIGHT USING GAS PHASE KINETICS AND GAS-PARTICLE PARTITIONING THEORY. (R826771)  

EPA Science Inventory

A kinetic mechanism was used to link and model the gas-phase reactions and aerosol accumulation resulting from -pinene reactions in the presence of sunlight, ozone (O3), and oxides of nitrogen (NO ...

72

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

SciTech Connect

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

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

1993-09-01

73

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

SciTech Connect

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

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

1993-02-01

74

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

75

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

NASA Astrophysics Data System (ADS)

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

Zhang, Guang-Hua; Jiang, Wei-Zhou

2013-03-01

76

Reactive plume model: Effect of stack exit conditions on gas phase precursors and sulfate formation  

NASA Astrophysics Data System (ADS)

A simple form of a carbon-bond smog mechanism has been introduced into a complete set of plume conservation equations. The conservation expressions for mass, momentum, energy and component species have been solved numerically for typical source and neutral or adiabatic ambient conditions to simulate the homogeneous gas phase chemistry for approximately two hours of travel time downwind from the stack exit. The influence of stack exit conditions including the ratios of momentum-to-buoyancy length lm/ lb, source-to-ambient velocity R and mixing-to-reaction time ? are demonstrated. It was found that homogeneous processes in the plume near-field do not significantly contribute to the overall conversion of SO 2 to SO 2-4. In the far-field maximum sulfate formation rates of 2.3% h -1 were predicted for clear summer noon hours, consistent with plume measurements. Variation of stack exit conditions were found to have little effect on the maximum SO 2 conversion rate or the peak OH radical concentration where local HC/NO x ratios between 16 and 22 were predicted. Parameter changes resulting in greater ambient entrainment rates, however, were found to shift the development of the radical pool closer to the source and to significantly increase the total molar flux of plume sulfate.

Forney, L. J.; Droescher, F. M.

77

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

NASA Astrophysics Data System (ADS)

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

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

78

Reaction dynamics on barrierless reaction surfaces - A model for isoergic gas-phase proton-transfer reactions  

NASA Astrophysics Data System (ADS)

The kinetics of some gas-phase alcohol/alkoxide proton-transfer reactions is slower than predicted by simple Rice-Ramsberger-Kassel-Marcus (RRKM) rate theory modeling on the near-barrierless reaction surfaces. Reaction dynamics can be investigated in isolation from nonequilibrium and/or thermodynamic considerations through the study of a generic isoergic ion-molecule system X(-) + X - H. Monte Carlo quasi-classical trajectory simulations on barrierless reaction surfaces show that the slow experimental kinetics is consistent with both locking of the external rotations of the reactants and passage over the (orbital angular momentum) centrifugal barrier being the rate-determining steps in bimolecular association, rather than only the latter process.

Lim, Kieran F.; Brauman, John I.

1991-06-01

79

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

SciTech Connect

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

Tsimpanogiannis, Ioannis N.; Yortsos, Yanis C.

2001-08-15

80

Gas phase kinetics during normal combustion  

NASA Technical Reports Server (NTRS)

The role of gas phase kinetics during combustion was explored in the steady state modeling efforts and in the analysis of ignition phenomena. In both cases it was shown that the combustion characteristics of some high energy ingredients and propellants are strongly affected, if not dictated, by the gas phase reactions which take place.

Price, C. F.; Boggs, T. L.; Eisel, J. L.; Atwood, A. I.; Zurn, D. E.

1980-01-01

81

A model coupling the liquid and gas phases for a totally wetting evaporative meniscus  

NASA Astrophysics Data System (ADS)

An hydrodynamic model has been developed to get a complete description of an evaporative meniscus in complete wetting configuration. The coupling between the liquid and gas is explicitly taken into account. Scaling laws are derived for the different domains of the meniscus and validated by numerical simulations. Results are compared with previous models of the literature that use the electrostatic analogy proposed by Deegan and co-authors to describe the evaporative flux. We show that the different approaches differ for the description of the tip of the meniscus in the domain corresponding to the decrease of the evaporative flux but lead to the same scaling for the apparent macroscopic contact angle.

Doumenc, F.; Guerrier, B.

2011-08-01

82

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

Microsoft Academic Search

As a result of new aerosol compositional information, the authors have implemented an exploratory model for predicting aerosol yields from the reaction of α-pinene with ozone in the atmosphere. This new approach has the ability to embrace a range of different atmospheric chemical conditions, which bring about biogenic aerosol formation. A kinetic mechanism was used to describe the gas-phase reactions

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

1999-01-01

83

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

PubMed

We study by kinetic Monte Carlo simulations the catalytic oxidation of carbon monoxide on a surface in the presence of contaminants in the gas phase. The process is simulated by a Ziff-Gulari-Barshad (ZGB) model that has been modified to include the effect of the contaminants and to eliminate an unphysical oxygen poisoned phase at very low CO partial pressures. The impurities can adsorb and desorb on the surface but otherwise remain inert. We find that if the impurities cannot desorb, no matter how small their proportion in the gas mixture, the reactive window and discontinuous transition to a CO poisoned phase at high CO pressures that characterize the original ZGB model disappear. The coverages become continuous, and once the surface has reached a steady state there is no production of CO(2). This is quite different from the behavior of systems in which the surface presents a fixed percentage of impurities. When the contaminants are allowed to desorb, the reactive phase appears again for CO pressures below a value that depends on the proportion of contaminants in the gas and on their desorption rate. PMID:22587074

Buendía, G M; Rikvold, P A

2012-03-01

84

Peptide models for membrane channels.  

PubMed Central

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

Marsh, D

1996-01-01

85

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

86

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

PubMed

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

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

2012-02-16

87

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

88

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

Microsoft Academic Search

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

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

2006-01-01

89

AEROSOL FORMATION FROM THE REACTION OF ? ?-PINENE AND OZONE USING A GAS PHASE KINETICS-PARTICLE PARTITIONING MODEL  

Microsoft Academic Search

A kinetic mechanism was used to describe the gas-phase reactions of ?-pinene with ozone. This reaction scheme produces low vapor pressure reaction products that distribute between gas and particle phases. Partitioning was treated as an equilibrium between the rate of particle uptake and rate of particle loss of semivolatile terpene reaction products. Given estimated liquid vapor pressures and activation energies

R. M. Kamens; M. Jaoui; S. Lee; C. J. Chien

90

A unified model for simulating liquid and gas phase, intermolecular energy transfer: N2 + C6F6 collisions.  

PubMed

Molecular dynamics simulations were used to study relaxation of a vibrationally excited C6F6* molecule in a N2 bath. Ab initio calculations were performed to develop N2-N2 and N2-C6F6 intermolecular potentials for the simulations. Energy transfer from "hot" C6F6 is studied versus the bath density (pressure) and number of bath molecules. For the large bath limit, there is no heating of the bath. As C6F6* is relaxed, the average energy of C6F6* is determined versus time, i.e., ?E(t)?, and for each bath density ?E(t)? is energy dependent and cannot be fit by a single exponential. In the long-time limit C6F6 is fully equilibrated with the bath. For a large bath and low pressures, the simulations are in the fixed temperature, independent collision regime and the simulation results may be compared with gas phase experiments of collisional energy transfer. The derivative d[?E(t)?]/dt divided by the collision frequency ? of the N2 bath gives the average energy transferred from C6F6* per collision ??Ec?, which is in excellent agreement with experiment. For the ?100-300 ps simulations reported here, energy transfer from C6F6* is to N2 rotation and translation in accord with the equipartition model, with no energy transfer to N2 vibration. The energy transfer dynamics from C6F6* is not statistically sensitive to fine details of the N2-C6F6 intermolecular potential. Tests, with simulation ensembles of different sizes, show that a relatively modest ensemble of only 24 trajectories gives statistically meaningful results. PMID:24852526

Paul, Amit K; Kohale, Swapnil C; Pratihar, Subha; Sun, Rui; North, Simon W; Hase, William L

2014-05-21

91

A unified model for simulating liquid and gas phase, intermolecular energy transfer: N2 + C6F6 collisions  

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations were used to study relaxation of a vibrationally excited C6F6* molecule in a N2 bath. Ab initio calculations were performed to develop N2-N2 and N2-C6F6 intermolecular potentials for the simulations. Energy transfer from "hot" C6F6 is studied versus the bath density (pressure) and number of bath molecules. For the large bath limit, there is no heating of the bath. As C6F6* is relaxed, the average energy of C6F6* is determined versus time, i.e., ?E(t)?, and for each bath density ?E(t)? is energy dependent and cannot be fit by a single exponential. In the long-time limit C6F6 is fully equilibrated with the bath. For a large bath and low pressures, the simulations are in the fixed temperature, independent collision regime and the simulation results may be compared with gas phase experiments of collisional energy transfer. The derivative d[?E(t)?]/dt divided by the collision frequency ? of the N2 bath gives the average energy transferred from C6F6* per collision ??Ec?, which is in excellent agreement with experiment. For the ˜100-300 ps simulations reported here, energy transfer from C6F6* is to N2 rotation and translation in accord with the equipartition model, with no energy transfer to N2 vibration. The energy transfer dynamics from C6F6* is not statistically sensitive to fine details of the N2-C6F6 intermolecular potential. Tests, with simulation ensembles of different sizes, show that a relatively modest ensemble of only 24 trajectories gives statistically meaningful results.

Paul, Amit K.; Kohale, Swapnil C.; Pratihar, Subha; Sun, Rui; North, Simon W.; Hase, William L.

2014-05-01

92

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

NASA Astrophysics Data System (ADS)

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

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

2012-01-01

93

Gas-phase separations of protease digests  

Microsoft Academic Search

A mixture of peptides from a complete tryptic digest of ubiquitin has been analyzed by ion mobility\\/time-of-flight mass spectrometry\\u000a techniques. All components of the mixture were electrosprayed and ions were separated in the gas phase based on differences\\u000a in their mobilities through helium before being dispersed into a time-of-flight mass spectrometer for mass-to-charge analysis.\\u000a The data show that ions separate

Stephen J. Valentine; Anne E. Counterman; Cherokee S. Hoaglund; James P. Reilly; David E. Clemmer

1998-01-01

94

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

95

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification  

PubMed Central

Motivation: Tandem mass spectrometry (MS/MS) is an indispensable technology for identification of proteins from complex mixtures. Proteins are digested to peptides that are then identified by their fragmentation patterns in the mass spectrometer. Thus, at its core, MS/MS protein identification relies on the relative predictability of peptide fragmentation. Unfortunately, peptide fragmentation is complex and not fully understood, and what is understood is not always exploited by peptide identification algorithms. Results: We use a hybrid dynamic Bayesian network (DBN)/support vector machine (SVM) approach to address these two problems. We train a set of DBNs on high-confidence peptide-spectrum matches. These DBNs, known collectively as Riptide, comprise a probabilistic model of peptide fragmentation chemistry. Examination of the distributions learned by Riptide allows identification of new trends, such as prevalent a-ion fragmentation at peptide cleavage sites C-term to hydrophobic residues. In addition, Riptide can be used to produce likelihood scores that indicate whether a given peptide-spectrum match is correct. A vector of such scores is evaluated by an SVM, which produces a final score to be used in peptide identification. Using Riptide in this way yields improved discrimination when compared to other state-of-the-art MS/MS identification algorithms, increasing the number of positive identifications by as much as 12% at a 1% false discovery rate. Availability: Python and C source code are available upon request from the authors. The curated training sets are available at http://noble.gs.washington.edu/proj/intense/. The Graphical Model Tool Kit (GMTK) is freely available at http://ssli.ee.washington.edu/bilmes/gmtk. Contact: noble@gs.washington.edu

Klammer, Aaron A.; Reynolds, Sheila M.; Bilmes, Jeff A.; MacCoss, Michael J.; Noble, William Stafford

2008-01-01

96

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

PubMed Central

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

Sitkiewicz, Ewa; Oledzki, Jacek; Poznanski, Jaroslaw; Dadlez, Michal

2014-01-01

97

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

98

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

SciTech Connect

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

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

1993-06-01

99

Gas-phase IR spectra of intact [alpha]-helical coiled coil protein complexes  

NASA Astrophysics Data System (ADS)

Electrospray ionization (ESI) is the softest ionization method that is currently available and it is widely accepted, that ESI generated ions of proteins and protein assemblies at certain conditions retain characteristic aspects of their solution-state conformation. ESI mass spectrometry (MS) therefore evolved as a useful tool to obtain information on composition, stoichiometry, and dynamics of non-covalently associated protein complexes. While tertiary structure information of proteins can be obtained from ion mobility spectrometry (IMS), only a few techniques yield direct information on the secondary structure of gas-phase peptides and proteins. We present here the mid-IR spectroscopic secondary structural analysis of three de novo designed [alpha]-helical coiled coil model peptides and their non-covalently associated complexes in the gas-phase. The conformational stability of such coiled coil peptides in solution is primarily driven by aggregation. Isolated monomers usually remain unfolded. Two of the investigated peptides were designed to assemble into stable [alpha]-helical complexes in acidic solution, while the third one remains monomeric and unfolded at these conditions. Monomer ions of all three peptides show comparable photodissociation IR spectra and therefore suggest an unfolded conformation in the gas phase. In contrast, considerable CO stretch (amide-I) and N-H bend (amide-II) band shifts have been observed for the dimers which is consistent with an elevated H-bond content. These findings provide evidence that at least a fraction of the condensed phase [alpha]-helical structure is retained in the gas-phase coiled coil complexes.

Pagel, Kevin; Kupser, Peter; Bierau, Frauke; Polfer, Nicolas C.; Steill, Jeffrey D.; Oomens, Jos; Meijer, Gerard; Koksch, Beate; von Helden, Gert

2009-06-01

100

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

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

101

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

PubMed

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

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

2007-06-01

102

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

103

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

104

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

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

105

Modeling nonaqueous proton wires built from helical peptides: biased proton transfer driven by helical dipoles.  

PubMed

We report gas-phase electronic structure calculations on helical peptides that act as scaffolds for imidazole-based hydrogen-bonding networks (proton wires). We have modeled various 21-residue polyalanine peptides substituted at regular intervals with histidines (imidazole-bearing amino acids), using a hybrid approach with a semiempirical method (AM1) for peptide scaffolds and density functional theory (B3LYP) for proton wires. We have computed energy landscapes including barriers for Grotthuss-shuttling-type proton motions though wires supported on 3(10)-, ?- and ?-helical structures, showing the 3(10)- and ?-helices to be attractive targets in terms of high proton affinities, low Grotthuss shuttling barriers, and high stabilities. Moreover, bias forces provided by the helical dipole moments were found to promote unidirectional proton translocation. PMID:22188565

López, Gustavo E; Colón-Díaz, Inara; Cruz, Anthony; Ghosh, Sumana; Nicholls, Samantha B; Viswanathan, Usha; Hardy, Jeanne A; Auerbach, Scott M

2012-02-01

106

Liquid-gas phase behavior of an argon-like fluid modelled by the hard-core two-Yukawa potential  

NASA Astrophysics Data System (ADS)

We study a model for an argon-like fluid parameterized in terms of a hard-core repulsion and a two-Yukawa potential. The liquid-gas phase behavior of the model is obtained from the thermodynamically Self-Consistent Ornstein-Zernike Approximation (SCOZA) of Høye and Stell, the solution of which lends itself particularly well to a pair potential of this form. The predictions for the critical point and the coexistence curve are compared to new high resolution simulation data and to other liquid-state theories, including the hierarchical reference theory (HRT) of Parola and Reatto. Both SCOZA and HRT deliver results that are considerably more accurate than standard integral-equation approaches. Among the versions of SCOZA considered, the one yielding the best agreement with simulation successfully predicts the critical point parameters to within 1%.

Pini, D.; Stell, G.; Wilding, N. B.

2001-08-01

107

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...

108

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

PubMed

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

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

2009-01-01

109

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

PubMed

In this work, we investigate the hydration of the halide ions fluoride, chloride, and bromide using classical molecular dynamics simulations at the 10 ns scale and based on a polarizable force-field approach, which treats explicitly the cooperative bond character of strong hydrogen bond networks. We have carried out a thorough analysis of the ab initio data at the MP2 or CCSD(T) level concerning anion/water clusters in gas phase to adjust the force-field parameters. In particular, we consider the anion static polarizabilities computed in gas phase using large atomic basis sets including additional diffuse functions. The information extracted from trajectories in solution shows well structured first hydration shells formed of 6.7, 7.0, and 7.6 water molecules at about 2.78 A?, 3.15 A?, and 3.36 A? for fluoride, chloride, and bromide, respectively. These results are in excellent agreement with the latest neutron- and x-ray diffraction studies. In addition, our model reproduces several other properties of halide ions in solution, such as diffusion coefficients, description of hydration processes, and exchange reactions. Moreover, it is also able to reproduce the electrostatic properties of the anions in solution (in terms of anion dipole moment) as reported by recent ab initio quantum simulations. All the results show the ability of the proposed model in predicting data, as well as the need of accounting explicitly for the cooperative character of strong hydrogen bonds to reproduce ab initio potential energy surfaces in a mean square sense and to build up a reliable force field. PMID:22299893

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

2012-01-28

110

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

NASA Astrophysics Data System (ADS)

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

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

2012-01-01

111

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

NASA Astrophysics Data System (ADS)

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

Bhaskaran, Renjith; Sarma, Manabendra

2013-07-01

112

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

113

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

2013-06-30

114

Modelling of emission of volatile organic compounds from building materials—estimation of gas-phase mass transfer coefficient  

Microsoft Academic Search

A mathematical model is developed to predict Volatile Organic Compound (VOC) emission rates from homogeneous materials. The model considers both mass diffusion and mass convection processes in the boundary layer between the material surface and the air flow. Establishing the relationship between the surface air flow and emission rate; the model, therefore can predict the material emission rate under different

Fariborz Haghighat; Ying Zhang

1999-01-01

115

Modelling peptide nanotubes for artificial ion channels.  

PubMed

We investigate the van der Waals interaction of D,L-Ala cyclopeptide nanotubes and various ions, ion-water clusters and C(60) fullerenes, using the Lennard-Jones potential and a continuum approach which assumes that the atoms are smeared over the peptide nanotube providing an average atomic density. Our results predict that Li(+), Na(+), Rb(+) and Cl(-) ions and ion-water clusters are accepted into peptide nanotubes of 8.5 Å internal diameter whereas the C(60) molecule is rejected. The model indicates that the C(60) molecule is accepted into peptide nanotubes of 13 Å internal diameter, suggesting that the interaction energy depends on the size of the molecule and the internal diameter of the peptide nanotube. This result may be useful for the design of peptide nanotubes for drug delivery applications. Further, we also find that the ions prefer a position inside the peptide ring where the energy is minimum. In contrast, Li(+)-water clusters prefer to be in the space between each peptide ring. PMID:21979746

Rahmat, Fainida; Thamwattana, Ngamta; Cox, Barry J

2011-11-01

116

Modelling peptide nanotubes for artificial ion channels  

NASA Astrophysics Data System (ADS)

We investigate the van der Waals interaction of D,L-Ala cyclopeptide nanotubes and various ions, ion-water clusters and C60 fullerenes, using the Lennard-Jones potential and a continuum approach which assumes that the atoms are smeared over the peptide nanotube providing an average atomic density. Our results predict that Li + , Na + , Rb + and Cl - ions and ion-water clusters are accepted into peptide nanotubes of 8.5 Å internal diameter whereas the C60 molecule is rejected. The model indicates that the C60 molecule is accepted into peptide nanotubes of 13 Å internal diameter, suggesting that the interaction energy depends on the size of the molecule and the internal diameter of the peptide nanotube. This result may be useful for the design of peptide nanotubes for drug delivery applications. Further, we also find that the ions prefer a position inside the peptide ring where the energy is minimum. In contrast, Li + -water clusters prefer to be in the space between each peptide ring.

Rahmat, Fainida; Thamwattana, Ngamta; Cox, Barry J.

2011-11-01

117

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...

118

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

119

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

Microsoft Academic Search

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

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

2005-01-01

120

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

PubMed Central

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

Rene, Eldon R.; Lopez, M. Estefania; Kim, Jung Hoon; Park, Hung Suck

2013-01-01

121

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

122

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

123

Model for the formation of airborne particulate matter based on the gas-phase adsorption on amorphous carbon blacks  

SciTech Connect

This paper reports the physicochemical properties that describe the adsorption of a series of solutes onto the surfaces of amorphous carbon blacks. Adsorption was studied at concentrations that correspond to low surface coverages and in the presence of volatile solvent diluents. The adsorbates and adsorbents were selected for their relevance as models for environmental agent-particle complexes originating from incomplete combustion. The data clearly show that the major factors that determine the strength of adsorption are the surface properties of the adsorbent and the intermolecular forces between the surface and the adsorbing molecule. The heat of adsorption data have been used to predict the lifetime of the absorbate-adsorbent complexes.

Risby, T.H.; Sehnert, S.S.

1988-04-01

124

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

NASA Technical Reports Server (NTRS)

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

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

1980-01-01

125

Spectroscopic and modeling investigations of the gas phase chemistry and composition in microwave plasma activated B2H6/CH4/Ar/H2 mixtures.  

PubMed

A comprehensive study of microwave (MW) activated B2H6/CH4/Ar/H2 plasmas used for the chemical vapor deposition of B-doped diamond is reported. Absolute column densities of ground state B atoms, electronically excited H(n = 2) atoms, and BH, CH, and C2 radicals have been determined by cavity ring down spectroscopy, as functions of height (z) above a molybdenum substrate and of the plasma process conditions (B2H6, CH4, and Ar partial pressures; total pressure, p; and supplied MW power, P). Optical emission spectroscopy has also been used to explore variations in the relative densities of electronically excited H atoms, H2 molecules, and BH, CH, and C2 radicals, as functions of the same process conditions. These experimental data are complemented by extensive 2D(r, z) modeling of the plasma chemistry, which result in substantial refinements to the existing B/C/H/O thermochemistry and chemical kinetics. Comparison with the results of analogous experimental/modeling studies of B2H6/Ar/H2 and CH4/Ar/H2 plasmas in the same MW reactor show that: (i) trace B2H6 additions have negligible effect on a pre-established CH4/Ar/H2 plasma; (ii) the spatial extent of the B and BH concentration profiles in a B2H6/CH4/Ar/H2 plasma is smaller than in a hydrocarbon-free B2H6/Ar/H2 plasma operating at the same p, P, etc.; (iii) B/C coupling reactions (probably supplemented by reactions involving trace O2 present as air impurity in the process gas mixture) play an important role in determining the local BHx (x = 0-3) radical densities; and (iv) gas phase B atoms are the most likely source of the boron that incorporates into the growing B-doped diamond film. PMID:20735120

Ma, Jie; Richley, James C; Davies, David R W; Ashfold, Michael N R

2010-09-23

126

Gas-Phase Reactivity of Carboxylic Acid Functional Groups with Carbodiimides  

PubMed Central

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

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

2012-01-01

127

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

128

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

129

Gas-phase photolysis of tungsten hexachloride  

NASA Astrophysics Data System (ADS)

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

Kullmer, R.

1994-07-01

130

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

SciTech Connect

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

Tsimpanogiannis, Ioannis N.; Yortsos, Yanis C.

2001-08-15

131

Gas-phase dissociation and ion\\/ion reactions of biomolecules in a quadrupole ion trap mass spectrometer  

Microsoft Academic Search

Quadrupole ion trap mass spectrometers can be used as reaction vessels for ion\\/ion reactions between positively and negatively charged ions. These reactions are useful in the gas-phase analysis of peptide and protein ions. Gas-phase fragmentation is another informative tool, which can be used in conjunction with ion\\/ion reactions for bioanalytical applications. In order to use gas-phase dissociation and ion\\/ion reactions

Sharon Joanna Pitteri

2005-01-01

132

Rate processes in gas phase  

NASA Technical Reports Server (NTRS)

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

Hansen, C. F.

1983-01-01

133

Theoretical Studies of Gas Phase Bioanions  

NASA Astrophysics Data System (ADS)

Theoretical studies provide insight into anionic states formed by some peptides and nucleic acid bases. A coexistence of conventional valence states and dipole-bound states will be demonstrated for some nucleic acid bases. It will be shown that the instability of zwitterion forms of amino acids in the gas phase relative to their canonical tautomers could be suppressed by attaching an excess electron. As demonstrated for zwitterions of glycine, betaine, and arginine, the solvation by an excess electron provides an extra stabilization by 6-8 kcal/mol relative to the corresponding canonical structures. Simple chemical reactions induced by electron attachment will be discussed. First, we will show that the tautomerization between zwitterionic and canonical forms of isolated amino acids is facilitated by excess electron attachment. For arginine, for example, the anionic tautomers are quasidegenerate in their electronic energies, and the reaction barrier is significantly lowered in comparison with the neutral species. Second, an intermolecular proton transfer induced by electron attachment in the uracil-glycine complex will be discussed. The theoretical results will be compared with the state-of-the-art experimental data from photoelectron spectroscopy and Rydberg electron transfer experiments.

Gutowski, Maciej

2002-03-01

134

Molecular dynamics and ion mobility spectrometry study of model ?-hairpin peptide, trpzip1.  

PubMed

Here, we explore the conformations of gas phase, protonated tryptophan zipper 1 (trpzip1) ions and its six derivatives by an enhanced sampling molecular dynamics, specially the integrated tempering sampling molecular dynamics simulation (ITS-MDS). The structural distributions obtained from ITS-MDS are compared with results obtained from matrix-assisted laser desorption ionization (MALDI)-ion mobility-mass spectrometry (IM-MS). The IM-MS measured collision cross-section (CCS) profiles compare well with the calculated CCS profiles obtained from ITS-MDS. Although ?-turn structures are preferred for solution phase species, the ITS-MDS and IM-MS structural analysis suggests that the ?-turn structures are preferred for gas-phase, unsolvated trpzip1 [M + H](+) ions. In addition, the data suggests that the energy landscape of the gas phase peptide ions is sensitive to the site of protonation as well as intramolecular interactions involving the lysine side chain. PMID:21476523

Chen, Liuxi; Shao, Qiang; Gao, Yi-Qin; Russell, David H

2011-05-01

135

Gas-Phase Infrared; JCAMP Format  

National Institute of Standards and Technology Data Gateway

SRD 35 NIST/EPA Gas-Phase Infrared; JCAMP Format (PC database for purchase)   This data collection contains 5,228 infrared spectra in the JCAMP-DX (Joint Committee for Atomic and Molecular Physical Data "Data Exchange") format.

136

Folding of Gas-Phase Polyalanines in a Static Electric Field: Alignment, Deformations, and Polarization Effects  

PubMed Central

Monte Carlo simulations of the temperature-induced unfolding of small gas-phase polyalanines in a static, homogeneous electric field are reported, based on the AMBER ff96 force field. The peptides exhibit a structural transition from the native ?-helix state to entropically favored ?-sheet conformations, before eventually turning to extended coil at higher temperatures. Upon switching the electric field, the molecules undergo preferential alignment of their dipole moment vector toward the field axis and a shift of the ?-? transition to higher temperatures. At higher field strengths (>108 V/m) the molecules stretch and the ?-? and ?-coil transitions merge. A simple three-state model is shown to account for the observed behavior. Under even higher fields, density functional theory calculations and a polarizable force field both show that electronic rearrangements tend to further increase the dipole moment, polarization effects being approximately half in magnitude with respect to stretching effect. Finally a tentative (temperature, field-strength) phase diagram is sketched.

Calvo, F.; Dugourd, P.

2008-01-01

137

Solid-phase sequencing on the gas-phase sequencer.  

PubMed

Automated Edman degradation has been successfully used for determining the primary structure of numerous peptides and proteins. Quantitative solid-phase Edman degradation has great potential use for amino acid sequence analysis of synthetic peptides assembled on resin support by the Merrifield procedure. We report here the combined use of a modified gas-phase sequencer program and our improved reversed-phase HPLC analysis for PTH-amino acids to carry out the sequence analysis on synthesized peptide resins. This approach is far more sensitive than using glass beads on the conventional solid-phase sequencer. The peptide was assembled on copoly (styrene-1% divinylbenzene) resin beads at an initial substitution of 0.54 mmol/g. On a routine basis, 10-15 resin beads are used, and a repetitive yield of 94% is obtained: as few as 4 beads can be successfully sequenced. The HPLC PTH-amino acid analysis is sensitive down to subpicomole quantities. This procedure offers a sensitive and rapid analytical tool for checking the purity of peptides as they are being assembled on solid support. PMID:2942055

Sarin, V K; Kim, Y; Fox, J L

1986-05-01

138

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

2012-05-01

139

A Fragmentation Event Model for Peptide Identification by Mass Spectrometry  

Microsoft Academic Search

We present in this paper a novel fragmentation event model for peptide identification by tandem mass spectrometry. Most current\\u000a peptide identification techniques suffer from the inaccuracies in the predicted theoretical spectrum, which is due to insufficient\\u000a understanding of the ion generation process, especially the b\\/y ratio puzzle.\\u000a \\u000a   To overcome this difficulty, we propose a novel fragmentation event model, which is

Yu Lin; Yantao Qiao; Shiwei Sun; Chungong Yu; Gongjin Dong; Dongbo Bu

2008-01-01

140

Photodissociation pathways of gas-phase photoactive yellow protein chromophores  

NASA Astrophysics Data System (ADS)

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

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

2008-11-01

141

Improved Mass Defect Model for Theoretical Tryptic Peptides  

PubMed Central

Improvements in the mass accuracy and resolution of mass spectrometers have greatly aided mass spectrometry-based proteomics in profiling complex biological mixtures. With the use of innovative bioinformatics approaches, high mass accuracy and resolution information can be used for filtering chemical noise in mass spectral data. Using our recent algorithmic developments, we have generated the mass distributions of all theoretical tryptic peptides composed of twenty natural amino acids and with masses limited to 3.5 kDa. Peptide masses are distributed discretely, with well defined peak clusters separated by empty or sparsely populated trough regions. Accurate models for peak centers and widths can be used to filter peptide signals from chemical noise. We modeled mass defects, the difference between monoisotopic and nominal masses, peak centers and widths in the peptide mass distributions. We found that peak widths encompassing 95% of all peptide sequences are substantially smaller than previously thought. The result has implications for filtering out larger stretches of the mass axis. Mass defects of peptides exhibit an oscillatory behavior which is damped at high mass values. The periodicity of the oscillations is about 14 Da which is the most common difference between the masses of the twenty natural amino acids. To determine the effects of amino acid modifications on our findings, we examined the mass distributions of peptides composed of the twenty natural amino acids, oxidized Met and phosphorylated Ser, Thr and Tyr. We found that extension of the amino acid set by modifications increases the 95% peak width. Mass defects decrease, reflecting the fact that the average mass defect of natural amino acids is larger than that of oxidized Met. We propose that a new model for mass defects and peak widths of peptides may improve peptide identifications by filtering chemical noise in mass spectral data.

Mitra, Indranil; Nefedov, Alexey V.; Brasier, Allan R.; Sadygov, Rovshan G.

2012-01-01

142

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

143

A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation  

NASA Astrophysics Data System (ADS)

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

Kang, Myungshim; Smith, Paul Edward

2010-05-01

144

Gas phase dynamics of triplet formation in benzophenone.  

PubMed

Benzophenone is a prototype molecule for photochemistry in the triplet state through its high triplet yield and reactivity. We have investigated its dynamics of triplet formation under the isolated gas phase conditions via femtosecond and nanosecond time resolved photoelectron spectroscopy. This represents the complete evolution from the excitation in S2 to the final decay of T1 to the ground state S0. We have found that the triplet formation can be described almost as a direct process in preparing T1, the lowest reacting triplet state, from the S1 state after S2 ? S1 internal conversion. The molecule was also deposited by a pick-up technique on cold argon clusters providing a soft relaxation medium without evaporation of the molecule and the mechanism was identical. This cluster technique is a model for medium influenced electronic relaxation and provides a continuous transition from the isolated gas phase to the relaxation dynamics in solution. PMID:24728443

Spighi, Gloria; Gaveau, Marc-André; Mestdagh, Jean-Michel; Poisson, Lionel; Soep, Benoît

2014-04-23

145

An Investigation of Gas Phase Ozonolysis Reactions.  

National Technical Information Service (NTIS)

A simple gas phase stopped-flow apparatus has been used to determine the rates and stoichiometry for the reactions of ozone with ethylene, propene, 1-butene, methylpropene, cis-2-butene, and trans-2-butene. Measurements of the intensity of light scattered...

D. G. Williamson

1976-01-01

146

Nuclear liquid-gas phase transition  

SciTech Connect

Calculations of the equation of state of nuclear matter strongly suggest the existence of a liquid-gas phase transition. However, how sharp the transition will appear in finite nuclei, and what the experimental signatures will be are questions which evoke considerable debate. The current status of these issues, particularly the experimental signature ambiguities, is reviewed here.

Boal, D.H.

1984-11-15

147

Continuous-Flow Gas-Phase Bioreactors  

NASA Technical Reports Server (NTRS)

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

Wise, Donald L.; Trantolo, Debra J.

1994-01-01

148

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

149

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

150

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

2013-01-01

151

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

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

152

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

NASA Astrophysics Data System (ADS)

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

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

153

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

154

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

155

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

NASA Astrophysics Data System (ADS)

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

Hoffmann, Marcin; Szarecka, Agnieszka; Rychlewski, Jacek

156

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

157

Gas phase chemistry of the transactinides  

NASA Astrophysics Data System (ADS)

In the past few years the gas phase chemistry of the first three transactinide elements rutherfordium (element 104), dubnium (element 105) and seaborgium (element 106) has been studied experimentally using OLGA, the On-line Gas chemistry Apparatus, developed at Paul Scherrer Institute. In each experiment, the investigated transactinide element was identified by measuring the characteristic decay properties of its isotopes. In the chemistry of rutherfordium and dubnium evidence for relativistic effects were found, as predicted previously in theoretical calculations. For the first time, the volatility of Sg oxychlorides in comparison to its lighter homologues W and Mo was measured. Also, the half-lives and SF-branches of the nuclides 265Sg and 266Sg were determined. Finally, prospects for a chemical separation of bohrium (element 107) and hassium (element 108) using gas phase chemistry will be discussed.

Türler, A.

1999-01-01

158

Gas-phase dehydrocyclization of diphenylamine  

Microsoft Academic Search

The gas-phase dehydrocyclization of diphenylamine to carbazole was studied in a fix-bed reactor over Pt and Pd catalysts. Alumina, magnesium oxide and silica were used as supports. The reaction was carried out at a temperature of 560°C in the presence of hydrogen. Pd catalysts are reasonably active but not selective compared to Pt catalysts which possess very high activity and

Miroslav Vl?ko; Zuzana Cvengrošová; Milan Hronec; Piyasan Praserthdam

2007-01-01

159

From the gas phase to aqueous solution  

NASA Astrophysics Data System (ADS)

Structural investigations of isolated and hydrated glucose, galactose and lactose structures in the gas phase based upon infra-red ion dip (IRID) spectroscopy conducted at low temperatures, are linked with parallel investigations conducted in aqueous solution at 298 K based upon measurements of their vibrational Raman and Raman optical activity (ROA) spectra. [`]Basis sets' of computed (gas phase) Raman and ROA spectra associated with their low-lying conformational structures are used to construct [`]weighted sums' which can approximate their experimental Raman and ROA spectra recorded in solution and provide estimates of their conformational population distributions in aqueous solution at 298 K; they are compared with estimates based upon analysis of NMR measurements and molecular mechanics and molecular dynamics calculations. The altered conformational preferences in the singly hydrated complexes of glucose and galactose isolated in the gas phase, appear to be sustained in aqueous solution, supporting the view that explicit hydration provides a key influence on their conformational preferences in solution. On the other hand, the conformational preference of the isolated [beta](1 --> 4) disaccharide, lactose which resists conformational alteration when singly hydrated, is altered when it is transferred to aqueous solution at 298 K. The computational evidence suggests the control is exerted by entropic effects associated with a loosening of the structure around the glycosidic linkage.

MacLeod, Neil A.; Johannessen, Christian; Hecht, Lutz; Barron, Laurence D.; Simons, John P.

2006-07-01

160

Evolutionary sequence modeling for discovery of peptide hormones.  

PubMed

There are currently a large number of "orphan" G-protein-coupled receptors (GPCRs) whose endogenous ligands (peptide hormones) are unknown. Identification of these peptide hormones is a difficult and important problem. We describe a computational framework that models spatial structure along the genomic sequence simultaneously with the temporal evolutionary path structure across species and show how such models can be used to discover new functional molecules, in particular peptide hormones, via cross-genomic sequence comparisons. The computational framework incorporates a priori high-level knowledge of structural and evolutionary constraints into a hierarchical grammar of evolutionary probabilistic models. This computational method was used for identifying novel prohormones and the processed peptide sites by producing sequence alignments across many species at the functional-element level. Experimental results with an initial implementation of the algorithm were used to identify potential prohormones by comparing the human and non-human proteins in the Swiss-Prot database of known annotated proteins. In this proof of concept, we identified 45 out of 54 prohormones with only 44 false positives. The comparison of known and hypothetical human and mouse proteins resulted in the identification of a novel putative prohormone with at least four potential neuropeptides. Finally, in order to validate the computational methodology, we present the basic molecular biological characterization of the novel putative peptide hormone, including its identification and regional localization in the brain. This species comparison, HMM-based computational approach succeeded in identifying a previously undiscovered neuropeptide from whole genome protein sequences. This novel putative peptide hormone is found in discreet brain regions as well as other organs. The success of this approach will have a great impact on our understanding of GPCRs and associated pathways and help to identify new targets for drug development. PMID:19132080

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

2009-01-01

161

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

162

Conformational preferences of flavone and isoflavone in the gas phase, aqueous solution and organic solution  

NASA Astrophysics Data System (ADS)

Flavone and isoflavone are an important class of secondary metabolites that are widely distributed in nature. In this Letter we have determined the conformational preferences of each compound in the gas phase, aqueous solution and organic solution. Gas-phase calculations were performed using AM1, MNDO, HF/3-21G, HF/6-31G(d) and B3-LYP/6-31G(d) calculations. Besides solution calculations were performed using the MST solvation model.

Ishiki, Hamilton Mitsugu; Alemán, Carlos; Galembeck, Sérgio Emanuel

1998-05-01

163

Interaction of S413-PV cell penetrating peptide with model membranes: relevance to peptide translocation across biological membranes.  

PubMed

Cell penetrating peptides (CPPs) have been successfully used to mediate the intracellular delivery of a wide variety of molecules of pharmacological interest both in vitro and in vivo, although the mechanisms by which the cellular uptake occurs remain unclear and controversial. Following our previous work demonstrating that the cellular uptake of the S4(13)-PV CPP occurs mainly through an endocytosis-independent mechanism, we performed a detailed biophysical characterization of the interaction of this peptide with model membranes. We demonstrate that the interactions of the S4(13)-PV peptide with membranes are essentially of electrostatic nature. As a consequence of its interaction with negatively charged model membranes, the S4(13)-PV peptide becomes buried into the lipid bilayer, which occurs concomitantly with significant peptide conformational changes that are consistent with the formation of a helical structure. Comparative studies using two related peptides demonstrate that the conformational changes and the extent of cell penetration are dependent on the peptide sequence, indicating that the helical structure acquired by the S4(13)-PV peptide is relevant for its nonendocytic uptake. Overall, our data suggest that the cellular uptake of the S4(13)-PV CPP is a consequence of its direct translocation through cell membranes, following conformational changes induced by peptide-membrane interactions. PMID:17437249

Mano, Miguel; Henriques, Ana; Paiva, Artur; Prieto, Manuel; Gavilanes, Francisco; Simões, Sérgio; de Lima, Maria C Pedroso

2007-05-01

164

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

PubMed Central

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

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

2013-01-01

165

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

NASA Astrophysics Data System (ADS)

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

Pilo, Alice L.; McLuckey, Scott A.

2014-03-01

166

Oxidation of methionine residues in polypeptide ions via gas-phase ion/ion chemistry.  

PubMed

The gas-phase oxidation of methionine residues is demonstrated here using ion/ion reactions with periodate anions. Periodate anions are observed to attach in varying degrees to all polypeptide ions irrespective of amino acid composition. Direct proton transfer yielding a charge-reduced peptide ion is also observed. In the case of methionine and, to a much lesser degree, tryptophan-containing peptide ions, collisional activation of the complex ion generated by periodate attachment yields an oxidized peptide product (i.e., [M?+?H?+?O](+)), in addition to periodic acid detachment. Detachment of periodic acid takes place exclusively for peptides that do not contain either a methionine or tryptophan side chain. In the case of methionine-containing peptides, the [M?+?H?+?O](+) product is observed at a much greater abundance than the proton transfer product (viz., [M?+?H](+)). Collisional activation of oxidized Met-containing peptides yields a signature loss of 64 Da from the precursor and/or product ions. This unique loss corresponds to the ejection of methanesulfenic acid from the oxidized methionine side chain and is commonly used in solution-phase proteomics studies to determine the presence of oxidized methionine residues. The present work shows that periodate anions can be used to 'label' methionine residues in polypeptides in the gas phase. The selectivity of the periodate anion for the methionine side chain suggests several applications including identification and location of methionine residues in sequencing applications. PMID:24671696

Pilo, Alice L; McLuckey, Scott A

2014-06-01

167

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

NASA Astrophysics Data System (ADS)

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

Pilo, Alice L.; McLuckey, Scott A.

2014-06-01

168

Mass Spectrometry of Protein-Ligand Complexes: Enhanced Gas Phase Stability of Ribonuclease-Nucleotide Complexes  

PubMed Central

Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS). Ligand binding stoichiometry can be determined easily by the ESI-MS method. The ability to detect noncovalent protein-ligand complexes depends, however, on the stability of the complexes in the gas phase environment. Solution binding affinities may or may not be accurate predictors of their stability in vacuo. Complexes composed of cytidine nucleotides bound to ribonuclease A (RNase A) and ribonuclease S (RNase S) were detected by ESI-MS and were further analyzed by MS/MS. RNase A and RNase S share similar structures and biological activity. Subtilisin-cleavage of RNase A yields an S-peptide and an S-protein; the S-peptide and S-protein interact through hydrophobic interactions with a solution binding constant in the nanomolar range to generate an active RNase S. Cytidine nucleotides bind to the ribonucleases through electrostatic interactions with a solution binding constant in the micromolar range. Collisionally activated dissociation (CAD) of the 1:1 RNase A-CDP and CTP complexes yields cleavage of the covalent phosphate bonds of the nucleotide ligands, releasing CMP from the complex. CAD of the RNase S-CDP and CTP complexes dissociates the S-peptide from the remaining S-protein/nucleotide complex; further dissociation of the S-protein/nucleotide complex fragments a covalent phosphate bond of the nucleotide with subsequent release of CMP. Despite a solution binding constant favoring the S-protein/S-peptide complex, CDP/CTP remains electrostatically bound to the S-protein in the gas phase dissociation experiment. This study highlights the intrinsic stability of electrostatic interactions in the gas phase and the significant differences in solution and gas phase stabilities of noncovalent complexes that can result.

Yin, Sheng; Xie, Yongming; Loo, Joseph A.

2008-01-01

169

Gas Phase Study of C+ Reactions of Interstellar Relevance  

NASA Astrophysics Data System (ADS)

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

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

2008-10-01

170

Gas phase thermochemistry of organogermanium compounds  

SciTech Connect

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

Engel, J.P.

1993-12-07

171

Approaching complete peroxisome characterization by gas-phase fractionation.  

PubMed

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 (microLC/ESI-MS/MS) analysis of the peptides produced by proteolytic digestion of unfractionated proteins from a yeast whole-cell lysate and in a peroxisomal membrane protein fraction derived from isolated yeast peroxisomes. We also investigated GPF in the relative ion intensity dimension and propose denoting the two types of GPF as GPF(m/z) and GPF(RI). Comparison of results of direct nuLC/ESI-MS/MS analysis of the unfractionated mixture of peptides from proteolysis of a yeast whole cell lysate by DD ion selection from 400-1800 m/z in triplicate and GPF(m/z) from 400-800, 800-1200 and 1200-1800 produced the following results: (i) 1.3 x more proteins were identified by GPF(m/z) for an equal amount of effort (i.e., 3 microLC/ESI-MS/MS) and (ii) proteins identified by GPF(m/z) had a lower average codon bias value. Use of GPF(RI) identified more proteins per m/z unit scanned than GPF(m/z) or triplicate analysis over a wide m/z range. After tryptic digestion of all the proteins from a discontinuous Nycodenz gradient fraction known to be enriched with yeast peroxisomal membrane proteins we detected 93% (38/41) of known peroxisomal proteins using GPF(m/z), but only 73% using a standard wide m/z range survey scan. PMID:12298092

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

2002-09-01

172

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

173

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

174

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

175

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

176

Impurity capture during the gas-phase epitaxy of gallium arsenide  

NASA Astrophysics Data System (ADS)

Attention is given to the possibility of using models of the equilibrium distribution of an impurity between phases and nonequilibrium capture limited by surface kinetics to describe the doping process during the gas-phase epitaxy of GaAs in halide-hydrogen (e.g., AsCl3-H2) systems. It is shown that the transition from the gas phase to the solid phase can be considered as consisting of three surface stages: adsorption, surface diffusion, and a step (building-in) reaction. A model is considered which makes it possible to determine which of these stages is limiting and to clarify the impurity growth and capture kinetics.

Lavrenteva, L. G.

1983-10-01

177

The gas-phase ozonolysis of ?-humulene.  

PubMed

?-Humulene contains three double bonds (DB), and after ozonolysis of the first DB the first-generation products are still reactive towards O(3) and produce second- and third-generation products. The primary aim of this study consisted of identifying the products of the three generations, focusing on the carboxylic acids, which are known to have a high aerosol formation potential. The experiments were performed in a 570 litre spherical glass reactor at 295 K and 730 Torr. Initial mixing ratios were 260-2090 ppb for O(3) and 250-600 ppb for ?-humulene in synthetic air. Reactants and gas-phase products were measured by in situ FTIR spectroscopy. Particulate products were sampled on Teflon filters, extracted with methanol and analyzed by LC-MS/MS-TOF. Using cyclohexane (10-100 ppm) as an OH-radical scavenger and by monitoring the yield of cyclohexanone by PTR-MS, an OH-yield of (10.5 ± 0.7)% was determined for the ozonolysis of the first DB, and (12.9 ± 0.7)% of the first-generation products. The rate constant of the reaction of O(3) with ?-humulene is known as k(0) = 1.17 × 10(-14) cm(3) molecule(-1) s(-1) [Y. Shu and R. Atkinson, Int. J. Chem. Kinet., 1994, 26, 1193-1205]. The reaction rate constants of O(3) with the first-generation products and the second-generation products were, respectively, determined as k(1) = (3.6 ± 0.9) × 10(-16) and k(2) = (3.0 ± 0.7) × 10(-17) cm(3) molecule(-1) s(-1) by Facsimile-simulation of the observed ozone decay by FTIR. A total of 37 compounds in the aerosol phase and 5 products in the gas phase were tentatively identified: 25 compounds of the first-generation products contained C13-C15 species, 9 compounds of the second-generation products contained C8-C11 species, whereas 8 compounds of the third-generation products contained C4-C6 species. The products of all three generations consisted of a variety of dicarboxylic-, hydroxy-oxocarboxylic- and oxo-carboxylic acids. The formation mechanisms of some of the products are discussed. The residual FTIR spectra indicate the formation of secondary ozonides (SOZ) in the gas phase, which are formed by the intramolecular reaction of the Criegee moiety with the carbonyl endgroup. These SOZ revealed to be stable over several hours and its formation was shown not to be affected by the addition of Criegee-radical scavengers such as HCOOH or H(2)O. This suggests that in the ozonolysis of ?-humulene at atmospheric pressures the POZ will decompose rapidly, and that a large fraction of the formed exited Criegee Intermediate will be stabilized to form stable SOZ, while the formation of OH-radicals via the hydroperoxide channel will be a minor process. PMID:21461420

Beck, M; Winterhalter, R; Herrmann, F; Moortgat, G K

2011-06-21

178

Insights into the molecular interactions between aminopeptidase and amyloid beta peptide using molecular modeling techniques.  

PubMed

Amyloid beta (A?) peptides play a central role in the pathogenesis of Alzheimer's disease. The accumulation of A? peptides in AD brain was caused due to overproduction or insufficient clearance and defects in the proteolytic degradation of A? peptides. Hence, A? peptide degradation could be a promising therapeutic approach in AD treatment. Recent experimental report suggests that aminopeptidase from Streptomyces griseus KK565 (SGAK) can degrade A? peptides but the interactive residues are yet to be known in detail at the atomic level. Hence, we developed the three-dimensional model of aminopeptidase (SGAK) using SWISS-MODEL, Geno3D and MODELLER. Model built by MODELLER was used for further studies. Molecular docking was performed between aminopeptidase (SGAK) with wild-type and mutated A? peptides. The docked complex of aminopeptidase (SGAK) and wild-type A? peptide (1IYT.pdb) shows more stability than the other complexes. Molecular docking and MD simulation results revealed that the residues His93, Asp105, Glu139, Glu140, Asp168 and His255 are involved in the hydrogen bonding with A? peptide and zinc ions. The interactions between carboxyl oxygen atoms of Glu139 of aminopeptidase (SGAK) with water molecule suggest that the Glu139 may be involved in the nucleophilic attack on Ala2-Glu3 peptide bond of A? peptide. Hence, amino acid Glu139 of aminopeptidase (SGAK) might play an important role to degrade A? peptides, a causative agent of Alzheimer's disease. PMID:24729013

Dhanavade, Maruti J; Sonawane, Kailas D

2014-08-01

179

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

180

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

2013-08-19

181

Pressure Dependence of Gas-Phase Reaction Rates  

ERIC Educational Resources Information Center

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

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

2004-01-01

182

Chemistry inside molecular containers in the gas phase.  

PubMed

Inner-phase chemical reactions of guest molecules encapsulated in a macromolecular cavity give fundamental insight into the relative stabilization of transition states by the surrounding walls of the host, thereby modelling the situation of substrates in enzymatic binding pockets. Although in solution several examples of inner-phase reactions are known, the use of cucurbiturils as macrocyclic hosts and bicyclic azoalkanes as guests has now enabled a systematic mass spectrometric investigation of inner-phase reactions in the gas phase, where typically the supply of thermal energy results in dissociation of the supramolecular host-guest assembly. The results reveal a sensitive interplay in which attractive and repulsive van der Waals interactions between the differently sized hosts and guests need to be balanced with a constrictive binding to allow thermally activated chemical reactions to compete with dissociation. The results are important for the understanding of supramolecular reactivity and have implications for catalysis. PMID:23609087

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

2013-05-01

183

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

PubMed

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

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

2012-02-01

184

Gas-phase reactions of halogen species of atmospheric importance  

NASA Astrophysics Data System (ADS)

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

Heard, Anne C.

185

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

186

Modeling the amide I bands of small peptides  

NASA Astrophysics Data System (ADS)

In this paper different floating oscillator models for describing the amide I band of peptides and proteins are compared with density functional theory (DFT) calculations. Models for the variation of the frequency shifts of the oscillators and the nearest-neighbor coupling between them with respect to conformation are constructed from DFT normal mode calculations on N-acetyl-glycine-N'-methylamide. The calculated frequencies are compared with those obtained from existing electrostatic models. Furthermore, a new transition charge coupling model is presented. We suggest a model which combines the nearest-neighbor maps with long-range interactions accounted for using the new transition charge model and an existing electrostatic map for long-range interaction frequency shifts. This model and others, which account for the frequency shifts by electrostatic maps exclusively, are tested by comparing the predicted IR spectra with those from DFT calculations on the pentapeptide [Leu]-enkephalin. The new model described above gives the best agreement and, after a systematic blueshift is accounted for, reproduces the DFT frequencies to within 3.5 cm-1. The correlation of the intensities for this model with intensities from DFT calculations is 0.94.

La Cour Jansen, Thomas; Dijkstra, Arend G.; Watson, Tim M.; Hirst, Jonathan D.; Knoester, Jasper

2006-07-01

187

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

PubMed Central

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

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

2013-01-01

188

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

189

Gas-phase structure of the E. coli OmpA dimer.  

PubMed

In this issue of Structure, Marcoux and colleagues use gas-phase collisional cross section (CCS) measured by ion-mobility mass spectrometry to analyze the CCS of oligomeric states of E. coli outer membrane OmpA. CCS of the dimer supports a model of paired periplasmic C-terminal domains projecting away from the transmembrane porins. PMID:24807077

Whitelegge, Julian

2014-05-01

190

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

PubMed

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

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

2010-07-01

191

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

PubMed Central

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

2013-01-01

192

Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions.  

PubMed

Peptide-protein interactions are among the most prevalent and important interactions in the cell, but a large fraction of those interactions lack detailed structural characterization. The Rosetta FlexPepDock web server (http://flexpepdock.furmanlab.cs.huji.ac.il/) provides an interface to a high-resolution peptide docking (refinement) protocol for the modeling of peptide-protein complexes, implemented within the Rosetta framework. Given a protein receptor structure and an approximate, possibly inaccurate model of the peptide within the receptor binding site, the FlexPepDock server refines the peptide to high resolution, allowing full flexibility to the peptide backbone and to all side chains. This protocol was extensively tested and benchmarked on a wide array of non-redundant peptide-protein complexes, and was proven effective when applied to peptide starting conformations within 5.5?Å backbone root mean square deviation from the native conformation. FlexPepDock has been applied to several systems that are mediated and regulated by peptide-protein interactions. This easy to use and general web server interface allows non-expert users to accurately model their specific peptide-protein interaction of interest. PMID:21622962

London, Nir; Raveh, Barak; Cohen, Eyal; Fathi, Guy; Schueler-Furman, Ora

2011-07-01

193

Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions  

PubMed Central

Peptide–protein interactions are among the most prevalent and important interactions in the cell, but a large fraction of those interactions lack detailed structural characterization. The Rosetta FlexPepDock web server (http://flexpepdock.furmanlab.cs.huji.ac.il/) provides an interface to a high-resolution peptide docking (refinement) protocol for the modeling of peptide–protein complexes, implemented within the Rosetta framework. Given a protein receptor structure and an approximate, possibly inaccurate model of the peptide within the receptor binding site, the FlexPepDock server refines the peptide to high resolution, allowing full flexibility to the peptide backbone and to all side chains. This protocol was extensively tested and benchmarked on a wide array of non-redundant peptide–protein complexes, and was proven effective when applied to peptide starting conformations within 5.5?Å backbone root mean square deviation from the native conformation. FlexPepDock has been applied to several systems that are mediated and regulated by peptide–protein interactions. This easy to use and general web server interface allows non-expert users to accurately model their specific peptide–protein interaction of interest.

London, Nir; Raveh, Barak; Cohen, Eyal; Fathi, Guy; Schueler-Furman, Ora

2011-01-01

194

Gas phase atomic and molecular processes  

NASA Astrophysics Data System (ADS)

We perform fully quantum mechanical calculations of the lithium 2 p -2 s and sodium 3 p -3 s resonance lines pressure broadened by collisions with helium atoms. Using carefully constructed potential energy surfaces and transition dipole moments, we have obtained the emission and absorption coefficients at temperatures from 200 to 3000 K at wavelengths between 500 and 1000 nm for lithium and at temperatures from 158 to 3000 K at wavelengths between 500 and 760 nm for sodium. Contributions from quasi-bound levels are included. Our results are in good agreement with experiment. These broadened line profiles are important in developing effective diagnostics on the temperatures, densities, albedos and composition of the atmospheres of brown dwarfs and extrasolar giant planets. We compute the diffusion coefficients of ground and excited-state lithium and sodium atoms in a helium gas. They are valuable in predicting the sign and magnitude of the light-induced drift for the gas mixture. We calculate the dispersion coefficients of the long range interactions of alkali-metal atoms with molecular hydrogen and helium atoms. The uncertainties in our results are less than 2%. We study the relaxation of the v = 1 vibrational level of carbon monoxide induced by collisions with helium three atoms in ultracold temperatures. We confirm the Wigner's threshold law which states that in the zero temperature limit the inelastic quenching cross sections are inversely proportional to the velocity of the incident atom. Our calculations agree well with experiment and we find enhanced rate coefficients as compared to those for 4 He-CO. We study the chemistry of hydrogen fluoride in the interstellar medium. We consider fine-structure collisions and find that most fluorine atoms reside in the ground 2 P 3/ 2 state. We calculate the rate coefficients for the reaction of F( 2 P 3/2 ) atoms in collisions with H 2 . Our results agree well with experiment. We confirm the conclusions of Neufeld et al. that in interstellar clouds HF is the major form of gas phase fluorine.

Zhu, Cheng

195

A model of random sequences for de novo peptide sequencing  

SciTech Connect

We present a model for the probability of random sequences appearing in product ion spectra obtained from tandem mass spectrometry experiments using collision-induced dissociation. We demonstrate the use of these probabilities for ranking candidate peptide sequences obtained using a de novo algorithm. Sequence candidates are obtained from a spectrum graph that is greatly reduced in size from those in previous graph-theoretical de novo approaches. Evidence of multiple instances of subsequences of each candidate, due to different fragment ion type series as well as isotopic peaks, is incorporated in a hierarchical scoring scheme. This approach is shown to be useful for confirming results from database search and as a first step towards a statistically rigorous de novo algorithm.

Jarman, Kenneth D.; Cannon, William R.; Jarman, Kristin H.; Heredia-Langner, Alejandro

2003-04-15

196

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

197

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

PubMed

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. PMID:22582033

Seo, Mikyung; Rauscher, Sarah; Pomès, Régis; Tieleman, D Peter

2012-05-01

198

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 (r(pred)2) and cross validated coefficient ( q(LOO)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. PMID:24105965

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

2013-11-15

199

Gas phase reaction of sulfur trioxide with water vapor  

Microsoft Academic Search

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

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

1994-01-01

200

Cationic peptide-induced remodelling of model membranes: direct visualization by in situ atomic force microscopy.  

PubMed

Our understanding of how antimicrobial and cell-penetrating peptides exert their action at cell membranes would benefit greatly from direct visualization of their modes of action and possible targets within the cell membrane. We previously described how the cationic antimicrobial peptide, indolicidin, interacted with mixed zwitterionic planar lipid bilayers as a function of both peptide concentration and lipid composition [Shaw, J.E. et al., 2006. J. Struct. Biol. 154 (1), 42-58]. In the present report, in situ atomic force microscopy was used to characterize the interactions between three families of cationic peptides: (1) tryptophan-rich antimicrobial peptides--indolicidin and two of its analogues, (2) an amphiphilic alpha-helical membranolytic peptide--melittin, and (3) an arginine-rich cell-penetrating peptide--Tat with phase-separated planar bilayers containing 1,2-dioleoyl-sn-glycerol-3-phosphocholine (DOPC)/1,2-distearoyl-sn-glycerol-3-phosphocholine (DSPC) or DOPC/N-stearoyl-D-erythro-sphingosylphosphorylcholine (SM)/cholesterol. We found that these cationic peptides all induced remodelling of the model membranes in a concentration, and family-dependent manner. At low peptide concentration, these cationic peptides, despite their different biological roles, all appeared to reduce the interfacial line tension at the domain boundary between the liquid-ordered and liquid-disordered domains. Only at high peptide concentration was the membrane remodelling induced by these peptides morphologically distinct among the three families. While the transformation caused by indolicidin and its analogues were structurally similar, the concentration required to initiate the transformation was strongly dependent on the hydrophobicity of the peptide. Our use of lipid compositions with no net charge minimized the electrostatic interactions between the cationic peptides and the model supported bilayers. These results suggest that peptides within the same functional family have a common mechanism of action, and that membrane insertion of short cationic peptides at low peptide concentration may also alter membrane structure through a common mechanism regardless of the peptide's origin. PMID:18180166

Shaw, James E; Epand, Raquel F; Hsu, Jenny C Y; Mo, Gary C H; Epand, Richard M; Yip, Christopher M

2008-04-01

201

Fragmentation of peptide negative molecular ions induced by resonance electron capture  

SciTech Connect

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

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

2009-07-28

202

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

203

Gas-phase acidities of aspartic acid, glutamic acid, and their amino acid amides  

NASA Astrophysics Data System (ADS)

Gas-phase acidities (GA or [Delta]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 Adam; Dixon, David A.; Cassady, Carolyn J.

2007-09-01

204

Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy.  

PubMed

The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems. PMID:24419903

Chaudret, R; de Courcy, B; Contreras-García, J; Gloaguen, E; Zehnacker-Rentien, A; Mons, M; Piquemal, J-P

2014-05-01

205

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

206

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

207

Infrared and electronic absorption spectra of formaldehyde in gas phase and astrophysical H2O ice  

NASA Astrophysics Data System (ADS)

This work reports theoretical infrared and electronic absorption spectra of formaldehyde and its ions in gas phase and H2O ice at different levels of theory. The vibrational frequencies from this work at B3LYP/6-311++G** level are in agreement with the experimental determinations. The gas phase dipole moment of neutral formaldehyde 2.4 D is in excellent agreement with the experimental value of 2.33 D. An influence of ice on vibrational frequencies of neutral formaldehyde molecule was obtained using Self Consistence Isodensity Polarizable Continuum Model (SCI-PCM) with dielectric constant 78.5. Significant shift in vibrational frequencies for neutral formaldehyde molecule when studied in H2O ice and upon ionization is observed. All the vibrational modes in cation and anion of formaldehyde in gas phase are red shifted than the corresponding modes in neutral formaldehyde. Two vibrational modes are blue shifted and all other modes are red shifted for neutral formaldehyde in H2O ice. Time dependent density functional theory (TDDFT) is used to study electronic absorption spectrum of neutral formaldehyde and its charged states. It is found that like neutral formaldehyde, its cation and anion also display strong ?? ? ? electronic transitions in vacuum and far UV regions. This study should help in detecting formaldehyde molecule and its ions in gas phase and in H2O ice in different astronomical environment.

Naganathappa, Mahadevappa; Waghmare, Shivaji; Chaudhari, Ajay

2011-04-01

208

Effects of hydrophobic interaction strength on the self-assembled structures of model peptides.  

PubMed

Stable and ordered self-assembled peptide nanostructures are formed as a result of cooperative effects of various relatively weak intermolecular interactions. We systematically studied the influence of hydrophobic interaction strength and temperature on the self-assembly of peptides with a coarse-grained model by Monte Carlo simulations. The simulation results show a rich phase behavior of peptide self-assembly, indicating that the formation and morphology of peptide assemblies may be tuned by varying the temperature and the strength of hydrophobic interactions. There exist optimal combinations of temperature and hydrophobic interaction strength where ordered fibrillar nanostructures are readily formed. Our simulation results not only facilitate the understanding of the self-assembly behavior of peptides at the molecular level, but also provide useful insights into the development of fabrication strategies for high-quality peptide fibrils. PMID:24888420

Mu, Yan; Yu, Meng

2014-07-21

209

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

PubMed

In the last decade, there has been renewed interest in biologically active peptides in fields like allergy, autoimmune diseases and antibiotic therapy. Mast cell degranulating peptides mimic G-protein receptors, showing different activity levels even among homologous peptides. Another important feature is their ability to interact directly with membrane phospholipids, in a fast and concentration-dependent way. The mechanism of action of peptide HR1 on model membranes was investigated comparatively to other mast cell degranulating peptides (Mastoparan, Eumenitin and Anoplin) to evidence the features that modulate their selectivity. Using vesicle leakage, single-channel recordings and zeta-potential measurements, we demonstrated that HR1 preferentially binds to anionic bilayers, accumulates, folds, and at very low concentrations, is able to insert and create membrane spanning ion-selective pores. We discuss the ion selectivity character of the pores based on the neutralization or screening of the peptides charges by the bilayer head group charges or dipoles. PMID:19328184

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

2009-06-01

210

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

PubMed

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

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

2011-11-01

211

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

PubMed Central

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

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

2012-01-01

212

Atomic and molecular physics in the gas phase  

SciTech Connect

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 has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process 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 leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. 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.

Toburen, L.H.

1990-09-01

213

Gas-phase SO 2 in absorption towards massive protostars  

NASA Astrophysics Data System (ADS)

We present the first detection of the nu3 ro-vibrational band of gas-phase SO2 in absorption in the mid-infrared spectral region around 7.3?m of a sample of deeply embedded massive protostars. Comparison with model spectra shows that the derived excitation temperatures correlate with previous C2H2 and HCN studies, indicating that the same warm gas component is probed. The SO2 column densities are similar along all lines of sight suggesting that the SO2 formation has saturated, but not destroyed, and the absolute abundances of SO2 are high ( ~ 10-7). Both the high temperature and the high abundance of the detected SO2 are not easily explained by standard hot core chemistry models. Likewise, indicators of shock induced chemistry are lacking. Based on observations with ISO, an ESA project with instruments funded by ESA Member States (especially the PI countries: France, Germany, The Netherlands and the UK) and with the participation of ISAS and NASA.

Keane, J. V.; Boonman, A. M. S.; Tielens, A. G. G. M.; van Dishoeck, E. F.

2001-09-01

214

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

PubMed

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

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

2013-11-26

215

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

Microsoft Academic Search

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

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

2005-01-01

216

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.

217

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

SciTech Connect

Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion intensities.

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

2005-09-01

218

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

219

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

NASA Astrophysics Data System (ADS)

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

Swihart, Mark T.

2005-02-01

220

Structure and orientation study of Ebola fusion peptide inserted in lipid membrane models.  

PubMed

The fusion peptide of Ebola virus comprises a highly hydrophobic sequence located downstream from the N-terminus of the glycoprotein GP2 responsible for virus-host membrane fusion. The internal fusion peptide of GP2 inserts into membranes of infected cell to mediate the viral and the host cell membrane fusion. Since the sequence length of Ebola fusion peptide is still not clear, we study in the present work the behavior of two fusion peptides of different lengths which were named EBO17 and EBO24 referring to their amino acid length. The secondary structure and orientation of both peptides in lipid model systems made of DMPC:DMPG:cholesterol:DMPE (6:2:5:3) were investigated using PMIRRAS and polarized ATR spectroscopy coupled with Brewster angle microscopy. The infrared results showed a structural flexibility of both fusion peptides which are able to transit reversibly from an ?-helix to antiparallel ?-sheets. Ellipsometry results corroborate together with isotherm measurements that EBO peptides interacting with lipid monolayer highly affected the lipid organization. When interacting with a single lipid bilayer, at low peptide content, EBO peptides insert as mostly ?-helices mainly perpendicular into the lipid membrane thus tend to organize the lipid acyl chains. Inserted in multilamellar vesicles at higher peptide content, EBO peptides are mostly in ?-sheet structures and induce a disorganization of the lipid chain order. In this paper, we show that the secondary structure of the Ebola fusion peptide is reversibly flexible between ?-helical and ?-sheet conformations, this feature being dependent on its concentration in lipids, eventually inducing membrane fusion. PMID:24055820

Agopian, Audrey; Castano, Sabine

2014-01-01

221

Surface plasmon sensing of gas phase contaminants using optical fiber.  

SciTech Connect

Fiber-optic gas phase surface plasmon resonance (SPR) detection of several contaminant gases of interest to state-of-health monitoring in high-consequence sealed systems has been demonstrated. These contaminant gases include H{sub 2}, H{sub 2}S, and moisture using a single-ended optical fiber mode. Data demonstrate that results can be obtained and sensitivity is adequate in a dosimetric mode that allows periodic monitoring of system atmospheres. Modeling studies were performed to direct the design of the sensor probe for optimized dimensions and to allow simultaneous monitoring of several constituents with a single sensor fiber. Testing of the system demonstrates the ability to detect 70mTorr partial pressures of H{sub 2} using this technique and <280 {micro}Torr partial pressures of H{sub 2}S. In addition, a multiple sensor fiber has been demonstrated that allows a single fiber to measure H{sub 2}, H{sub 2}S, and H{sub 2}O without changing the fiber or the analytical system.

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

2009-10-01

222

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

223

Using support vector machine regression to model the retention of peptides in immobilized metal-affinity chromatography  

Microsoft Academic Search

Retention of histidine-containing peptides in immobilized metal-affinity chromatography (IMAC) has been studied using several hundred model peptides. Retention in a Nickel column is primarily driven by the number of histidine residues; however, the amino acid composition of the peptide also plays a significant role. A regression model based on support vector machines was used to learn and subsequently predict the

B. G. Kermani; I. Kozlov; P. Melnyk; C. Zhao; J. Hachmann; D. Barker; M. Lebl

2007-01-01

224

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

NASA Astrophysics Data System (ADS)

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

Liu, Xiaohua; Cole, Richard B.

2013-12-01

225

Analysis on conformational stability of C-peptide of ribonuclease A in water using the reference interaction site model theory and Monte Carlo simulated annealing  

NASA Astrophysics Data System (ADS)

Solvation structure and conformational stability of the C-peptide fragment of ribonuclease A in pure water have been analyzed using the full reference interaction site model (RISM) theory. The charged groups in the side chains of Lys-1+, Glu-2-, Lys-7+, Arg-10+, and His-12+ (in particular, the four like-charged groups) play substantial roles in stabilizing the conformations. The solvation free energy and the conformational energy are governed by the contribution from the electrostatic interaction with water and the intramolecular Coulombic energy, respectively, and the conformational stability is determined by competition of these two factors. The contributions from the hydrophobic hydration and the van der Waals and torsion terms in the conformational energy are less important, which is in contrast to the result for Met-enkephalin. The Monte Carlo simulated annealing combined with the RISM theory has been applied to the C-peptide using an almost fully extended conformation as the initial one. The conformation first changes in the direction that the charged groups in the side chains are more exposed to water, and in particular, the positively charged groups are closer together. Thus, the solvation free energy decreases greatly in the initial stage. Although this leads to a significant increase in the intramolecular Coulombic repulsion energy, the decrease in the solvation free energy dominates. In the later stage, however, a further decrease in the solvation free energy gives rise to an even larger increase in the intramolecular Coulombic repulsion energy, and the conformational change is greatly decelerated. The conformations thus stabilized in four different runs of the combined program are quite similar. The peptide conformation in water is stabilized far more rapidly than in the gas phase.

Kinoshita, Masahiro; Okamoto, Yuko; Hirata, Fumio

1999-02-01

226

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

PubMed

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

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

2005-07-01

227

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

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

228

Dermaseptins as models for the elucidation of membrane-acting helical amphipathic antimicrobial peptides.  

PubMed

Antimicrobial peptides (AMPs) produced by a wide variety of organisms are major actors of the host defense systems against invading pathogenic microorganisms. These peptides exhibit a broad spectrum of action against bacteria, yeasts, fungi, protozoa and viruses. It is widely believed that a large part of their antimicrobial effect derives from direct interactions with the lipid membrane surrounding the target cells, causing its permeabilization and cell lysis. However, the exact nature of these interactions is presently unclear. The skin of the amphibians has proved to be a remarkably rich storehouse of AMPs that encompass a wide variety of structural motifs. This natural AMP bank is used in combined approaches, based on biophysical and cellular biology methods, to elucidate how these peptides perturb the membrane and whether such membrane perturbations are related to the antimicrobial activity of these peptides. Here we review our current knowledge about the structure and the mechanism of action of the dermaseptin super-family, ?-helical amphipathic AMPs isolated from the skin of frogs of the Phyllomedusa genus. Dermaseptins are genetically related, with a remarkable identity in signal sequences and acidic propieces of their preproforms but have clearly diverged to yield several families of microbicidal cationic peptides that are structurally distinct. Particularly, we focused on the orthologous peptides dermaseptin S and B of which the shortening from the carboxy terminal extremity causes a drastic change in their membrane disruption activity. These peptides could be good models to study the membrane-peptide interactions discussed in this review. PMID:21470155

Amiche, Mohamed; Galanth, Cécile

2011-08-01

229

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

PubMed Central

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

McLarnon, James G.

2014-01-01

230

Interaction of synthetic HA2 influenza fusion peptide analog with model membranes.  

PubMed Central

The interaction of the synthetic 21 amino acid peptide (AcE4K) with 1-oleoyl-2-[caproyl-7-NBD]-sn-glycero-3-phosphocholine membranes is used as a model system for the pH-sensitive binding of fusion peptides to membranes. The sequence of AcE4K (Ac-GLFEAIAGFIENGWEGMIDGK) is based on the sequence of the hemagglutinin HA2 fusion peptide and has similar partitioning into phosphatidylcholine membranes as the viral peptide. pH-dependent partitioning in the membrane, circular dichroism, tryptophan fluorescence, change of membrane area, and membrane strength, are measured to characterize various key aspects of the peptide-membrane interaction. The experimental results show that the partitioning of AcE4K in the membrane is pH dependent. The bound peptide inserts in the membrane, which increases the overall membrane area in a pH-dependent manner, however the depth of insertion of the peptide in the membrane is independent of pH. This result suggests that the binding of the peptide to the membrane is driven by the protonation of its three glutamatic acids and the aspartic acid, which results in an increase of the number of bound molecules as the pH decreases from pH 7 to 4.5. The transition between the bound state and the free state is characterized by the Gibbs energy for peptide binding. This Gibbs energy for pH 5 is equal to -30.2 kJ/mol (-7.2 kcal/mol). Most of the change of the Gibbs energy during the binding of AcE4K is due to the enthalpy of binding -27.3 kJ/mol (-6.5 kcal/mol), while the entropy change is relatively small and is on the order of 6.4 J/mol.K (2.3 cal/mol.K). The energy barrier separating the bound and the free state, is characterized by the Gibbs energy of the transition state for peptide adsorption. This Gibbs energy is equal to 51.3 kJ/mol (12.3 kcal/mol). The insertion of the peptide into the membrane is coupled with work for creation of a vacancy for the peptide in the membrane. This work is calculated from the measured area occupied by a single peptide molecule (220 A(2)) and the membrane elasticity (190 mN/m), and is equal to 15.5 kJ/mol (3.7 kcal/mol). The comparison of the work for creating a vacancy and the Gibbs energy of the transition state shows that the work for creating a vacancy may have significant effect on the rate of peptide insertion and therefore plays an important role in peptide binding. Because the work for creating a vacancy depends on membrane elasticity and the elasticity of the membrane is dependent on membrane composition, this provides a tool for modulating the pH for membrane instability by changing membrane composition. The insertion of the peptide in the membrane does not affect the membrane permeability for water, which shows that the peptide does not perturb substantially the packing of the hydrocarbon region. However, the ability of the membrane to retain solutes in the presence of peptide is compromised, suggesting that the inserted peptide promotes formation of short living pores. The integrity of the membrane is substantially compromised below pH 4.8 (threshold pH), when large pores are formed and the membrane breaks down. The binding of the peptide in the pore region is reversible, and the pore size varies on the experimental conditions, which suggests that the peptide in the pore region does not form oligomers.

Zhelev, D V; Stoicheva, N; Scherrer, P; Needham, D

2001-01-01

231

Interaction of synthetic HA2 influenza fusion peptide analog with model membranes.  

PubMed

The interaction of the synthetic 21 amino acid peptide (AcE4K) with 1-oleoyl-2-[caproyl-7-NBD]-sn-glycero-3-phosphocholine membranes is used as a model system for the pH-sensitive binding of fusion peptides to membranes. The sequence of AcE4K (Ac-GLFEAIAGFIENGWEGMIDGK) is based on the sequence of the hemagglutinin HA2 fusion peptide and has similar partitioning into phosphatidylcholine membranes as the viral peptide. pH-dependent partitioning in the membrane, circular dichroism, tryptophan fluorescence, change of membrane area, and membrane strength, are measured to characterize various key aspects of the peptide-membrane interaction. The experimental results show that the partitioning of AcE4K in the membrane is pH dependent. The bound peptide inserts in the membrane, which increases the overall membrane area in a pH-dependent manner, however the depth of insertion of the peptide in the membrane is independent of pH. This result suggests that the binding of the peptide to the membrane is driven by the protonation of its three glutamatic acids and the aspartic acid, which results in an increase of the number of bound molecules as the pH decreases from pH 7 to 4.5. The transition between the bound state and the free state is characterized by the Gibbs energy for peptide binding. This Gibbs energy for pH 5 is equal to -30.2 kJ/mol (-7.2 kcal/mol). Most of the change of the Gibbs energy during the binding of AcE4K is due to the enthalpy of binding -27.3 kJ/mol (-6.5 kcal/mol), while the entropy change is relatively small and is on the order of 6.4 J/mol.K (2.3 cal/mol.K). The energy barrier separating the bound and the free state, is characterized by the Gibbs energy of the transition state for peptide adsorption. This Gibbs energy is equal to 51.3 kJ/mol (12.3 kcal/mol). The insertion of the peptide into the membrane is coupled with work for creation of a vacancy for the peptide in the membrane. This work is calculated from the measured area occupied by a single peptide molecule (220 A(2)) and the membrane elasticity (190 mN/m), and is equal to 15.5 kJ/mol (3.7 kcal/mol). The comparison of the work for creating a vacancy and the Gibbs energy of the transition state shows that the work for creating a vacancy may have significant effect on the rate of peptide insertion and therefore plays an important role in peptide binding. Because the work for creating a vacancy depends on membrane elasticity and the elasticity of the membrane is dependent on membrane composition, this provides a tool for modulating the pH for membrane instability by changing membrane composition. The insertion of the peptide in the membrane does not affect the membrane permeability for water, which shows that the peptide does not perturb substantially the packing of the hydrocarbon region. However, the ability of the membrane to retain solutes in the presence of peptide is compromised, suggesting that the inserted peptide promotes formation of short living pores. The integrity of the membrane is substantially compromised below pH 4.8 (threshold pH), when large pores are formed and the membrane breaks down. The binding of the peptide in the pore region is reversible, and the pore size varies on the experimental conditions, which suggests that the peptide in the pore region does not form oligomers. PMID:11423414

Zhelev, D V; Stoicheva, N; Scherrer, P; Needham, D

2001-07-01

232

Ion yields for some salts in MALDI: mechanism for the gas-phase ion formation from preformed ions.  

PubMed

Preformed ion emission is the main assumption in one of the prevailing theories for peptide and protein ion formation in matrix-assisted laser desorption ionization (MALDI). Since salts are in preformed ion forms in the matrix-analyte mixture, they are ideal systems to study the characteristics of preformed ion emission. In this work, a reliable method to measure the ion yield (IY) in MALDI was developed and used for a solid salt benzyltriphenylphosphonium chloride and two room-temperature ionic liquids 1-butyl-3-methylimidazolium hexafluorophosphate and trihexyltetradecylphosphonium bis(2,4,4-trimethylpentyl)phosphinate. IY for the matrix (?-cyano-4-hydroxycinnamic acid, CHCA) was also measured. Taking 1 pmol salts in 25 nmol CHCA as examples, IYs for three salts were similar, (4-8) × 10(-4), and those for CHCA were (0.8-1.2) × 10(-7). Even though IYs for the salts and CHCA remained virtually constant at low analyte concentration, they decreased as the salt concentrations increased. Two models, Model 1 and Model 2, were proposed to explain low IYs for the salts and the concentration dependences. Both models are based on the fact that the ion-pair formation equilibrium is highly shifted toward the neutral ion pair. In Model 1, the gas-phase analyte cations were proposed to originate from the same cations in the solid that were dielectrically screened from counter anions by matrix neutrals. In Model 2, preformed ions were assumed to be released from the solid sample in the form of neutral ion pairs and the anions in the ion pairs were assumed to be eliminated via reactions with matrix-derived cations. PMID:22048904

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

2012-01-01

233

Physicochemical characterization of GBV-C E1 peptides as potential inhibitors of HIV-1 fusion peptide: interaction with model membranes.  

PubMed

Four peptide sequences corresponding to the E1 protein of GBV-C: NCCAPEDIGFCLEGGCLV (P7), APEDIGFCLEGGCLVALG (P8), FCLEGGCLVALGCTICTD (P10) and QAGLAVRPGKSAAQLVGE (P18) were studied as they were capable of interfering with the HIV-1 fusion peptide (HIV-1 FP). In this work, the surface properties of the E1 peptide sequences are investigated and their physicochemical characterization is done by studying their interaction with model membranes; moreover, their mixtures with HIV-1 FP were also studied in order to observe whether they are capable to modify the HIV-1 FP interaction with model membranes as liposomes or monolayers. Physicochemical properties of peptides (pI and net charge) were predicted showing similarities between P7 and P8, and P10 and HIV-1 FP, whereas P18 appears to be very different from the rest. Circular dichroism experiments were carried out showing an increase of the percentage of ?-helix of P7 and P8 when mixed with HIV-1 FP corroborating a conformational change that could be the cause of their inhibition ability. Penetration experiments show that all the peptides can spontaneously insert into phospholipid membranes. Analysis of compression isotherms indicates that the peptides interact with phospholipids and the E1 peptides modify the compression isotherms of HIV-1 FP, but there is one of the peptides that excelled as the best candidate for inhibiting the activity of HIV-1 FP, P7, and therefore, that could be potentially used in future anti-HIV-1 research. PMID:22868231

Sánchez-Martín, Maria Jesús; Cruz, Antonio; Busquets, M Antònia; Haro, Isabel; Alsina, M Asunción; Pujol, Montserrat

2012-10-15

234

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

PubMed Central

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

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

2007-01-01

235

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

236

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

NASA Astrophysics Data System (ADS)

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

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

2010-05-01

237

Laboratory spectra of gas-phase coronene at elevated temperatures  

NASA Technical Reports Server (NTRS)

Gas-phase infrared spectra of coronene from 4000 to 400/cm are presented in emission and absorption at temperatures from 350 to 450 C. Peak positions are compared to KBr pellet data and to a previously published neon matrix-isolated coronene spectrum. Relative feature strengths are analyzed and used to estimate a temperature of interstellar PAHs assuming thermal emission.

Kurtz, J.

1992-01-01

238

Selected Examples of Gas-Phase Ion Chemistry Studies  

PubMed Central

Gas-phase ion chemistry is an area in mass spectrometry that has received much research interest since the mid fifties of the last century. Although the focus of mass spectrometric research has shifted the last twenty years largely to life science studies, including proteomics, genomics and metabolomics, there are still several groups in the world active in gas-phase ion chemistry of both positive and negative ions, either unimolecularly and/or bimolecularly. In this tutorial lecture the formation and determination of tautomeric ion structures and intra-ionic catalyzed tautomerization in the gas phase will be discussed. In addition, an example of formation of different tautomeric structures in protic and aprotic solvents under electrospray ionization conditions will be given, as established by gas-phase infrared multiphoton dissociation spectroscopy. This will be followed by presenting an example of time-resolved MS/MS which enables to identify the structure of an ion, generated at a particular molecular ion lifetime. At the end of the lecture the power of ion mobility will be shown in elucidating the mechanism of epimerization of bis-Tröger bases having chiral nitrogen centers.

Nibbering, Nico M. M.

2013-01-01

239

Fragment production and the liquid-gas phase transition  

SciTech Connect

An inclusive experiment in which isotopically resolved fragments, 3less than or equal toZless than or equal to13, were produced in high energy proton-nucleus collisions has provided evidence for a liquid-gas phase transition in nuclei. We review briefly the data and its description in terms of a critical phenomenon.

Hirsch, A.S.

1984-11-15

240

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

241

Statistical and Microscopic Approach to Gas Phase Chemical Kinetics.  

ERIC Educational Resources Information Center

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

Perez, J. M.; Quereda, R.

1983-01-01

242

Stochastic Lindemann kinetics for unimolecular gas-phase reactions.  

PubMed

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

Saha, Soma; Dua, Arti

2013-08-22

243

Kinetics of the initial stage of isothermal gas phase formation  

SciTech Connect

A theoretical description is proposed of the kinetics of the initial stage of gas phase formation in supersaturated liquids at constant temperature. General expressions are given for the time dependence of the number [ital N] of bubbles nucleated, of the probability [ital P] of appearance of at least one nucleus bubble and of the total volume [ital V][sub [ital g

Kashchiev, D.; Firoozabadi, A. (Reservoir Engineering Research Institute, Palo Alto, California 94304 (United States))

1993-03-15

244

First measurements of gas phase sulphuric acid in the stratosphere  

Microsoft Academic Search

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

F. Arnold; R. Fabian

1980-01-01

245

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

246

Reticulated vitreous carbon electrodes for gas phase pulsed corona reactors  

Microsoft Academic Search

A new design for gas phase pulsed corona reactors incorporating reticulated vitreous carbon electrodes is demonstrated to be effective for the removal of nitrogen oxides from synthetic air mixtures. The reactor consists of a plexiglass tube with porous reticulated carbon disk electrodes placed perpendicularly to the cylinder axis. Streamers propagate between the reticulated carbon disks providing a uniform exposure of

B. R. Looke; M. Kirkpatrick; H. Hanson; W. C. Finney

1998-01-01

247

Reticulated vitreous carbon electrodes for gas phase pulsed corona reactors  

Microsoft Academic Search

A new design for gas phase pulsed corona reactors incorporating reticulated vitreous carbon (RVC) electrodes is demonstrated to be effective for the removal of nitrogen oxides from various gas mixtures containing O2, N2, water vapor and ethylene. The reactor consists of either a Plexiglass or glass cylindrical tube with macro-porous RVC electrodes placed perpendicularly to the cylinder axis. Streamers propagate

Michael Kirkpatrick; Wright C. Finney; Bruce R. Locke

2000-01-01

248

Optically-Based Diagnostics for Gas-Phase Laser Development.  

National Technical Information Service (NTIS)

In this paper we describe several diagnostics that we have developed to assist the development of high power gas phase lasers including COIL, EOIL, and DPAL. For COIL we discuss systems that provide sensitive measurements of O2(a), small signal gain, iodi...

A. J. Hicks K. L. Galbally-Kinney S. Lee W. J. Kessler W. T. Rawlins

2010-01-01

249

Optically based diagnostics for gas-phase laser development  

Microsoft Academic Search

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

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

2010-01-01

250

KL? peptide induces reversible collapse structures on multiple length scales in model lung surfactant.  

PubMed

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

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

2011-12-21

251

Gas-Phase Combustion Synthesis of Nonoxide Nanoparticles in Microgravity  

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

252

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

253

The partitioning of Nitric Acid between the gas phase and condensed phase of aqueous sulfate aerosols.  

NASA Astrophysics Data System (ADS)

The heterogeneous hydrolysis of N2O_5 on aqueous aerosol surfaces is an important source of atmospheric HNO3. We generated HNO3 by heterogeneous hydrolysis of N2O_5 on aqueous ammonium and sodium sulfate aerosols and studied its partitioning between the gas phase and the aerosol phase. The experiments were performed in the large aerosol chamber at the FZ-Jülich at several relative humidities. Gas phase processes and the composition of the aerosols were monitored on-line simultaneously by FTIR spectroscopy and by Steam Jet Aerosol Collection/Ion Chromatography. The aerosol size distributions in the range of 20 nm to 5 ? m were measured by differential electromobility classification and by aerodynamic particle sizing. In the presence of aqueous bisulfate and sulfate aerosols a fast heterogeneous formation HNO3 is observed. (The reaction probability of N2O_5 is about 0.02.) In the case of the acidic bisulfate aerosols the major fraction of heterogeneously formed HNO3 resides in the gas phase. For neutral sulfate aerosols a significant fraction of HNO3 is taken up by the condensed phase of the aerosols. This leads to a distinctive growth of the aerosol population during the heterogeneous hydrolysis of N2O_5, which is observable in the number size distribution as well as in IR extinction measurements. The observed partitioning of HNO3 between gas phase and aqueous aerosol phase can be quantitatively understood by a Pitzer based thermodynamic model for salt solutions of high ionic strength. The model calculations and low resolution FTIR spectroscopy demonstrate that protonation of sulfate to bisulfate is the driving force for the uptake of HNO3 in neutral sulfate aerosols.

Mentel, T. F.; Folkers, M.; Sebald, H.; Wahner, A.

2001-12-01

254

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

255

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

PubMed

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

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

2014-01-01

256

Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage  

PubMed Central

Background Type I signal peptidases (SPases) are essential membrane-bound serine proteases responsible for the cleavage of signal peptides from proteins that are translocated across biological membranes. The crystal structure of SPase in complex with signal peptide has not been solved and their substrate-binding site and binding specificities remain poorly understood. We report here a structure-based model for Escherichia coli DsbA 13–25 in complex with its endogenous type I SPase. Results The bound structure of DsbA 13–25 in complex with its endogenous type I SPase reported here reveals the existence of an extended conformation of the precursor protein with a pronounced backbone twist between positions P3 and P1'. Residues 13–25 of DsbA occupy, and thereby define 13 subsites, S7 to S6', within the SPase substrate-binding site. The newly defined subsites, S1' to S6' play critical roles in the substrate specificities of E. coli SPase. Our results are in accord with available experimental data. Conclusion Collectively, the results of this study provide interesting new insights into the binding conformation of signal peptides and the substrate-binding site of E. coli SPase. This is the first report on the modeling of a precursor protein into the entire SPase binding site. Together with the conserved precursor protein binding conformation, the existing and newly identified substrate binding sites readily explain SPase cleavage fidelity, consistent with existing biochemical results and solution structures of inhibitors in complex with E. coli SPase. Our data suggests that both signal and mature moiety sequences play important roles and should be considered in the development of predictive tools.

Choo, Khar Heng; Tong, Joo Chuan; Ranganathan, Shoba

2008-01-01

257

Gas phase stripping of alkali cations from biomolecules via reaction with crown ethers  

NASA Astrophysics Data System (ADS)

Electrospray mass spectra of biomolecules produced from salty solutions can exhibit a large number of alkali adducts. Often the number of attached alkali metal atoms exceeds the net charge state of the ion. For example, the spectral intensity of the 2+ charge state of gramicidin S, cyclo[Val-Orn-Leu--Phe-Pro]2, (GS), withdrawn from a sodium-containing water:methanol solution, is distributed over (GS + 2H)2+, (GS + H + Na)2+, (GS + 2Na)2+, (GS-H + 3Na)2+, (GS-2H + 4Na)2+, (GS-3H + 5Na)2+, and (GS-4H + 6Na)2+. Each additional metal cation displaces a proton without affecting the net charge of the biomolecule. Hence, in (GS-2H + 4Na)2+, at least two of the alkali metal adducts must involve displacement of protons from non-traditional basic sites. The character of these coordination sites must be either "salt-like" or zwitterionic. Alkali adducts of trapped polypeptide ions may be removed via gas phase ion-molecule "stripping" reactions with crown ethers 12-crown-4, 15-crown-5, or 18-crown-6. Both products of the stripping reaction, the desalted biomolecule of reduced charge and the alkali-metal-attached crown, are observed in the FTICR mass spectra. For gas phase, "hyper-metallated" peptides, in which the number of adducted alkali metal ions exceeds the net charge, we suggest that some of the attached cations replace amide protons by coordinating as a salt or zwitterion to a tautomerized, deprotonated amide link in the backbone of the peptide. Alkali adduction to these non-traditional base sites leads to slightly higher stripping rates, probably by removing the secondary constraints of transannular NH[middle dot][middle dot][middle dot]O = C hydrogen bonds, which makes attached alkali cations more accessible to the stripping reagent. Stripping of K+ is faster than stripping of Na+, as may be expected for electrostatically bound cations.

Pope, R. Marshall; Shen, Nanzhu; Hofstadler, Steven A.; Dearden, David V.

1998-05-01

258

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

259

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

260

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

NASA Astrophysics Data System (ADS)

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

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

2012-07-01

261

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

262

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

263

Computer Modeling of Protocellular Functions: Peptide Insertion in Membranes  

NASA Technical Reports Server (NTRS)

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

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

2006-01-01

264

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

PubMed

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

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

2007-06-01

265

Effects of polarity on the structures and charge states of native-like proteins and protein complexes in the gas phase.  

PubMed

Native mass spectrometry and ion mobility spectrometry were used to investigate the gas-phase structures of selected cations and anions of proteins and protein complexes with masses ranging from 6 to 468 kDa. Under the same solution conditions, the average charge states observed for all native-like anions were less than those for the corresponding cations. Using an rf-confining drift cell, similar collision cross sections were measured in positive and negative ion mode suggesting that anions and cations have very similar structures. This result suggests that for protein and protein complex ions within this mass range, there is no inherent benefit to selecting a specific polarity for capturing a more native-like structure. For peptides and low-mass proteins, polarity and charge-state dependent structural changes may be more significant. The charged-residue model is most often used to explain the ionization of large macromolecules based on the Rayleigh limit, which defines the upper limit of charge that a droplet can hold. Because ions of both polarities have similar structures and the Rayleigh limit does not depend on polarity, these results cannot be explained by the charged-residue model alone. Rather, the observed charge-state distributions are most consistent with charge-carrier emissions during the final stages of analyte desolvation, with lower charge-carrier emission energies for anions than the corresponding cations. These results suggest that the observed charge-state distributions in most native mass spectrometry experiments are determined by charge-carrier emission processes; although the Rayleigh limit may determine the gas-phase charge states of larger species, e.g., virus capsids. PMID:24224685

Allen, Samuel J; Schwartz, Alicia M; Bush, Matthew F

2013-12-17

266

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

EPA Science Inventory

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

267

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

268

Substituent effects on the gas-phase acidity of silane  

SciTech Connect

In a previous paper, the gas-phase acidities of XH{sub n} compounds (X = C, N, O, F, Si, P, S, Cl) were predicted with ab initio wave functions. At the MP4{sup 2} level of theory with extended basis sets acidities for these species were determined to be within 2 kcal/mol of experimental value. In the present work, with 6-31G(d) geometries and full MP4/MC-311++G{sup 6}(3df,2pd) energies, the effects of CH{sub 3}, NH{sub 2}, OH, F, SiH{sub 3}, PH{sub 2}, SH, and Cl on the gas-phase acidity of silane are examined. Only a few related calculations have been carried out. All calculations were performed with Gaussian86, and all structures were verified as minima by diagonalizing the analytically determined hessians. Only the valence electrons were correlated in the perturbation theory calculations.

Gordon, M.S.; Volk, D.E. (North Dakota State Univ., Fargo (USA)); Gano, D.R. (Minot State Univ., ND (USA))

1989-12-20

269

Pr:YAG temperature imaging in gas-phase flows  

NASA Astrophysics Data System (ADS)

In this study, a new thermographic phosphor for planar gas-phase thermometry is investigated. The thermographic phosphor used is composed of trivalent praseodymium (Pr3+) ions doped into a yttrium aluminum garnet (YAG) host. Spectrally-resolved emission data were taken in a furnace for temperatures up to 1,300 K. The emission spectra were used to develop a temperature measurement strategy utilizing a non-equilibrium population ratio. The developed temperature measurement technique was demonstrated in a turbulent heated air jet for exit temperatures ranging from 300 to 750 K. The results demonstrate the promise of the Pr:YAG phosphor for obtaining high-precision single-shot temperature measurements in gas-phase flows.

Jordan, Jonathan; Rothamer, David A.

2013-03-01

270

Gas-phase reactivity of ruthenium carbonyl cluster anions  

Microsoft Academic Search

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

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

2009-01-01

271

Micro-structured reactors for gas phase reactions  

Microsoft Academic Search

This paper deals with reviewing on the application of micro-structured reactors for heterogeneously catalysed gas phase reactions. After a brief introduction covering some estimation criteria for the performance of micro-structured reactors, an overview of the work performed to date in the field is given. The reactors are classified by the type of catalyst applied (porous or non-porous) and according to

Gunther Kolb; Volker Hessel

2004-01-01

272

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

273

Femtosecond analysis of free molecular rotation in the gas phase  

NASA Astrophysics Data System (ADS)

The time-resolved S 1?S *n absorption anisotropy decay resulting from rotation of free gas phase POPOP molecules at 593 K and PPO molecules at 483 K was studied after S 0?S *1 excitation by femtosecond linearly polarized pulses at 308 nm. The time evolution of the anisotropy measured through a few picoseconds after excitation is in agreement with the results of calculations made for POPOP and PPO using orientational correlation functions developed for rigid asymmetric top molecules.

Borisevich, N. A.; Khoroshilov, E. V.; Kryukov, I. V.; Kryukov, P. G.; Sharkov, A. V.; Blokhin, A. P.; Tolstorozhev, G. B.

1992-04-01

274

Preconceptual design of the gas-phase decontamination demonstration cart  

Microsoft Academic Search

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

Munday

1993-01-01

275

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

276

Gas phase decontamination of gaseous diffusion process equipment  

SciTech Connect

D&D of the process facilities at the gaseous diffusion plants (GDPs) will be an enormous task. The EBASCO estimate places the cost of D&D of the GDP at the K-25 Site at approximately $7.5 billion. Of this sum, nearly $4 billion is associated with the construction and operation of decontamination facilities and the dismantlement and transport of contaminated process equipment to these facilities. In situ long-term low-temperature (LTLT) gas phase decontamination is being developed and demonstrated at the K-25 site as a technology that has the potential to substantially lower these costs while reducing criticality and safeguards concerns and worker exposure to hazardous and radioactive materials. The objective of gas phase decontamination is to employ a gaseous reagent to fluorinate nonvolatile uranium deposits to form volatile LJF6, which can be recovered by chemical trapping or freezing. The LTLT process permits the decontamination of the inside of gas-tight GDP process equipment at room temperature by substituting a long exposure to subatmospheric C1F for higher reaction rates at higher temperatures. This paper outlines the concept for applying LTLT gas phase decontamination, reports encouraging laboratory experiments, and presents the status of the design of a prototype mobile system. Plans for demonstrating the LTLT process on full-size gaseous diffusion equipment are also outlined briefly.

Bundy, R.D.; Munday, E.B.; Simmons, D.W.; Neiswander, D.W.

1994-03-01

277

Performance of efficient minimization algorithms as applied to models of peptides and proteins  

Microsoft Academic Search

We test the efficiency of three minimization algorithms as applied to models of peptides and proteins. These include: the limited memory quasi- . . Newton L-BFGS of Liu and Nocedal; the truncated Newton TN with . automatic preconditioner of Nash; and the nonlinear conjugate gradients CG of Shanno and Phua. The molecules are modeled by two energy functions, one is

Canan Baysal; Hagai Meirovitch; I. Michael Navon

1999-01-01

278

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

Microsoft Academic Search

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

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

2000-01-01

279

Lipid tail protrusion in simulations predicts fusogenic activity of influenza fusion peptide mutants and conformational models.  

PubMed

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

Larsson, Per; Kasson, Peter M

2013-01-01

280

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

PubMed Central

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

Larsson, Per; Kasson, Peter M.

2013-01-01

281

A Thermodynamic Approach to the Mechanism of Cell-Penetrating Peptides in Model Membranes†  

PubMed Central

We report a first test of the hypothesis that the mechanism of antimicrobial, cytolytic, and amphipathic cell-penetrating peptides in model membranes is determined by the thermodynamics of peptide insertion into the lipid bilayer from the surface-associated state. Three peptides were designed with minimal mutations relative to the sequence of TP10W, the Y3W variant of transportan 10, which is a helical, amphipathic cell-penetrating peptide previously studied. Binding to 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) membranes and dye release from those vesicles were measured by stopped-flow fluorescence, and the secondary structure of the peptides on the membranes was determined by circular dichroism. The Gibbs energy of binding determined experimentally was in excellent agreement with that calculated using the Wimley-White interfacial hydrophobicity scale, taking into account the helical content of the membrane-associated peptide. Dye release from POPC vesicles remained graded, as predicted by the hypothesis. More significantly, as the Gibbs energy of insertion into the bilayer became more unfavorable, which was estimated using the Wimley-White octanol hydrophobicity scale, dye release became slower in quantitative agreement with the prediction.

McKeown, Alesia N.; Naro, Jeffrey L.; Huskins, Laura J.; Almeida, Paulo F.

2010-01-01

282

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:23363529

Polyansky, Anton A; Chugunov, Anton O; Vassilevski, Alexander A; Grishin, Eugene V; Efremov, Roman G

2012-11-01

283

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

284

Mass-sensitive detection of gas-phase volatile organics using disk microresonators.  

PubMed

The detection of volatile organic compounds (VOCs) in the gas phase by mass-sensitive disk microresonators is reported. The disk resonators were fabricated using a CMOS-compatible silicon micromachining process and subsequently placed in an amplifying feedback loop to sustain oscillation. Sensing of benzene, toluene, and xylene was conducted after applying controlled coatings of an analyte-absorbing polymer. An analytical model of the resonator's chemical sensing performance was developed and verified by the experimental data. Limits of detection for the analytes tested were obtained, modeled, and compared to values obtained from other mass-sensitive resonant gas sensors. PMID:21469667

Truax, Stuart B; Demirci, Kemal S; Beardslee, Luke A; Luzinova, Yulia; Hierlemann, Andreas; Mizaikoff, Boris; Brand, Oliver

2011-05-01

285

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...

286

Quantification of isotopically overlapping deamidated and 18o-labeled peptides using isotopic envelope mixture modeling.  

PubMed

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

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

2009-03-01

287

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

288

Gas phase self-association of Eudistomin U controlled by gas phase acidity and origin of its interaction with nucleobases  

Microsoft Academic Search

Electrospray ionization mass spectrometry was used to investigate the intrinsic chemical properties of ?-carbolines: Eudistomin U (as EU) and 5-Br-Eudistomin U (as BrEU) yielding self-association in negative ion mode. It was observed that the deprotonated homodimer of EU was more stable in the gas phase than BrEU. Indeed, BrEU presents a higher polarizability that could influence the dimerization energy. On

Ying Xu; Carlos Afonso; Yves Gimbert; Françoise Fournier; Xiaochun Dong; Ren Wen; Jean-Claude Tabet

2009-01-01

289

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

PubMed

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. PMID:23750078

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

2013-01-01

290

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

291

Peptides in membranes: assessment of environmental effects via simulations using an implicit solvation model  

Microsoft Academic Search

.   A recently developed implicit solvation model is applied to Monte Carlo simulations of peptides in bilayer-mimetic and polar\\u000a environments. The model employs the formalism of atomic solvation parameters and reproduces experimental data. Solvent effects\\u000a on the?structure of the following peptides were studied: 20-residue poly-Leu and poly-Val, transmembrane helix A of bacteriorhodopsin,\\u000a magainin2. It was shown that a?membrane-like environment considerably

Roman G. Efremov; Dmitry E. Nolde; Gérard Vergoten; Alexander S. Arseniev

1999-01-01

292

Sequence-dependent reactivity of model peptides with glyceraldehyde.  

PubMed

Glyceraldehyde reacted faster with tripeptides than with dipeptides. The pH profiles of the reactions with tripeptides displayed optima in the range of 8.5-10.0, approximately 1-2 pH units higher than found with dipeptides. The second amino acid residue influences not only the rate of reaction but also the extent of formation of the product of the Amadori rearrangement, the ketoamine. The presence of histidine as the second amino acid residue of either di- or tri-peptides greatly accelerated the rate of reaction perhaps by facilitating the rearrangement. Conventional amino acid analysis and liquid chromatography procedures have been used to detect intermediates and the ketoamine product. 1H-N.m.r. analysis of the reduced adducts was consistent with the assigned structures. PMID:2776139

Mori, N; Bai, Y; Ueno, H; Manning, J M

1989-06-15

293

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

2013-01-10

294

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

PubMed Central

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

2012-01-01

295

Use of PTFE membrane for in-situ gas phase extraction from natural waters  

NASA Astrophysics Data System (ADS)

The extraction of the dissolved gas phase in natural waters is a delicate operation which can frequently invalidate the analytical data. Several methodologies were developed in order to separate the dissolved gaseous phase from water. They can be divided in two main groups: the extraction laboratory technique (ELT) (Mazor, 1977; Sugisaki & Taki, 1987; Andrews et al.,1989; Holt et al. 1995; Capasso & Inguaggiato, 1998) and the extraction field technique (EFT) (Tonani, 1971; Chiodini, 1996). Recently, new EFT method have been developed using PDMS membrane, (Sanford et al., 1996; Jacinthe & Groffman, 2001). We perform a method based on semi-permeable polymeric membrane PTFE (waterproof and permeable to the gases).The sampling device consists of a PTFE tube, sealed at one end, and connected to a glass vessel. The evacuated system is plunged in the natural water for one or more days. During this time the dissolved gases flows inside the system. The equilibrium is reached after 10 days, but a theoretical model was developed to recalculate the partial pressure of each gas species, from not equilibrated gas sample. The recalculation model was developed combining Mass Balance with "Diffusion-Solution Model", the best model to describe the gas permeation through the PTFE membrane. The recalculation model was experimentally validated by several laboratory tests and compared with ELT methods. The new method was applied in groundwater of Vulcano Island, and allows us to carry out chemical and isotopic data of dissolved gas phase from a same gas sample

de Gregorio, S.; Gurrieri, S.; Valenza, M.

2003-12-01

296

The molecular structure of cyclopentadienyl vanadium tetracarbonyl determined by gas-phase electron diffraction  

Microsoft Academic Search

The molecular structure of cyclopentadienyl vanadium tetracarbonyl, C5H5V(CO)4, has been determined by gas-phase electron diffraction at 95°C assuming local C4v symmetry for the V?(CO)4 moiety and C5v symmetry for the C5H5?V group. The relative positions of these two groups could not be determined unequivocally. Models with an eclipsed (torsion angle, ?(C?V?X?C) = 0° where X is the centre of the

Matthew J. Almond; Elizabeth M. Page; David A. Rice; Kolbjørn Hagen

1996-01-01

297

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

2013-11-01

298

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

PubMed

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

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

1992-01-01

299

A photothermal interferometer for gas-phase ammonia detection.  

PubMed

Detection of gas-phase ammonia is particularly challenging because ambient ammonia concentrations may be less than 1 ppb (molecules of NH(3) per 10(9) molecules of air), ammonia sticks to many materials commonly used to sample air, and particles containing ammonium may interfere with gas-phase measurements. We have built a new and sensitive photothermal interferometer to detect gas-phase ammonia in situ, under typical atmospheric conditions. Ammonia molecules in sampled air absorb infrared radiation from a CO(2) laser at 9.22 ?m, with consequent collisional heating, expansion, and refractive index change. This change in refractive index is detected as a phase shift in one arm of a homodyne interferometer. Measurements of vibrational and electrical noise in the interferometer correlate to an instrumental lower limit of detection of 6.6 ppt ammonia in 1 s. The CO(2) laser output is modulated at 1.2 kHz, and the ac signal from the interferometer is measured with a lock-in amplifier. The detector is zeroed by sampling through a H(3)PO(4)-coated denuder tube and is calibrated by dynamic dilution of two permeation tube outputs and by standard addition. Signal gain is insensitive to CO(2) or H(2)O in the sample, and the signal is linear over 5 orders of magnitude. The instrument 2? precision is 31 ppt when the signal is integrated for 100 s and 250 ppt with a 1-s integration time. The windowless sample cell and inlet is fabricated entirely of glass to minimize sample loss and hysteresis. The instrument response time is demonstrated to be about 1 s. PMID:21662962

Owens, M A; Davis, C C; Dickerson, R R

1999-04-01

300

Fluorescence Spectroscopy of Gas-phase Polycyclic Aromatic Hydrocarbons  

NASA Astrophysics Data System (ADS)

The purpose of this investigation was to produce fluorescence spectra of polycyclic aromatic hydrocarbon (PAH) molecules in the gas-phase for comparison with blue luminescence (BL) emission observed in astrophysical sources te{ref2,ref3,ref4}. The BL occurs roughly from 350 to 450 nm, with a sharp peak near 380 nm. PAHs with three to four rings, e.g. anthracene and pyrene, were found to produce luminescence in the appropriate spectral region, based on existing studies. Relatively few studies of the gas-phase fluorescence of PAHs exist; those that do exist have dealt primarily with the same samples commonly available for purchase such as pyrene and anthracene. In an attempt to understand the chemistry of the nebular environment we also obtained several nitrogen substituted PAHs from our colleagues at NASA Ames. In order to simulate the astrophysical environment we also took spectra by heating the PAHs in a flame. The flame environment counteracts the formation of eximers and permits the spectroscopy of free-flying neutral molecules. Experiments with coal tar demonstrate that fluorescence spectroscopy reveals primarily the presence of the smallest molecules, which are most abundant and which possess the highest fluorescence efficiencies. One gas-phase PAH that seems to fit the BL spectrum most closely is phenanthridine. In view of the results from the spectroscopy of coal tar, a compound containing a mixture of PAHs ranging from small to very large PAH molecules, we can not preclude the presence of larger PAHs in interstellar sources exhibiting BL.

Thomas, J. D.; Witt, A. N.

301

Gas-phase basicities around and below water revisited.  

PubMed

This work employs Fourier transform ion cyclotron resonance (FT-ICR) and the Gaussian quantum chemistry composite methods W1 and G2 to experimentally and computationally analyze gas-phase basicities (GB) for a series of weak bases in the basicity region around and below water. The study aims to clarify the long-standing discrepancy between reported GB values for weak bases obtained via high-pressure mass spectrometry (HPMS) and ICR; the ICR scale is observed to be more than 2 times contracted compared to the HPMS scale. The computational results of this work support published HPMS data. This agreement improves with increasing sophistication of the computational method and is excellent at the W1 level. Several equilibria were also re-examined experimentally using FT-ICR. In the experiments with some polyfluorinated weak bases (hexafluoro-2-propanol and nonafluoro-2-methyl-2-propanol), it was found that two protonation processes compete in the gas phase: protonation on oxygen and protonation on fluorine. In these species, protonation on fluorine proceeds faster and is statistically favored over protonation on oxygen but leads to cations that are thermodynamically less stable than oxygen-protonated cations. The process may also lead to the irreversible loss of HF. The rearrangement of fluorine-protonated cations to oxygen-protonated cations is very slow and is further suppressed by the process of HF abstraction. These results at least partially explain the discrepancy between published HPMS data and earlier FT-ICR findings and call for the utmost care in using FT-ICR for gas-phase basicity measurements of heavily fluorinated compounds. The narrower dynamic range of ICR necessitates the measurement of several problematic bases and produces some differences between the ICR results in the present work and the published HPMS data; the wider dynamic range allows HPMS to overcome these difficulties in connecting the ladder. PMID:20831239

Leito, Ivo; Koppel, Ilmar A; Burk, Peeter; Tamp, Sven; Kutsar, Martin; Mishima, Masaaki; Abboud, José-Luis M; Davalos, Juan Z; Herrero, Rebeca; Notario, Rafael

2010-10-01

302

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

303

Laser and Fourier Transform Spectroscopy of Gas Phase Molecules  

Microsoft Academic Search

Laser and Fourier transform spectroscopy were used to study a variety of gas phase molecules. A series of calcium and strontium monoalkoxides, CaOR and SrOR (R=H, CH_3, CH _2CH_3, CH(CH _3)_2, CH_2CH _2CH_3, CH _2(CH_2)_2 CH_3, CH_2 (CH_3)CH_2 CH_3 and C(CH_3) _3) was studied by laser induced fluorescence and laser excitation techniques. The A - X and B - X

Leah Christine O'Brien

1987-01-01

304

Neurotransmitters in the Gas Phase: La-Mb Studies  

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

305

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

Microsoft Academic Search

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

James J. Schauer; Glen R. Cass

2000-01-01

306

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

NASA Astrophysics Data System (ADS)

A series of photooxidation experiments were conducted in an atmospheric simulation chamber in order to investigate the secondary organic aerosol (SOA) formed from the anthropogenic model gas phase precursor, 1,3,5-trimethylbenzene. Alongside specific aerosol measurements, comprehensive gas phase measurements, primarily by chemical ionisation reaction time-of-flight mass spectrometry (CIR-TOF-MS), were carried out to provide detailed insight into the composition and behaviour of the organic components of the gas phase matrix during SOA formation. An array of gas phase organic compounds was measured during the oxidation process, including several previously unmeasured primary bicyclic compounds possessing various functional groups. Analysis of results obtained during this study implies that these peroxide bicyclic species along with a series of furanones and organic acids contribute to SOA growth. The effect of varying the VOC/NOx ratio on SOA formation was explored, as was the effect of acid seeding. It was found that low NOx conditions favour more rapid aerosol formation and a higher aerosol yield, a finding that points towards a role for organic peroxides in the nucleation process and SOA growth.

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

2008-06-01

307

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

308

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

309

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

PubMed

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

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

2007-06-27

310

Improved storage stability of model infant formula by whey peptides fractions.  

PubMed

The purpose of this study was to evaluate the shelf-life stability (6 months) of model infant formula with whey protein hydrolysates or peptidic fractions as carrageenan replacers. Whey protein hydrolysates were prepared with trypsin and followed by ultrafiltration of the hydrolyzed mixture, and peptidic fractions were isolated from the ultrafiltered tryptic hydrolysate by anion- or cation-exchange chromatography. The stability of the model infant formula was evaluated using a stratification method based on fat content differences between the top and bottom strata of the samples. With protein hydrolysate-based formulations, the creaming rate of the fat in the product was slightly higher than in the standard formulation (with carrageenan), which is indicative of lower storage stability. The addition of cationic fractions to model infant formula also resulted in lower product stability, whereas the fat creaming rate was retarded in anionic fraction based formulations. The physicochemical characteristics of certain peptides combined with the reported high emulsifying properties of peptidic sequences found within these fractions may account for their ability to act as carrageenan replacers. PMID:11308359

Lajoie, N; Gauthier, S F; Pouliot, Y

2001-04-01

311

Multiscale Models of the Antimicrobial Peptide Protegrin-1 on Gram-Negative Bacteria Membranes  

PubMed Central

Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in our lab aimed at understanding this unique mechanism of action, in particular the development of models that provide a quantitative connection between molecular-level biophysical phenomena and relevant biological effects. Our work is focused on protegrins, a potent class of AMPs that attack bacteria by associating with the bacterial membrane and forming transmembrane pores that facilitate the unrestricted transport of ions. Using fully atomistic molecular dynamics simulations, we have computed the thermodynamics of peptide-membrane association and insertion, as well as peptide aggregation. We also present a multi-scale analysis of the ion transport properties of protegrin pores, ranging from atomistic molecular dynamics simulations to mesoscale continuum models of single-pore electrodiffusion to models of transient ion transport from bacterial cells. Overall, this work provides a quantitative mechanistic description of the mechanism of action of protegrin antimicrobial peptides across multiple length and time scales.

Bolintineanu, Dan S.; Vivcharuk, Victor; Kaznessis, Yiannis N.

2012-01-01

312

Multiscale models of the antimicrobial Peptide protegrin-1 on gram-negative bacteria membranes.  

PubMed

Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in our lab aimed at understanding this unique mechanism of action, in particular the development of models that provide a quantitative connection between molecular-level biophysical phenomena and relevant biological effects. Our work is focused on protegrins, a potent class of AMPs that attack bacteria by associating with the bacterial membrane and forming transmembrane pores that facilitate the unrestricted transport of ions. Using fully atomistic molecular dynamics simulations, we have computed the thermodynamics of peptide-membrane association and insertion, as well as peptide aggregation. We also present a multi-scale analysis of the ion transport properties of protegrin pores, ranging from atomistic molecular dynamics simulations to mesoscale continuum models of single-pore electrodiffusion to models of transient ion transport from bacterial cells. Overall, this work provides a quantitative mechanistic description of the mechanism of action of protegrin antimicrobial peptides across multiple length and time scales. PMID:23109834

Bolintineanu, Dan S; Vivcharuk, Victor; Kaznessis, Yiannis N

2012-01-01

313

Gas phase self-association of Eudistomin U controlled by gas phase acidity and origin of its interaction with nucleobases  

NASA Astrophysics Data System (ADS)

Electrospray ionization mass spectrometry was used to investigate the intrinsic chemical properties of [beta]-carbolines: Eudistomin U (as EU) and 5-Br-Eudistomin U (as BrEU) yielding self-association in negative ion mode. It was observed that the deprotonated homodimer of EU was more stable in the gas phase than BrEU. Indeed, BrEU presents a higher polarizability that could influence the dimerization energy. On the contrary, the stability energies calculated at B3LYP/6-31+G*//AM1 level showed a small difference for these two dimers. To understand the experimental stability variation, the experimental and theoretical gas phase acidities of these two [beta]-carbolines have been estimated. It has been shown that EU is less acidic than BrEU in the gas phase, which could explain the lower stability of the [2BrEU-H]- dimer. In addition, the investigation of non-covalent interaction of [beta]-carbolines and nucleobases has been carried out. It was experimentally demonstrated that the deprotonated heterodimer's relative stability scale was [Gua + M-H]- >> [Thy + M-H]- > [Ade + M-H]-, but the Cyt/[beta]-carboline complexes were not observed. However, the absence of Cyt/[beta]-carboline complexes could be explained by the great acidity difference between Cyt and [beta]-carbolines, yielding unstable non-covalent complexes. The studied [beta]-carbolines showed a particular affinity with guanine which suggested a strong interaction, from a structural and reactivity point of view. Calculated reaction pathways rationalize the set of experimental results concerning the heterodimer stabilisation reflected by the V1/2 value of breakdown curves of deprotonated heterodimers.

Xu, Ying; Afonso, Carlos; Gimbert, Yves; Fournier, Françoise; Dong, Xiaochun; Wen, Ren; Tabet, Jean-Claude

2009-09-01

314

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

NASA Astrophysics Data System (ADS)

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

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

2003-04-01

315

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

316

DSMC Convergence for Microscale Gas-Phase Heat Conduction  

NASA Astrophysics Data System (ADS)

The convergence of Bird's Direct Simulation Monte Carlo (DSMC) method is investigated for gas-phase heat conduction at typical microscale conditions. A hard-sphere gas is confined between two fully accommodating walls of unequal temperature. Simulations are performed for small system and local Knudsen numbers, so continuum flow exists outside the Knudsen layers. The ratio of the DSMC thermal conductivity to the Chapman-Enskog value in the central region is determined for over 200 combinations of time step, cell size, and number of computational molecules per cell. In the limit of vanishing error, this ratio approaches 1.000 to within the correlation uncertainty. In the limit of infinite computational molecules per cell, the difference from unity depends quadratically on time step and cell size as these quantities become small. The coefficients of these quadratic terms are in good agreement with Green-Kubo values found by Hadjiconstantinou, Garcia, and co-workers. These results demonstrate that DSMC can accurately simulate microscale gas-phase heat conduction. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

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

2004-11-01

317

Gas phase absorption studies of photoactive yellow protein chromophore derivatives.  

PubMed

Photoabsorption spectra of deprotonated trans p-coumaric acid and two of its methyl substituted derivatives have been studied in gas phase both experimentally and theoretically. We have focused on the spectroscopic effect of the location of the two possible deprotonation sites on the trans p-coumaric acid which originate to either a phenoxide or a carboxylate. Surprisingly, the three chromophores were found to have the same absorption maximum at 430 nm, in spite of having different deprotonation positions. However, the absorption of the chromophore in polar solution is substantially different for the distinct deprotonation locations. We also report on the time scales and pathways of relaxation after photoexcitation for the three photoactive yellow protein chromophore derivatives. As a result of these experiments, we could detect the phenoxide isomer within the deprotonated trans p-coumaric acid in gas phase; however, the occurrence of the carboxylate is uncertain. Several computational methods were used simultaneously to provide insights and assistance in the interpretation of our experimental results. The calculated excitation energies S(0)-S(1) are in good agreement with experiment for those systems having a negative charge on a phenoxide moiety. Although our augmented multiconfigurational quasidegenerate perturbation theory calculations agree with experiment in the description of the absorption spectrum of anions with a carboxylate functional group, there are some puzzling disagreements between experiment and some calculational methods in the description of these systems. PMID:19642665

Rocha-Rinza, Toms; Christiansen, Ove; Rajput, Jyoti; Gopalan, Aravind; Rahbek, Dennis B; Andersen, Lars H; Bochenkova, Anastasia V; Granovsky, Alexander A; Bravaya, Ksenia B; Nemukhin, Alexander V; Christiansen, Kasper Lincke; Nielsen, Mogens Brøndsted

2009-08-27

318

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

319

Determinants of Gas-Phase Disassembly Behavior in Homodimeric Protein Complexes with Related yet Divergent Structures  

PubMed Central

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

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

2011-01-01

320

Investigating site-specific effects of the -X glutamate in a parvalbumin CD site model peptide.  

PubMed

The -X glutamate in a 33-residue model peptide comprising the CD site of carp parvalbumin 4.25 (ParvCD) was replaced with aspartate (ParvCD-XD) and the effect on calcium-dependent dimerization and calcium affinity assessed. The peptide ParvCD demonstrates a 10(5)-fold lower calcium affinity than the same site in the native protein. Both the ParvCD and ParvCD-XD model peptides fail to bind magnesium. The low calcium affinity and failure of the model ParvCD site to bind magnesium may be due to higher enthalpic costs of chelation by the -X glutamate. Replacement of the -X glutamate with an aspartate resulted in a twofold increase in the calcium affinity of both the monomer and dimer forms and a twofold increase in the calcium dependent dimerization of the peptide. A -X glutamate to aspartate replacement in 33-residue model peptides corresponding to bovine brain calmodulin site 3 (R. M. Procyshyn and R. E. Reid, Arch. Biochem. Biophys. 311, 425-429, 1994) and in Escherichia coli d-galactose-binding protein (S. K. Drake, K. L. Lee, and J. J. Falke, Biochemistry 35, 6697-6705, 1996) agree with results in the ParvCD site. However, in rat oncomodulin a -X glutamate to aspartate replacement increases calcium affinity (R. C. Hapak, P. J. Lammers, W. A. Palmisano, E. R. Birnbaum, and M. T. Henzl, J. Biol. Chem. 264, 18751-18760, 1989). The different effect of a -X glutamate to aspartate substitution in the different sites suggests site-specific factors dictating the thermodynamic contribution of the -X glutamate to calcium affinity. PMID:10562419

Franchini, P L; Reid, R E

1999-12-01

321

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

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

322

Distance estimates from paramagnetic enhancements of nuclear relaxation in linear and flexible model peptides.  

PubMed Central

The distance dependence of electron-nuclear dipole-dipole coupling was tested using a series of poly-L-proline based peptides of different length. The poly-proline based peptides were synthesized with a nitroxide spin label on the N-terminus and a tryptophan on the C-terminus, and paramagnetic enhancements of nuclear spin-lattice relaxation rates were measured for the aromatic protons on the tryptophan as a function of the number of proline spacers in the sequence. As expected, paramagnetic enhancements decrease with distance, but the distances deduced from the NMR relaxation rates were shorter than expected for every peptide studied compared to a rigid linear poly-L-proline type II helix structure. Calculations of cross-relaxation rates indicate that this difference is not the result of spin-diffusion or the creation of a spin-temperature gradient in the proton spins caused by the nitroxide. Molecular dynamics simulations were used to estimate dynamically averaged value of (2). These weighted average distances were close to the experimentally determined distances, and suggest that molecular motion may account for differences between the rigid linear models and the distances implied by the NMR relaxation data. A poly-L-prolone peptide synthesized with a central glycine hinge showed dramatic relaxation rate enhancements compared to the peptide of the same length lacking the hinge. Molecular dynamics simulations for the hinged peptide support the notion that the NMR data is a representation of the weighted average distance, which in this case is much shorter than that expected for an extended conformation. These results demonstrate that intermoment distances based on NMR relaxation rates provide a sensitive indicator of intramolecular motions.

Jacob, J; Baker, B; Bryant, R G; Cafiso, D S

1999-01-01

323

Sequence dependent self-assembly of ?-peptides: Insights from a coarse-grained model  

NASA Astrophysics Data System (ADS)

The sequence-directed self-assembly of amphiphilic ?-peptides is studied using Monte Carlo simulations. A phenomenological model is employed where each molecule is modeled as a rigid nanorod with side groups located at positions to mimic globally amphiphilic (GA) and nonglobally amphiphilic (non-GA) isomers of ?-peptides. The strength and the range of interactions between side groups are chosen based on the types of residues. The simulations show that the aggregation of ?-peptides is sensitive to the sequence and the residue types. For one type of ?-peptide the GA isomer has a greater tendency to aggregate while for the other the non-GA isomer has a greater tendency to aggregate. The trends observed in the simulations are consistent with recent experiments [Pomerantz et al., J. Am. Chem. Soc. 128, 8730 (2006); Pomerantz et al., Angew. Chem., Int. Ed. 47, 1 (2008)], although the molecules do not spontaneously form the hollow fibers seen in experiment. Simulations with initial configurations as hollow fibers show that the stability of the fibers follows the same trend as the tendency for aggregation. The simulations demonstrate that the details matter: the self-assembly of the molecules is sensitive to the strength of the short-ranged interactions and the size of the side groups, in addition to the global amphiphilicity of the molecules. This suggests the possibility of designing molecules for desired nanostructures.

Mondal, Jagannath; Sung, Bong June; Yethiraj, Arun

2010-02-01

324

Human cathelicidin LL-37-derived peptide IG-19 confers protection in a murine model of collagen-induced arthritis.  

PubMed

Current therapies for autoimmune chronic inflammatory diseases e.g. rheumatoid arthritis (RA) include inhibitors of inflammatory cytokines. However, these therapies can result in increased risk of infections. There is a need to explore alternate strategies that can control inflammation without compromising the innate ability to resolve infections. In this study, we examined the effect of small peptides derived from endogenous cathelicidin peptides in a murine model of collagen-induced arthritis (CIA). Cathelicidins are immunomodulatory peptides known to control infections. We demonstrate that the administration of the peptide IG-19, which represents an internal segment of the human cathelicidin LL-37, decreased disease severity and significantly reduced the serum levels of antibodies against collagen type II in the CIA model. IG-19 peptide reduced cellular infiltration in joints, prevented cartilage degradation and suppressed pro-inflammatory cytokines in the CIA mice. We also showed that not all cathelicidin-derived peptides exhibit similar functions. A bovine cathelicidin-derived peptide IDR-1018 did not exhibit the beneficial effects observed with the human cathelicidin LL-37-derived peptide IG-19, in the same murine model of CIA. This is the first study to provide evidence demonstrating the ability of a peptide derived from the human cathelicidin LL-37 to alleviate the arthritic disease process in a murine model of RA. Our results has lead us to propose a new approach for controlling autoimmune chronic inflammatory disorders such as RA, by using specific synthetic derivatives of endogenous host defence peptides. Cathelicidin-derived peptides are particularly attractive for their dual antimicrobial and anti-inflammatory actions. PMID:24091294

Chow, Leola N Y; Choi, Ka-Yee Grace; Piyadasa, Hadeesha; Bossert, Maike; Uzonna, Jude; Klonisch, Thomas; Mookherjee, Neeloffer

2014-02-01

325

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

Microsoft Academic Search

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

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

2002-01-01

326

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

327

Ion Trap Collisional Activation of c and z• Ions Formed via Gas-Phase Ion/Ion Electron Transfer Dissociation  

PubMed Central

A series of c- and z•-type product ions formed via gas-phase electron transfer ion/ion reactions between protonated polypeptides with azobenzene radical anions are subjected to ion trap collision activation in a linear ion trap. Fragment ions including a-, b-, y-type and ammonia-loss ions are typically observed in collision induced dissociation (CID) of c ions, showing almost identical CID patterns as those of the C-terminal amidated peptides consisting of the same sequences. Collisional activation of z• species mainly gives rise to side-chain losses and peptide backbone cleavages resulting in a-, b-, c-, x-, y-and z-type ions. Most of the fragmentation pathways of z• species upon ion trap CID can be accounted for by radical driven processes. The side-chain losses from z• species are different from the small losses observed from the charge-reduced peptide molecular species in electron transfer dissociation (ETD), which indicates rearrangement of the radical species. Characteristic side-chain losses are observed for several amino acid residues, which are useful to predict their presence in peptide/protein ions. Furthermore, the unique side-chain losses from leucine and isoleucine residues allow facile distinction of these two isomeric residues.

Han, Hongling; Xia, Yu; McLuckey, Scott A.

2008-01-01

328

Gaussian process: an alternative approach for QSAM modeling of peptides  

Microsoft Academic Search

Different statistical modeling methods (SMMs) are used for nonlinear system classification and regression. On the basis of\\u000a Bayesian probabilistic inference, Gaussian process (GP) is preliminarily used in the field of quantitative structure-activity\\u000a relationship (QSAR) but has not yet been applied to quantitative sequence-activity model (QSAM) of biosystems. This paper\\u000a proposes the application of GP as an alternative tool for the

Peng Zhou; Xiang Chen; Yuqian Wu; Zhicai Shang

2010-01-01

329

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

330

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

331

Optically based diagnostics for gas-phase laser development  

NASA Astrophysics Data System (ADS)

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

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

2010-09-01

332

Raman study of vibrational dynamics of aminopropylsilanetriol in gas phase  

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

333

Silicon nanowire-based devices for gas-phase sensing.  

PubMed

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

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

2013-01-01

334

Tautomeric properties and gas-phase structure of acetylacetone.  

PubMed

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

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

2014-06-20

335

Conformational Study of Taurine in the Gas Phase  

NASA Astrophysics Data System (ADS)

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

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

2009-08-01

336

The gas-phase thermochemistry of FeH  

NASA Astrophysics Data System (ADS)

The guided-ion-beam mass spectrometer apparatus and procedures described by Ervin and Armentrout (1985) and Sunderlin and Armentrout (1990) are used to investigate the gas-phase endothermic hydride-abstraction reactions of Fe(+) with propane, cyclopropane, n-butane, cyclopentane, and acetaldehyde as a function of ion translational energy. The results are presented in graphs and briefly characterized. Values determined (for temperature 298 K) include D0 Fe-H = 1.63 + or - 0.08 eV, D0 Fe(+)-H(-) = 8.77 + or - 0.08 eV, IE FeH = 7.37 + or - 0.10 eV, PA Fe(-) = 347.6 + or - 1.9 kcal/mol, and Delta(f)H FeH = 113.9 + or - 1.9 kcal/mol.

Schultz, Richard H.; Armentrout, P. B.

1991-02-01

337

Gas-phase generation and cyclisation reactions of imidoyl radicals.  

PubMed

Some 1,2-diarylimidoyl radicals were generated in the gas-phase by intramolecular radical translocation from ortho-imino-aryloxyl radicals, in turn generated under flash vacuum pyrolysis (FVP) conditions. The imidoyls reacted with XR ortho'-substituents in the N-aryl group to give (in most cases) modest yields of cyclisation products. Depending on the nature of the bridging atom (X), the formation of these products was initiated either by a further hydrogen atom translocation (X = CH(2)), or by ipso-attack onto the aryl group (R = Ph), or by direct substitution at the heteroatom (X = S). With XR = N(Me)Ph, the major reaction product was probably the result of a competing pathway not involving the corresponding imidoyl. PMID:22116614

Leardini, Rino; McNab, Hamish; Nanni, Daniele; Tenan, Anton G; Thomson, Andrew

2012-01-21

338

Reaction of atomic fluorine with silicon: The gas phase products  

SciTech Connect

SiF/sub 2/ and SiF/sub 4/ have been identified as gas phase products of the reaction between atomic fluorine and silicon. Atomic fluorine is supplied by a low density molecular beam hitting a silicon target in a high vacuum. Reaction products were detected by mass spectrometric measurements. Activation energies for the production of SiF/sub 2/ and SiF/sub 4/ were found to be 0.09 +- 0.02 and 0.15 +- 0.02 eV//sup 0/K, respectively, in good agreement with the values measured by flowing afterglow techniques. The reaction probability for the reaction 4F+Si..-->..SiF/sub 4/ was found to be 0.016 at 100 /sup 0/C.

Vasile, M.J.; Stevie, F.A.

1982-05-01

339

Gas Phase Analysis of Diamond Growth Chemical Vapor Deposition Systems.  

NASA Astrophysics Data System (ADS)

The gas composition of two diamond film chemical vapor deposition (CVD) systems is probed with absorption spectroscopy. The gas temperature in a hot filament diamond CVD system is derived from the vacuum ultraviolet absorption spectrum of the H_2 molecule using synchrotron continuum radiation. The gas temperature is influenced most strongly by the substrate temperature, less strongly by heat conduction from the filament, and is nearly unaffected by heat deposited or absorbed by chemical reactions. The density of methyl radicals (CH _3) and the mole fraction of acetylene are measured in a hot filament CVD system both during and after an initial pretreatment that is intended to enhance the crystal nucleation density. The measurements suggest that the surface condition of the filament is the primary factor affecting the gas phase chemistry both during and after the pretreatment. The densities of CH_3 and CH and the hydrogen dissociation fraction are measured in a hot filament diamond CVD system for each of five different hydrocarbon input gases. The crystal growth rate and morphology of the diamond grown from the different input gases are also examined. The results indicate that the nature of the input hydrocarbon is relatively unimportant, and that the addition of oxygen greatly alters the gas phase chemistry and the filament surface condition. The absolute column densities of CH_3 and CH and the hydrogen dissociation ratio are measured in a DC hollow cathode plasma-assisted CVD system. The plasma gas temperature is determined using the H _2 emission spectrum near 460 nm. The CH _3 and CH densities are compared with measurements made in the hot filament CVD system.

Menningen, Kenneth Lee

1995-01-01

340

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

341

Surfactants from the gas phase may promote cloud droplet formation.  

PubMed

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

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

2013-02-19

342

Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers.  

PubMed

We report altogether 3-?s molecular dynamics (MD) simulations of the antimicrobial peptide CM15 to systematically investigate its interaction with two model lipid bilayers, pure POPC and mixed POPG:POPC (1:2). Starting with either an ?-helical or a random-coil conformation, CM15 is found to insert into both bilayers. Peptide-lipid interaction is stronger with the anionic POPG:POPC than the zwitterionic POPC, which is largely attributed to the electrostatic attraction between CM15 and the negatively charged POPG. Simulations initiated with CM15 as a random coil allowed us to study peptide folding at the lipid-water interface. Interestingly, CM15 folding appears to be faster in POPC than POPG:POPC, which may be explained by a lower activation energy barrier of structural rearrangement in the former system. Our data also suggest that compared with the random-coil conformation, CM15 in a pre-folded ?-helix has significantly reduced interactions with the lipids, indicating that peptide initial structures may bias the simulation results considerably on the 100-ns timescale. The implications of this result should be considered when preparing and interpreting future AMP simulations. PMID:22387432

Wang, Yi; Schlamadinger, Diana E; Kim, Judy E; McCammon, J Andrew

2012-05-01

343

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

344

The Menshutkin reaction in the gas phase and in aqueous solution: a valence bond study.  

PubMed

The recently developed (L. Song, W. Wu, Q. Zhang, S. Shaik, J. Phys. Chem. A 2004, 108, 6017-6024) valence bond method coupled to a polarized continuum model (VBPCM) is applied to the Menshutkin reaction, NH3+CH3Cl-->CH3NH3(+)+Cl-, in the gas phase and in aqueous solution. The computed barriers and reaction energies at the level of the breathing orbital VB method (P. C. Hiberty, J. P. Flament, E. Noizet, Chem. Phys. Lett. 1992, 189, 259), BOVB and VBPCM//BOVB, are comparable to CCSD(T) and CCSD(T)//PCM results and to experimental values in solution. The gas-phase reaction is endothermic and leads to an ion-pair complex via a late transition state. By contrast, the reaction in the aqueous phase is exothermic and leads to separate solvated ions as reaction products, via an early transition state. The VB calculations provide also the reactivity parameters needed to apply the valence bond state correlation diagram method, VBSCD (S. Shaik, A. Shurki, Angew. Chem. Int. Ed. 1999, 38, 586). It is shown that the reactivity parameters along with their semiempirical derivations provide together a satisfactory qualitative and quantitative account of the barriers. PMID:18061916

Su, Peifeng; Ying, Fuming; Wu, Wei; Hiberty, Philippe C; Shaik, Sason

2007-12-21

345

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

PubMed

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

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

2014-03-27

346

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

PubMed Central

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

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

2008-01-01

347

The gas-phase iron abundance in Herbig-Haro objects  

NASA Technical Reports Server (NTRS)

The gas-phase abundance ratios Fe/S and Fe/O have been determined for the Herbig-Haro objects HH 1, HH 7, HH 11, HH 43A, and 'Burnham's Nebula' (HH 255). It is the purpose of this study to decide whether a sizeable fraction of the Fe in these HH objects is still bound in dust grains or whether the observed matter has gone through sufficiently fast shock waves so that the dust grains have been essentially destroyed and most of the iron has gone back into the gas phase. We have determined the abundance ratios using statistical equilibrium calculations for the ions Fe(+), S(+), and O(+). (These are the most abundant ions of the elements in question.) Abundance determinations have been made using homogeneous models of the HH objects for which electron temperatures and densities have been determined observationally from forbidden line ratios. The results show that the Fe/S ratio in the objects HH 1, HH 7, HH 11, and HH 43A agrees very well with the Population I abundance ratio. Only Burnham's Nebula (HH255) shows an Fe/S ratio which is about three times lower indicating a shock-wave history which is quite different from that of the other HH objects.

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

1994-01-01

348

Gas-phase Mechanisms of Sulfur Isotope Mass-independent Fractionation  

NASA Astrophysics Data System (ADS)

Mass-independent fractionation (MIF) in sulfur isotopes in ancient sulfur-bearing rocks (Farquhar et al. 2000a) is interpreted as evidence for gas-phase MIF processes in the early Earth atmosphere. This interpretation is made by analogy with oxygen isotope MIF in the modern atmosphere (produced during ozone formation), and by laboratory photolysis experiments on SO2 (Farquhar et al. 2001; Wing et al. 2004) that yield both elemental sulfur and sulfate with S MIF signatures at wavelengths above and below the SO2 dissociation limit. What is lacking is a quantitative understanding of the mechanisms of gas-phase S MIF. Quantification is essential in order to extract the full implications of sulfur MIF throughout Earth history, including for bacterial sulfate reduction processes which largely conserve D33S and D36S. Several sulfur MIF mechanisms are possible. The most obvious is the gas-phase thiozone reaction, which is isovalent to the ozone formation reaction. Ozone formation produces a well-known MIF signature in oxygen isotopes (Thiemens and Heidenreich 1983), and a symmetry-dependent non-RRKM mechanism has been proposed as the origin of O MIF (Gao and Marcus 2001). It is possible and perhaps likely that S3 formation also proceeds by a non-RRKM process. Data are lacking on isotopic (an even non-isotopic) rates of S3 formation, so it is not possible to make definitive statements about MIF in S3 at this time. However modeling results suggest that the vapor pressure of S2 is too low for gas-phase S3 formation to be significant. Two additional species that may exhibit a non-RRKM MIF signature are S2O2 and S4. Again, there is a lack of isotopomer-specific kinetic data for these reactions, and gas-phase formation of S4 is likely inconsequential. Perhaps the most obvious mechanism is simply the primary act of SO2 photolysis. The SO2 absorption spectrum is highly structured, with strong vibronic bands above and below the dissociation limit. In contrast H2S, with its mostly unstructured absorption spectrum, yields a small MIF signature (Farquhar et al. 2000b; Wing pers. comm.). The modeling work of Pavlov and Kasting (2002) assigned MIF to SO2 and SO photodissociation, but without specifying a mechanism. I have preformed radiative transfer modeling of a column of SO2 gas with all sulfur isotopologues included, and observe a large mass-dependent fractionation associated with small frequency shifts. Larger frequency shifts, as would be expected for high vibrational quantum numbers in the upper state, yield MIF signatures; anharmonic effects may be evident in these MIF signatures. Additionally, some vibronic bands are rotationally resolved, and line-type self-shielding also leads to a MIF signature. The significance of these results for the ancient atmosphere will be discussed. References Farquhar, J. et al. (2000a) Science 289, 756-758. Farquhar, J. et al. (2000b) Nature 404, 50-52. Farquhar, J. et al. (2001) J. Geophys. Res. 106, 32829-32839. Gao, Y. and R. Marcus (2001) Science 293, 259-263. Pavlov, A. A. and J. F. Kasting, (2002) Astrobiology 2, 27-41. Savarino, J. et al. (2003) Geophys. Res. Lett. 30, 11-1, 11-4. Thiemens, M. H. and H. Heindenreich, Science 219, 1073-1075. Wing, B. et al. (2004) 228th ACS meeting, Aug. 22-26, Philadelphia.

Lyons, J. R.

2006-12-01

349

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

PubMed

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

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

2013-01-01

350

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

351

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

PubMed

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

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

2009-10-01

352

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

NASA Astrophysics Data System (ADS)

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

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

2009-09-01

353

Molecular structures of 3-hydroxybenzoic acid and 4-hydroxybenzoic acid, obtained by gas-phase electron diffraction and theoretical calculations.  

PubMed

The structures of 3-hydroxybenzoic acid and 4-hydroxybenzoic acid have been determined by gas-phase electron diffraction using results from quantum chemical calculations to inform the choice of restraints applied to some of the structural parameters. The results from the study presented here demonstrate that resonance hybrids are not as helpful in rationalizing the structures of 2-, 3-, and 4-hydroxybenzoic acids as are models based upon electrostatic effects. PMID:18798606

Aarset, Kirsten; Page, Elizabeth M; Rice, David A

2008-10-01

354

Identification of core functional region of murine IL4 using peptide phage display and molecular modeling  

Microsoft Academic Search

Murine IL-4 is a pleiotropic cytokine with undefined core functional region for eliciting downstream signaling. We used molecular modeling to predict the binding sites recognized by an anti-IL-4- neutralizing mAb (11B.11) and peptide phage display to delineate their makeup. The results of these approaches were confirmed by site-directed mutagenesis analysis. The results suggest that the amino acid residues spanning from

Gang Yao; Weiyan Chen; Haibin Luo; Qunfeng Jiang; Zongxiang Xia; Lei Zang; Jianping Zuo; Xin Wei; Zhengjun Chen; Xu Shen; Chen Dong; Bing Sun

2005-01-01

355

Abeta peptide immunization reduces behavioural impairment and plaques in a model of Alzheimer's disease  

Microsoft Academic Search

Much evidence indicates that abnormal processing and extracellular deposition of amyloid-beta peptide (Abeta), a proteolytic derivative of the beta-amyloid precursor protein (betaAPP), is central to the pathogenesis of Alzheimer's disease (reviewed in ref. 1). In the PDAPP transgenic mouse model of Alzheimer's disease, immunization with Abeta causes a marked reduction in burden of the brain amyloid. Evidence that Abeta immunization

Christopher Janus; Jacqueline Pearson; JoAnne McLaurin; Paul M. Mathews; Ying Jiang; Stephen D. Schmidt; M. Azhar Chishti; Patrick Horne; Donna Heslin; Janet French; Howard T. J. Mount; Ralph A. Nixon; Marc Mercken; Catherine Bergeron; Paul E. Fraser; Peter St George-Hyslop; David Westaway

2000-01-01

356

On Utilizing Optimal and Information Theoretic Syntactic Modeling for Peptide Classification  

Microsoft Academic Search

Syntactic methods in pattern recognition have been used extensively in bioinformatics, and in particular, in the analysis\\u000a of gene and protein expressions, and in the recognition and classification of bio-sequences. These methods are almost universally\\u000a distance-based. This paper concerns the use of an Optimal and Information Theoretic (OIT) probabilistic model [11] to achieve\\u000a peptide classification using the information residing in

Eser Aygün; B. John Oommen; Zehra Cataltepe

2009-01-01

357

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

PubMed

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

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

2012-01-01

358

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

359

Energy and Entropy Effects in the Gas-Phase Dissociation of Peptides and Proteins  

SciTech Connect

In the last decade characterization of complex molecules, particularly biomolecules, became a focus of both fundamental and applied research in mass spectrometry. Most of these studies utilize tandem mass spectrometry (MS/MS) for obtaining structural information for complex molecules. MS/MS typically involves the mass selection of a primary ion, its activation by collision or photon excitation, unimolecular decay into fragment ions characteristic of the ion structure and its internal excitation, and mass analysis of the fragment ions. A wide variety of mass filters and ion excitation methods can be employed in these experiments, making tandem mass spectrometry an extremely flexible analytical technique that can be implemented on almost any type of mass spectrometer.

Laskin, Julia

2006-10-06

360

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

361

Peptide identification  

DOEpatents

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

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

2011-07-12

362

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

PubMed

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

Nayar, Divya; Chakravarty, Charusita

2014-06-01

363

Testing the diffusing boundary model for the helix-coil transition in peptides.  

PubMed

The dynamics of peptide ?-helices have been studied extensively for many years, and the kinetic mechanism of the helix-coil dynamics has been discussed controversially. Recent experimental results have suggested that equilibrium helix-coil dynamics are governed by movement of the helix/coil boundary along the peptide chain, which leads to slower unfolding kinetics in the helix center compared with the helix ends and position-independent helix formation kinetics. We tested this diffusion of boundary model in helical peptides of different lengths by triplet-triplet energy transfer measurements and compared the data with simulations based on a kinetic linear Ising model. The results show that boundary diffusion in helical peptides can be described by a classical, Einstein-type, 1D diffusion process with a diffusion coefficient of 2.7?10(7) (amino acids)(2)/s or 6.1?10(-9) cm(2)/s. In helices with a length longer than about 40 aa, helix unfolding by coil nucleation in a helical region occurs frequently in addition to boundary diffusion. Boundary diffusion is slowed down by helix-stabilizing capping motifs at the helix ends in agreement with predictions from the kinetic linear Ising model. We further tested local and nonlocal effects of amino acid replacements on helix-coil dynamics. Single amino acid replacements locally affect folding and unfolding dynamics with a ?f-value of 0.35, which shows that interactions leading to different helix propensities for different amino acids are already partially present in the transition state for helix formation. Nonlocal effects of amino acid replacements only influence helix unfolding (?f = 0) in agreement with a diffusing boundary mechanism. PMID:23878243

Neumaier, Sabine; Reiner, Andreas; Büttner, Maren; Fierz, Beat; Kiefhaber, Thomas

2013-08-01

364

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

NASA Technical Reports Server (NTRS)

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

Radhakrishnan, Krishnan; Bittker, David A.

1993-01-01

365

Comparison of the rates of deamidation, diketopiperazine formation, and oxidation in recombinant human vascular endothelial growth factor and model peptides  

Microsoft Academic Search

In this work, we examine the way in which stability information obtained from studies on small model peptides correlates with\\u000a similar information acquired from a protein. The rates of deamidation, oxidation, and diketopiperazine reactions in model\\u000a peptide systems were compared to those of recombinant human vascular endothelial growth factor (rhVEGF). The N-terminal residues\\u000a of rhVEGF, a potent mitogen in angiogenesis,

Chimanlall Goolcharran; Andrew J. S. Jones; Ronald T. Borchardt

2000-01-01

366

Computational modelling of H+-coupled peptide transport via human PEPT1  

PubMed Central

H+-coupled peptide transporter 1 (PEPT1) mediates the transport of small peptides and peptide-like drugs in a pH- and voltage-dependent manner. Here, we investigated the transport mechanisms of PEPT1 for neutral and charged substrates by experimental studies and computational simulation. Uptake studies revealed that the Michaelis-Menten constant (Km) of glycylsarcosine (Gly-Sar), a neutral substrate, decreased with a fall in pH from 7.4 to 5.5, but at pH 5.0, the Km increased again. In contrast, the Km value of an anionic substrate, ceftibuten, declined steadily with decreasing pH. Based on these findings and information from the literature, we hypothesized the transport mechanisms in which (1) H+ binds to not only the H+-binding site, but also the substrate-binding site; and (2) H+ at the substrate-binding site inhibits the interaction of neutral and cationic substrates, but is necessary for that of anionic substrates. To validate these hypotheses, a computational model was constructed and various properties of substrate transport by PEPT1 were simulated. Our model reproduced the voltage dependence, hyperbolic saturation and bell-shaped pH-profile of Gly-Sar transport. Moreover, the various transport properties of negatively and positively charged substrates were also reconstructed. These findings indicated that the inferred mechanisms are able to sufficiently interpret the transport of both neutral and charged substrates by PEPT1.

Irie, Megumi; Terada, Tomohiro; Katsura, Toshiya; Matsuoka, Satoshi; Inui, Ken-ichi

2005-01-01

367

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

PubMed Central

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

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

2010-01-01

368

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

369

A model for the role of isomerization in nascent peptide movement through the ribosomal tunnel.  

PubMed

The ribosome is a molecular machine whose manner of controlling the progression of the nascent chain through the ribosomal exit tunnel is currently unknown. A novel model for the mechanism driving the nascent chain motion is hereby presented, in which the ?180° rotatory motion performed by each C-terminal amino acid of the nascent chain during its translocation from the A site to the P site, is suggested to twist the newly formed peptide bond into cis conformation. By catalyzing the cis to trans isomerization, the ribosome is proposed to release the potential energy stored within the cis conformer and to utilize it to push the chain down the tunnel, thus operating as a molecular motor. This hypothetical isomerization mechanism is supported by its ability to provide an explanation for the peculiar conduct observed in translational events of nascent chains with C-terminal prolines: the slow peptide bond formation with puromycin, translation arrest, and tmRNA tagging. PMID:22389440

Agmon, Ilana C

2012-06-01

370

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

PubMed Central

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

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

2011-01-01

371

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

SciTech Connect

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

Garrison, W.M.

1982-08-01

372

Gas Phase Conformations of Tetrapeptide Glycine-Phenylalanine-Glycine-Glycine  

NASA Astrophysics Data System (ADS)

Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine-glycine-glycine (GFGG) in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search method is described in detail. The relative electronic energies, zero point vibrational energies, dipole moments, rotational constants, vertical ionization energies and the temperature dependent conformational distributions for a number of important conformers are obtained. The structural characteristics of these conformers are analyzed and it is found that the entropic effect is a dominating factor in determining the relative stabilities of the conformers. The measurements of dipole moments and some characteristic IR mode are shown to be effective approaches to verify the theoretical prediction. The structures of the low energy GFGG conformers are also analyzed in their connection with the secondary structures of proteins. Similarity between the local structures of low energy GFGG conformers and the ?-helix is discussed and many ?- and ?-turn local structures in GFGG conformers are found.

Chen, Hui-bin; Wang, Yao; Chen, Xin; Lin, Zi-jing

2012-02-01

373

Directed gas-phase formation of the ethynylsulfidoboron molecule.  

PubMed

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

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

2014-06-11

374

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

375

Project ARGO: Gas phase formation in simulated microgravity  

NASA Technical Reports Server (NTRS)

The ARGO study investigated the reduced incidence of joint pain decompression sickness (DCS) encountered in microgravity as compared with an expected incidence of joint pain DCS experienced by test subjects in Earth-based laboratories (unit gravity) with similar protocols. Individuals who are decompressed from saturated conditions usually acquire joint pain DCS in the lower extremities. Our hypothesis is that the incidence of joint pain DCS can be limited by a significant reduction in the tissue gas micronuclei formed by stress-assisted nucleation. Reductions in dynamic and kinetic stresses in vivo are linked to hypokinetic and adynamic conditions of individuals in zero g. We employed the Doppler ultrasound bubble detection technique in simulated microgravity studies to determine quantitatively the degree of gas phase formation in the upper and lower extremities of test subjects during decompression. We found no evidence of right-to-left shunting through pulmonary vasculature. The volume of gas bubble following decompression was examined and compared with the number following saline contrast injection. From this, we predict a reduced incidence of DCS on orbit, although the incidence of predicted mild DCS still remains larger than that encountered on orbit.

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

1993-01-01

376

Gas phase chemistry of dinitramide and nitroacetylide ions  

NASA Astrophysics Data System (ADS)

Using the tandem flowing afterglow-selected-ion flow tube, we have examined the basicity, reactivity, electron binding energy and collision-induced dissociation of two novel nitro species, the dinitramide ion (N(NO2)-2) and the nitroacetylide ion (O2NC[triple bond; length as m-dash]C-). Dinitraminic acid is among the strongest known gas phase acids with [Delta]H°acid [less-than-or-equals, slant] 310 kcal mol-1. The conjugate base, dinitramide anion, has a high electron binding energy, is extremely unreactive and is a very poor nucleophile. Collision-induced dissociation of dinitramide anion generates the O2N=N- anion. Nitroacetylene is a moderately strong acid with [Delta]H°acid = 354 ± 4 kcal mol-1; this value is similar to those of other nitro compounds and substituted acetylenes. The nitroacetylide ion is generally unreactive but exhibits a rich chemistry upon reaction with hydrogen sulfide. The anion has a high electron binding energy and generates four ions upon collision-induced dissociation, ONC-, C-2, C2O-, and CN-.

Schmitt, Robert J.; Krempp, Michele; Bierbaum, Veronica M.

1992-09-01

377

Role of hydrophobic interactions and desolvation in determining the structural properties of a model alpha beta peptide.  

PubMed Central

Model AB, a 20-amino acid peptide that was designed to adopt an alpha beta tertiary structure stabilized by hydrophobic interactions between residues in adjacent helical and extended segments, exhibited large pKa shifts of several ionizable groups and slow hydrogen/deuterium exchange rates of nearly all the peptide amide groups [Butcher, D. J., Bruch, M. D. & Moe, G. T. (1995) Biopolymers 36, 109-120]. These properties, which depend on structure and hydration, are commonly observed in larger proteins but are quite unusual for small peptides. To identify which of several possible features of the peptide design are most important in determining these properties, several closely related analogs of Model AB were characterized by CD and NMR spectroscopy. The results show that hydrophobic interactions between adjacent helical and extended segments are structure-determining and have the additional effect of altering water-peptide interactions over much of the peptide surface. These results may have important implications for understanding mechanisms of protein folding and for the design of independently folding peptides.

Butcher, D J; Moe, G R

1996-01-01

378

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

PubMed Central

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

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

2013-01-01

379

Research in Korea on Gas Phase Synthesis and Control of Nanoparticles  

Microsoft Academic Search

Research activity into the gas phase synthesis of nanoparticles has witnessed rapid growth on a worldwide basis, which is also reflected by Korean research efforts. Nanoparticle research is inherently a multi-disciplinary activity involving both science and engineering. In this paper, the recent studies undertaken in Korea on the gas phase synthesis and control of nanoparticles are reviewed. Studies on the

Mansoo Choi

2001-01-01

380

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 ...

381

Gas-Phase Deposition of Polychlorinated Biphenyls (PCBs) to a Water Surface Sampler  

Microsoft Academic Search

In this study a water surface sampler (WSS) was utilized to directly measure gas phase deposition of polychlorinated biphenyls (PCBs). The measured gas phase PCB fluxes averaged about 880 ± 660 ngmd, which was higher than the fluxes calculated using simultaneously measured air and water concentrations for natural surface waters. These large fluxes were due to fact that the measured

YÜCEL TASDEMIR; THOMAS M. HOLSEN

2006-01-01

382

Photofragment fluorescence as a sensitive probe for gas-phase alkali compounds and their photochemistry  

Microsoft Academic Search

Sensitive techniques are needed for the detection of highly corrosive gas-phase alkali compounds in coal gasifier gas turbine streams. We report on the use of photofragment fluorescence as a very sensitive, selective probe for alkali compounds. Photodissociation of a gas-phase alkali compound using a laser at suitably short ultraviolet (uv) wavelengths produces an electronically excited alkali atom. Detection of fluorescence

R. C. Oldenborg; S. L. Baughcum; D. Hof; K. E. Winn

1985-01-01

383

Calculation of CO 2 gas phase diffusion in leaves and its relation to stomatal resistance  

Microsoft Academic Search

A new theory and experimental method was developed to measure the diffusion resistance to CO2 in the gas phase of mesophyll leaf tissue. Excised leaves were placed in a chamber and their net evaporation and CO2 assimilation rates measured at two different ambient pressures. These data were used to calculate CO2 gas phase diffusion resistances. A variety of field grown

J. W. Cary

1981-01-01

384

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

385

WHERE ARE THE LIMITS OF THE GAS-PHASE FLUORESCENCE ON THE POLYCYCLIC AROMATIC COMPOUND ANALYSIS?  

Microsoft Academic Search

The aim of this work has been centered on the development of a detection system which could be useful to determine polycyclic aromatic hydrocarbon (PAH) emissions in power generation processes where PAHs are released to the atmosphere in the gas phase. In this way, a suitable sensor based on gas phase fluorescence spectroscopy was designed to facilitate the PAH analysis,

A. M. Mastral; T. García; J. M. López; R. Murillo; M. S. Callén; M. V. Navarro

2004-01-01

386

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

National Technical Information Service (NTIS)

Gas-phase parasitic reactions among TMG, TMA, and NH3, are investigated by monitoring of the growth rate/incorporation efficiency of GaN and AlN using an in-situ optical reflectometer. It is suggested that gas phase adduct (TMA: NH(sub 3)) reactions not o...

J. Han J. J. Figiel M. H. Crawford M. A. Banas M. E. Bartram

1998-01-01