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Sample records for abundant fragment ions

  1. Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS.

    PubMed

    Gandhi, Tejas; Puri, Pranav; Fusetti, Fabrizia; Breitling, Rainer; Poolman, Bert; Permentier, Hjalmar P

    2012-08-01

    The identification of proteins in proteomics experiments is usually based on mass information derived from tandem mass spectrometry data. To improve the performance of the identification algorithms, additional information available in the fragment peak intensity patterns has been shown to be useful. In this study, we consider the effect of iTRAQ labeling on the fragment peak intensity patterns of singly charged peptides from MALDI tandem MS data. The presence of an iTRAQ-modified basic group on the N-terminus leads to a more pronounced set of b-ion peaks and distinct changes in the abundance of specific peptide types. We performed a simple intensity prediction by using a decision-tree machine learning approach and were able to show that the relative ion abundance in a spectrum can be correctly predicted and distinguished from closely related sequences. This information will be useful for the development of improved method-specific intensity-based protein identification algorithms. PMID:22770492

  2. Fragmentation pathways of polymer ions.

    PubMed

    Wesdemiotis, Chrys; Solak, Nilüfer; Polce, Michael J; Dabney, David E; Chaicharoen, Kittisak; Katzenmeyer, Bryan C

    2011-01-01

    Tandem mass spectrometry (MS/MS) is increasingly applied to synthetic polymers to characterize chain-end or in-chain substituents, distinguish isobaric and isomeric species, and determine macromolecular connectivities and architectures. For confident structural assignments, the fragmentation mechanisms of polymer ions must be understood, as they provide guidelines on how to deduce the desired information from the fragments observed in MS/MS spectra. This article reviews the fragmentation pathways of synthetic polymer ions that have been energized to decompose via collisionally activated dissociation (CAD), the most widely used activation method in polymer analysis. The compounds discussed encompass polystyrenes, poly(2-vinyl pyridine), polyacrylates, poly(vinyl acetate), aliphatic polyester copolymers, polyethers, and poly(dimethylsiloxane). For a number of these polymers, several substitution patterns and architectures are considered, and questions regarding the ionization agent and internal energy of the dissociating precursor ions are also addressed. Competing and consecutive dissociations are evaluated in terms of the structural insight they provide about the macromolecular structure. The fragmentation pathways of the diverse array of polymer ions examined fall into three categories, viz. (1) charge-directed fragmentations, (2) charge-remote rearrangements, and (3) charge-remote fragmentations via radical intermediates. Charge-remote processes predominate. Depending on the ionizing agent and the functional groups in the polymer, the incipient fragments arising by pathways (1)-(3) may form ion-molecule complexes that survive long enough to permit inter-fragment hydrogen atom, proton, or hydride transfers. PMID:20623599

  3. Heavy Ion Fragmentation Experiments at the Bevatron

    NASA Technical Reports Server (NTRS)

    Heckman, H. H.

    1975-01-01

    Fragmentation processes of heavy nuclei in matter using the heavy-ion capability of the Bevatron were studied. The purpose was to obtain the single particle inclusive spectra of secondary nuclei produced at 0 deg by the fragmentation of heavy ion beam projectiles. The process being examined is B+T yields F + anything, where B is the beam nucleus, T is the target nucleus, and F is the detected fragment. The fragments F are isotopically identified by experimental procedures involving magnetic analysis, energy loss and time-of-flight measurements. Attempts were also made to: (1) measure the total and partial production cross section for all isotopes, (2) test the applicability of high-energy multi-particle interaction theory to nuclear fragmentation, (3) apply the cross-section data and fragmentation probabilities to cosmic ray transport theory, and (4) search for systematic behavior of fragment production as a means to improve existing semi-empirical theories of cross sections.

  4. Fragmentation of Macromolecules Resulting from Ion Impact

    NASA Astrophysics Data System (ADS)

    Storey, D. M.; Dubois, R. D.

    1997-04-01

    Ion induced fragmentation of macromolecules is being investigated by bombarding various amino acids, which have been deposited on solid substrates, with few-keV singly-charged ions. Ionized particles, ejected from the target, are extracted with an electric field and time-of-flight mass spectroscopy is used to determine the degree of ionization and fragmentation which has occured. The goal of this study is to investigate how macromolecules respond to different energy deposition mechanisms. For example, the patterns we observe indicates that slow, low-charged ions primarily remove electrons from the molecule, thus producing varying degrees of ionization for the entire molecule. In contrast, for slow, highly-charged ions, where the potential energy of the incoming ion is extremely large, considerable fragmentation and ejection of intact molecules is observed(C. Ruehliche, D. Schneider, R. DuBois and R. Balhorn, Nucl. Inst. and Meth. (in press) 1997.). Data for various macromolecules will be presented and discussed.

  5. Heavy ion fragmentation experiments at the bevatron

    NASA Technical Reports Server (NTRS)

    Heckman, H. H.

    1976-01-01

    Collaborative research efforts to study the fragmentation processes of heavy nuclei in matter using heavy ion beams of the Bevatron/Bevalac are described. The goal of the program is to obtain the single particle inclusive spectra of secondary nuclei produced at 0 deg by the fragmentation of heavy ion beam projectiles. The process being examined is B+T yields F + anything, where B is the beam nucleus, T is the target nucleus, and F is the detected fragment. The fragments F are isotopically identified by experimental procedures involving magnetic analysis, energy loss and time-of-flight measurements. Effects were also made to: (a) study processes of heavy nuclei in matter, (b) measure the total and partial production cross section for all isotopes, (c) test the applicability of high energy multiparticle interaction theory to nuclear fragmentation, (d) apply the cross section data and fragmentation probabilities to cosmic ray transport theory, and (e) search for systematic behavior of fragment production as a means to improve existing semi-empirical theories of cross-sections.

  6. Relativistic heavy ion fragmentation at HISS (Heavy Ion Spectrometer System)

    SciTech Connect

    Tull, C.E.

    1990-10-01

    An experiment was conducted at the Lawrence Berkeley Laboratory to measure projectile fragmentation of relativistic heavy ions. Charge identification was obtained by the use of a Cerenkov Hodoscope operating above the threshold for total internal reflection, while velocity measurement was performed by use of a second set of Cerenkov radiators operating at the threshold for total internal reflection. Charge and mass resolution for the system was {sigma}{sub Z} = 0.2 e and {sigma}{sub A} = 0.2 u. Measurements of the elemental and isotopic production cross sections for the fragmentation of {sup 40}Ar at 1.65{center dot}A GeV have been compared with an Abrasion-Ablation Model based on the evaporation computer code GEMINI. The model proves to be an accurate predictor of the cross sections for fragments between Chlorine and Boron. The measured cross section were reproduced using simple geometry with charge dispersions induced by zero-point vibrations of the giant dipole resonance for the prompt abrasion stage, and injecting an excitation energy spectrum based on a final state interaction with scaling factor E{sub fsi} = 38.8 MeV/c. Measurement of the longitudinal momentum distribution widths for projectile fragments are consistent with previous experiment and can be interpreted as reflecting the Fermi momentum distribution in the initial projectile nucleus. Measurement of the transverse momentum indicate an additional, unexplained dependence of the reduced momentum widths on fragment mass. This dependence has the same sign and similar slope to previously measured fragments of {sup 139}La, and to predictions based on phase-space constraints on the final state of the system.

  7. High Abundance of Ions in Cosmic Ices

    NASA Technical Reports Server (NTRS)

    Gudipati, Murthy S.; Allamandola, Louis J.; Fonda, Mark (Technical Monitor)

    2002-01-01

    Water-rich, mixed molecular ices and polycyclic aromatic hydrocarbons (PAHs) are common throughout interstellar molecular clouds and the Solar System. Vacuum ultraviolet (VUV) irradiation and particle bombardment of these abiotic ices produces complex organic species, including important biogenic molecules such as amino acids and functionalized PAHs which may have played a role in the origin of life. This ability of such water-rich, oxygen dominated ices to promote production of complex organic species is surprising and points to an important, unusual, but previously overlooked mechanism at play within the ice. Here we report the nature of this mechanism using electronic spectroscopy. VUV-irradiation of PAH/H2O ices leads to an unprecedented and efficient (greater than 70 %) conversion of the neutral PAHs to their cation form (PAH+). Further, these H2O/PAH+ ices are stabile at temperatures below 50 K, a temperature domain common throughout interstellar clouds and the Solar System. Between 50 and 125 K they react to form the complex organics. In view of this, we conclude that charged PAHs and other molecular ions should be common and abundant in many cosmic ices. The chemical, spectroscopic and physical properties of these ion-rich ices can be of fundamental importance for objects as diverse as comets, planets, and molecular clouds and may account for several poorly understood phenomena associated with each of these object classes.

  8. DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Neumann, Elizabeth K.; Solouki, Touradj

    2015-08-01

    Collision-induced dissociation (CID) of m/z-isolated w type fragment ions and an intact 5' phosphorylated DNA oligonucleotide generated rearranged product ions. Of the 21 studied w ions of various nucleotide sequences, fragment ion sizes, and charge states, 18 (~86%) generated rearranged product ions upon CID in a Synapt G2-S HDMS (Waters Corporation, Manchester, England, UK) ion mobility-mass spectrometer. Mass spectrometry (MS), ion mobility spectrometry (IMS), and theoretical modeling data suggest that purine bases can attack the free 5' phosphate group in w type ions and 5' phosphorylated DNA to generate sequence permuted [phosphopurine]- fragment ions. We propose and discuss a potential mechanism for generation of rearranged [phosphopurine]- and complementary y-B type product ions.

  9. Isomeric signatures in the fragmentation of pyridazine and pyrimidine induced by fast ion impact

    SciTech Connect

    Wolff, Wania Luna, Hugo; Montenegro, Eduardo C.

    2015-07-28

    We present fast proton impact induced fragmentations of pyrimidine and pyridazine as an experimental resource to investigate isomeric signatures. Major isomeric imprints are identified for few fragment ions and differences of more than an order of magnitude for the cross sections of fragments of the same mass were measured. The observation of the molecular structure of these isomers gives no apparent indication for the reasons for such substantial differences. It is verified that the simple displacement of the position of one nitrogen atom strongly inhibits or favors the production of some ionic fragment species. The dependency of the fragmentation cross sections on the proton impact energy, investigated by means of time of flight mass spectroscopy and of a model calculation based in first order perturbation theory, allows us to disentangle the complex collision dynamics of the ionic fragments. The proton-induced fragmentation discriminates rather directly the association between a molecular orbital ionization and the fragment-ions creation and abundance, as well as how the redistribution of the energy imparted to the molecules takes place, triggering not only single but also double vacancy and leads to specific fragmentation pathways.

  10. Timeframe Dependent Fragment Ions Observed in In-Source Decay Experiments with β-Casein Using MALDI MS

    NASA Astrophysics Data System (ADS)

    Sekiya, Sadanori; Nagoshi, Keishiro; Iwamoto, Shinichi; Tanaka, Koichi; Takayama, Mitsuo

    2015-09-01

    The fragment ions observed with time-of-flight (TOF) and quadrupole ion trap (QIT) TOF mass spectrometers (MS) combined with matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) experiments of phosphorylated analytes β-casein and its model peptide were compared from the standpoint of the residence timeframe of analyte and fragment ions in the MALDI ion source and QIT cell. The QIT-TOF MS gave fragment c-, z'-, z-ANL, y-, and b-ions, and further degraded fragments originating from the loss of neutrals such as H2O, NH3, CH2O (from serine), C2H4O (from threonine), and H3PO4, whereas the TOF MS merely showed MALDI source-generated fragment c-, z'-, z-ANL, y-, and w-ions. The fragment ions observed in the QIT-TOF MS could be explained by the injection of the source-generated ions into the QIT cell or a cooperative effect of a little internal energy deposition, a long residence timeframe (140 ms) in the QIT cell, and specific amino acid effects on low-energy CID, whereas the source-generated fragments (c-, z'-, z-ANL, y-, and w-ions) could be a result of prompt radical-initiated fragmentation of hydrogen-abundant radical ions [M + H + H]+ and [M + H - H]- within the 53 ns timeframe, which corresponds to the delayed extraction time. The further degraded fragment b/y-ions produced in the QIT cell were confirmed by positive- and negative-ion low-energy CID experiments performed on the source-generated ions (c-, z'-, and y-ions). The loss of phosphoric acid (98 u) from analyte and fragment ions can be explained by a slow ergodic fragmentation independent of positive and negative charges.

  11. Formation and fragmentation of quadruply charged molecular ions by intense femtosecond laser pulses.

    PubMed

    Yatsuhashi, Tomoyuki; Nakashima, Nobuaki

    2010-07-22

    We investigated the formation and fragmentation of multiply charged molecular ions of several aromatic molecules by intense nonresonant femtosecond laser pulses of 1.4 mum with a 130 fs pulse duration (up to 2 x 10(14) W cm(-2)). Quadruply charged states were produced for 2,3-benzofluorene and triphenylene molecular ion in large abundance, whereas naphthalene and 1,1'-binaphthyl resulted only in up to triply charged molecular ions. The laser wavelength was nonresonant with regard to the electronic transitions of the neutral molecules, and the degree of fragmentation was strongly correlated with the absorption of the singly charged cation radical. Little fragmentation was observed for naphthalene (off-resonant with cation), whereas heavy fragmentation was observed in the case of 1,1'-binaphthyl (resonant with cation). The degree of H(2) (2H) and 2H(2) (4H) elimination from molecular ions increased as the charge states increased in all the molecules examined. A striking difference was found between triply and quadruply charged 2,3-benzofluorene: significant suppression of molecular ions with loss of odd number of hydrogen was observed in the quadruply charged ions. The Coulomb explosion of protons in the quadruply charged state and succeeding fragmentation resulted in the formation of triply charged molecular ions with an odd number of hydrogens. The hydrogen elimination mechanism in the highly charged state is discussed. PMID:20578764

  12. Anatomy of a cluster IDP. Part 2: Noble gas abundances, trace element geochemistry, isotopic abundances, and trace organic chemistry of several fragments from L2008#5

    NASA Technical Reports Server (NTRS)

    Thomas, K. L.; Clemett, S. J.; Flynn, G. J.; Keller, L. P.; Mckay, David S.; Messenger, S.; Nier, A. O.; Schlutter, D. J.; Sutton, S. R.; Walker, R. M.

    1994-01-01

    The topics discussed include the following: noble gas content and release temperatures; trace element abundances; heating summary of cluster fragments; isotopic measurements; and trace organic chemistry.

  13. Long-term landscape change and bird abundance in Amazonian rainforest fragments.

    PubMed

    Stouffer, Philip C; Bierregaard, Richard O; Strong, Cheryl; Lovejoy, Thomas E

    2006-08-01

    The rainforests of the Amazon basin are being cut by humans at a rate >20,000 km2/year leading to smaller and more isolated patches of forest, with remaining fragments often in the range of 1-100 ha. We analyzed samples of understory birds collected over 20 years from a standardized mist-netting program in 1- to 100-ha rainforest fragments in a dynamic Amazonian landscape near Manaus, Brazil. Across bird guilds, the condition of second growth immediately surrounding fragments was often as important as fragment size or local forest cover in explaining variation in abundance. Some fragments surrounded by 100 m of open pasture showed reductions in insectivorous bird abundance of over 95%, even in landscapes dominated by continuous forest and old second growth. These extreme reductions may be typical throughout Amazonia in small (< or =10 ha), isolated fragments of rainforest. Abundance for some guilds returned to preisolation levels in 10- and 100-ha fragments connected to continuous forest by 20-year-old second growth. Our results show that the consequences of Amazonian forest loss cannot be accurately described without explicit consideration of vegetation dynamics in matrix habitat. Any dichotomous classification of the landscape into 'forest" and "nonforest" misses essential information about the matrix. PMID:16922237

  14. Fragmentation efficiencies of peptide ions following low energy collisional activation

    NASA Astrophysics Data System (ADS)

    Summerfield, Scott G.; Gaskell, Simon J.

    1997-11-01

    Low energy fragmentations of protonated peptides in the gas phase are generally attributed to charge-directed processes. The extent and location of peptide backbone fragmentation is accordingly influenced by the extent to which charge is sequestered on amino acid side-chains. We describe systematic studies of the efficiencies of decomposition of peptide ions to assess in particular the influence of the presence of basic amino acid residues and of the protonation state. In a set of analogues containing two arginine, two histidine or two lysine residues, the extent of fragmentation of [M + 2H]2+ ions decreases with increased basicity, reflecting decreased backbone protonation. The collisionally activated dissociation of multiply protonated melittin ions shows an increase in fragmentation efficiency with higher charge state (using activation conditions which are similar for each charge state). For a single charge state, acetylation of primary amine groups increases fragmentation efficiency, consistent with the reduction in basicity of lysine side-chains. Conversion of arginine residues to the less basic dimethylpyrimidylornithine, however, decreases fragmentation efficiency, suggesting more effective sequestering of ionizing protons; the effect may be attributable to a disfavouring of proton-bridged structures but this hypothesis requires further study. Preliminary data for the decompositions of [M- 2H]2- ions derived from peptides containing two acidic residues suggest that the sequestration of charge away from the backbone is again detrimental to efficient fragmentation. Apparently diagnostic cleavages adjacent to aspartic acid residues are observed.

  15. Effects of Habitat Fragmentation on Abundance, Larval Food and Parasitism of a Spider-Hunting Wasp

    PubMed Central

    Coudrain, Valérie; Herzog, Felix; Entling, Martin H.

    2013-01-01

    Habitat fragmentation strongly affects species distribution and abundance. However, mechanisms underlying fragmentation effects often remain unresolved. Potential mechanisms are (1) reduced dispersal of a species or (2) altered species interactions in fragmented landscapes. We studied if abundance of the spider-hunting and cavity-nesting wasp Trypoxylon figulus Linnaeus (Hymenoptera: Crabronidae) is affected by fragmentation, and then tested for any effect of larval food (bottom up regulation) and parasitism (top down regulation). Trap nests of T. figulus were studied in 30 agricultural landscapes of the Swiss Plateau. The sites varied in the level of isolation from forest (adjacent, in the open landscape but connected, isolated) and in the amount of woody habitat (from 4 % to 74 %). We recorded wasp abundance (number of occupied reed tubes), determined parasitism of brood cells and analysed the diversity and abundance of spiders that were deposited as larval food. Abundances of T. figulus were negatively related to forest cover in the landscape. In addition, T. figulus abundances were highest at forest edges, reduced by 33.1% in connected sites and by 79.4% in isolated sites. The mean number of spiders per brood cell was lowest in isolated sites. Nevertheless, structural equation modelling revealed that this did not directly determine wasp abundance. Parasitism was neither related to the amount of woody habitat nor to isolation and did not change with host density. Therefore, our study showed that the abundance of T. figulus cannot be fully explained by the studied trophic interactions. Further factors, such as dispersal and habitat preference, seem to play a role in the population dynamics of this widespread secondary carnivore in agricultural landscapes. PMID:23516622

  16. Multi-scale models of grassland passerine abundance in a fragmented system in Wisconsin

    USGS Publications Warehouse

    Renfrew, R.B.; Ribic, C.A.

    2008-01-01

    Fragmentation of grasslands has been implicated in grassland bird population declines. Multi-scale models are being increasingly used to assess potential factors that influence grassland bird presence, abundance, and productivity. However, studies rarely assess fragmentation metrics, and seldom evaluate more than two scales or interactions among scales. We evaluated the relative importance of characteristics at multiple scales to patterns in relative abundance of Savannah Sparrow (Passerculus sandwichensis), Grasshopper Sparrow (Ammodramus savannarum), Eastern Meadowlark (Sturnella magna), and Bobolink (Dolichonyx oryzivorus). We surveyed birds in 74 southwestern Wisconsin pastures from 1997 to 1999 and compared models with explanatory variables from multiple scales: within-patch vegetation structure (microhabitat), patch (macrohabitat), and three landscape extents. We also examined interactions between macrohabitat and landscape factors. Core area of pastures was an important predictor of relative abundance, and composition of the landscape was more important than configuration. Relative abundance was frequently higher in pastures with more core area and in landscapes with more grassland and less wooded area. The direction and strength of the effect of core pasture size on relative abundance changed depending on amount of wooded area in the landscape. Relative abundance of grassland birds was associated with landscape variables more frequently at the 1200-m scale than at smaller scales. To develop better predictive models, parameters at multiple scales and their interactive effects should be included, and results should be evaluated in the context of microhabitat variability, landscape composition, and fragmentation in the study area. ?? 2007 Springer Science+Business Media B.V.

  17. The fragmentation pattern of 1,4-dioxane ion

    NASA Astrophysics Data System (ADS)

    Dunbar, Robert C.; Huang, Fu-Shiuan; Klippenstein, Stephen J.

    1993-09-01

    Fragmentation of 1,4-dioxane ions at low internal energies was studied by photodissociation in the ion cyclotron resonance (ICR) ion trap. Branching ratios, rate--energy curves and kinetic parameters were assigned for the m/z 58, 57 and 45 fragment ions. M/z 58 is formed through a slightly tight rate-limiting transition state (E0 = 1.46 eV, [Delta]S+1000K = -1.4 e.u.) which probably corresponds to rupture of the dioxane ring. M/z 45 is formed through a tight transition state (E0 = 1.42 eV, [Delta]S++1000K = -10.9 eV) which presumably reflects a cyclic rearrangement pathway. The kinetic data for formation of 57 are almost equally well fitted by assuming competitive (RRKM) fragmentation from the parent ion, or assuming sequential fragmentation through an intermediate 58 ion. If the mechanism is solely competitive, the transition state is extraordinary loose (E0 = 1.87 eV, [Delta]S++1000K = 14.8 e.u.) which would be very surprising for this rearrangement dissociation. Accordingly we lean toward a sequential dissociation mechanism leading to the 57 product, and suggest further experimental testing of this possibility via structural studies of the 57 fragment.

  18. Fragmentation of peptide negative molecular ions induced by resonance electron capture

    PubMed Central

    Vasil’ev, Yury V.; Figard, Benjamin J.; Morré, Jeff; Deinzer, Max L.

    2009-01-01

    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 zn−1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M–H]− 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 cn+1 ions. Instead, cn ions arose without hydrogen∕proton transfer albeit with lower abundances than that observed for zn−1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the cn ions than for the zn−1 ions. The mechanisms for the N–Cα bond cleavage are discussed. PMID:19655877

  19. Optical model analyses of heavy ion fragmentation in hydrogen targets

    NASA Technical Reports Server (NTRS)

    Townsend, Lawrence W.

    1994-01-01

    Quantum-mechanical optical-model methods for calculating cross sections for the fragmentation of high-energy heavy ions by hydrogen targets are presented. The cross sections are calculated with a knockout-ablation collision formalism which has no arbitrary fitting parameters. Predictions of elemental production cross sections from the fragmentation of 1.2A Ge(V(La-139) nuclei and of isotope production cross sections from the fragmentation of 400A MeV(S-32) nuclei are in good agreement with recently reported experimental measurements.

  20. Hadronic and electromagnetic fragmentation of ultrarelativistic heavy ions at LHC

    NASA Astrophysics Data System (ADS)

    Braun, H. H.; Fassò, A.; Ferrari, A.; Jowett, J. M.; Sala, P. R.; Smirnov, G. I.

    2014-02-01

    Reliable predictions of yields of nuclear fragments produced in electromagnetic dissociation and hadronic fragmentation of ion beams are of great practical importance in analyzing beam losses and interactions with the beam environment at the Large Hadron Collider (LHC) at CERN as well as for estimating radiation effects of galactic cosmic rays on the spacecraft crew and electronic equipment. The model for predicting the fragmentation of relativistic heavy ions is briefly described, and then applied to problems of relevance for LHC. The results are based on the fluka code, which includes electromagnetic dissociation physics and dpmjet-iii as hadronic event generator. We consider the interaction of fully stripped lead ions with nuclei in the energy range from about one hundred MeV to ultrarelativistic energies. The yields of fragments close in the mass and charge to initial ions are calculated. The approach under discussion provides a good overall description of Pb fragmentation data at 30 and 158A GeV as well as recent LHC data for √sNN =2.76 TeV Pb-Pb interactions. Good agreement with the calculations in the framework of different models is found. This justifies application of the developed simulation technique both at the LHC injection energy of 177A GeV and at its collision energies of 1.38, 1.58, and 2.75A TeV, and gives confidence in the results obtained.

  1. Fragmentation of Multiply-Charged Intact Protein Ions Using MALDI TOF-TOF Mass Spectrometry

    PubMed Central

    Liu, Zhaoyang; Schey, Kevin L.

    2008-01-01

    Top down proteomics in a TOF-TOF instrument was further explored by examining the fragmentation of multiply charged precursors ions generated by matrix-assisted laser desorption ionization. Evaluation of sample preparation conditions allowed selection of solvent/matrix conditions and sample deposition methods to produce sufficiently abundant doubly and triply charged precursor ions for subsequent CID experiments. As previously reported, preferential cleavage was observed at sites C-terminal to acidic residues and N-terminal to proline residues for all ions examined. An increase in non-preferential fragmentation as well as additional low mass product ions was observed in the spectra from multiply charged precursor ions providing increased sequence coverage. This enhanced fragmentation from multiply charged precursor ions became increasingly important with increasing protein molecular weight and facilitates protein identification using database searching algorithms. The useable mass range for MALDI TOF-TOF analysis of intact proteins has been expanded to 18.2 kDa using this approach. PMID:17693096

  2. Travelling-wave ion mobility and negative ion fragmentation of high-mannose N-glycans.

    PubMed

    Harvey, David J; Scarff, Charlotte A; Edgeworth, Matthew; Struwe, Weston B; Pagel, Kevin; Thalassinos, Konstantinos; Crispin, Max; Scrivens, Jim

    2016-03-01

    The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility mass spectrometry for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra, and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed, but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers or anomers were being separated. Collision cross sections of the isomers in positive and negative fragmentation mode were estimated from travelling-wave ion mobility mass spectrometry data using dextran glycans as calibrant. More complete collision cross section data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross-sectional data, details of the negative ion collision-induced dissociation spectra of all resolved isomers are discussed. PMID:26956389

  3. Richness and Abundance of Ichneumonidae in a Fragmented Tropical Rain Forest.

    PubMed

    Ruiz-Guerra, B; Hanson, P; Guevara, R; Dirzo, R

    2013-10-01

    Because of the magnitude of land use currently occurring in tropical regions, the local loss of animal species due to habitat fragmentation has been widely studied, particularly in the case of vertebrates. Many invertebrate groups and the ichneumonid wasps in particular, however, have been poorly studied in this context, despite the fact that they are one of the most species-rich groups and play an important role as regulators of other insect populations. Here, we recorded the taxonomic composition of ichneumonid parasitoids and assessed their species richness, abundance, similarity, and dominance in the Los Tuxtlas tropical rain forest, Mexico. We compared two forest types: a continuous forest (640 ha) and a forest fragment (19 ha). We sampled ichneumonids using four malaise traps in both forest types during the dry (September-October) and rainy (March-April) seasons. A total of 104 individuals of Ichneumonidae belonging to 11 subfamilies, 18 genera, and 42 species were collected in the continuous forest and 11 subfamilies, 15 genera, and 24 species were collected in the forest fragment. Species richness, abundance, and diversity of ichneumonids were greater in the continuous forest than in the forest fragment. We did not detect differences between seasons. Species rank/abundance curves showed that the ichneumonid community between the forest types was different. Species similarity between forest types was low. The most dominant species in continuous forest was Neotheronia sp., whereas in the forest fragment, it was Orthocentrus sp. Changes in the ichneumonid wasp community may compromise important tropical ecosystem processes. PMID:23949980

  4. Fragmentation of negative ions in a strong laser field

    NASA Astrophysics Data System (ADS)

    Berry, Ben; Jochim, Bethany; Severt, T.; Feizollah, Peyman; Rajput, Jyoti; Hayes, D.; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.

    2016-05-01

    The fragmentation of negative ions in a strong laser field can provide a testing ground for a variety of unique phenomena. For example, anions with a loosely bound electron allow for the study of rescattering phenomena at lower laser intensities than for neutral targets. We study the behavior of keV anion beams in an ultrafast, intense laser field. The use of a fast-beam target facilitates the measurement of neutral fragments. This capability allows us to explore laser-induced dynamics in both ionic and neutral charge states. Using a coincidence 3D momentum imaging technique, we obtain the full 3D momentum of all nuclear fragments. In this preliminary work, we study atomic (H-) and molecular (H2-,F2-)systems with the goal of identifying and controlling their fragmentation pathways. This work was supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy.

  5. Polarization dependent fragmentation of ions produced by laser desorption from nanopost arrays.

    PubMed

    Stolee, Jessica A; Vertes, Akos

    2011-05-28

    Tailored silicon nanopost arrays (NAPA) enable controlled and resonant ion production in laser desorption ionization experiments and have been termed nanophotonic ion sources (Walker et al., J. Phys. Chem. C, 2010, 114, 4835-4840). As the post dimensions are comparable to or smaller than the laser wavelength, near-field effects and localized electromagnetic fields are present in their vicinity. In this contribution, we explore the desorption and ionization mechanism by studying how surface derivatization affects ion yields and fragmentation. We demonstrate that by increasing the laser fluence on derivatized NAPA with less polar surfaces that have decreased interaction energy between the structured silicon substrate and the adsorbate, the spectrum changes from exhibiting primarily molecular ions to showing a growing variety and abundance of fragments. The polarization angle of the laser beam had been shown to dramatically affect the ion yields of adsorbates. For the first time, we report that by rotating the plane of polarization of the desorption laser, the internal energy of the adsorbate can also be modulated resulting in polarization dependent fragmentation. This polarization effect also resulted in selective fragmentation of vitamin B(12). To explore the internal energy of NAPA generated ions, the effect of the post aspect ratios on the laser desorption thresholds and on the internal energy of a preformed ion was studied. Elevated surface temperatures and enhanced near fields in the vicinity of high aspect ratio posts are thought to contribute to desorption and ionization from NAPA. Comparison of the fluence dependence of the internal energies of ions produced from nanoporous silicon and NAPA substrates indicates that surface restructuring or transient melting by the desorption laser is a prerequisite for the former but not for the latter. PMID:21437297

  6. Hybrid molecular ions emitted from CO-NH3 ice bombarded by fission fragments

    NASA Astrophysics Data System (ADS)

    Martinez, R.; Ponciano, C. R.; Farenzena, L. S.; Iza, P.; Homem, M. G. Pe; Naves de Brito, A.; da Silveira, E. F.; Wien, K.

    2007-05-01

    CO-NH3 ice at 25 K is bombarded by 65 MeV fission fragments and the emitted secondary ions are analyzed by time-of-flight mass spectrometry. The yields of the specific ion species (those formed only from CO or from NH3 molecules) and of the hybrid ion species (formed from both CO and NH3 molecules) are determined as a function of the ice temperature. The time-temperature dependence of desorption yields has been used for secondary ion identification because its behavior characterizes the ion's origin around the sublimation temperature of CO ice (~30 K). The mass spectrum of positive ions measured before CO sublimation is decomposed into three spectra corresponding to CO specific ions, NH3 specific ions and hybrid molecular ions, respectively. The observed spectrum after CO sublimation is very similar to that of a pure NH3 specific spectrum. The total yield of all positive hybrid molecular ions over 600 u mass range is found to be about 2 ions/impact: 20% of this is attributed to N and NH3 containing ions and 80% are ions having the CnOmHl+ structure. The ions Cnions is about 20 times lower than that of positive ions, the most abundant species being the cyanide ion CN-. Observation of cluster ions based on (HCN)n indicates the formation of hydrogen cyanide.

  7. FIRST experiment: Fragmentation of Ions Relevant for Space and Therapy

    NASA Astrophysics Data System (ADS)

    Agodi, C.; Abou-Haidar, Z.; Alvarez, M. A. G.; Aumann, T.; Balestra, F.; Battistoni, G.; Bocci, A.; Bohlen, T. T.; Bondì, M.; Boudard, A.; Brunetti, A.; Carpinelli, M.; Cappuzzello, F.; Cavallaro, M.; Carbone, D.; Cirrone, G. A. P.; Cortes-Giraldo, M. A.; Cuttone, G.; De Napoli, M.; Durante, M.; Fernandez-Garcia, J. P.; Finck, C.; Foti, A.; Gallardo, M. I.; Golosio, B.; Iarocci, E.; Iazzi, F.; Ickert, G.; Introzzi, R.; Juliani, D.; Krimmer, J.; Kurz, N.; Labalme, M.; Lavagno, A.; Leifels, Y.; Le Fevre, A.; Leray, S.; Marchetto, F.; Monaco, V.; Morone, M. C.; Nicolosi, D.; Oliva, P.; Paoloni, A.; Patera, V.; Piersanti, L.; Pleskac, R.; Quesada, J. M.; Randazzo, N.; Romano, F.; Rossi, D.; Rosso, V.; Rousseau, M.; Sacchi, R.; Sala, P.; Sarti, A.; Scheidenberger, C.; Schuy, C.; Sciubba, A.; Sfienti, C.; Simon, H.; Sipala, V.; Spiriti, E.; Stuttge, L.; Tropea, S.; Younis, H.

    2013-03-01

    Nuclear fragmentation processes are relevant in different fields of basic research and applied physics and are of particular interest for tumor therapy and for space radiation protection applications. The FIRST (Fragmentation of Ions Relevant for Space and Therapy) experiment at SIS accelerator of GSI laboratory in Darmstadt, has been designed for the measurement of different ions fragmentation cross sections at different energies between 100 and 1000 MeV/nucleon. The experiment is performed by an international collaboration made of institutions from Germany, France, Italy and Spain. The experimental apparatus is partly based on an already existing setup made of the ALADIN magnet, the MUSIC IV TPC, the LAND2 neutron detector and the TOFWALL scintillator TOF system, integrated with newly designed detectors in the interaction Region (IR) around the carbon removable target: a scintillator Start Counter, a Beam Monitor drift chamber, a silicon Vertex Detector and a Proton Tagger for detection of light fragments emitted at large angles (KENTROS). The scientific program of the FIRST experiment started on summer 2011 with the study of the 400 MeV/nucleon 12C beam fragmentation on thin (8mm) carbon target.

  8. Composition and abundance of small mammal communities in forest fragments and vegetation corridors in Southern Minas Gerais, Brazil.

    PubMed

    Mesquita, Andréa O; Passamani, Marcelo

    2012-09-01

    Habitat fragmentation leads to isolation and reduce habitat areas, in addition to a series of negative effects on natural populations, affecting richness, abundance and distribution of animal species. In such a context, habitat corridors serve as an alternative for connectivity in fragmented landscapes, minimizing the effects of structural isolation of different habitat areas. This study evaluated the richness, composition and abundance of small mammal communities in forest fragments and in the relevant vegetation corridors that connect these fragments, located in Southern Minas Gerais, Southeastern Brazil. Ten sites were sampled (five forest fragments and five vegetation corridors) using the capture-mark-recapture method, from April 2007-March 2008. A total sampling effort of 6 300 trapnights resulted in 656 captures of 249 individuals. Across the 10 sites sampled, 11 small mammal species were recorded. Multidimensional scaling (MDS) ordinations and ANOSIM based on the composition of small mammal communities within the corridor and fragment revealed a qualitative difference between the two environments. Regarding abundance, there was no significant difference between corridors and fragments. In comparing mean values of abundance per species in each environment, only Cerradomys subflavus showed a significant difference, being more abundant in the corridor environment. Results suggest that the presence of several small mammal species in the corridor environment, in relatively high abundances, could indicate corridors use as habitat, though they might also facilitate and/or allow the movement of individuals using different habitat patches (fragments). PMID:23025102

  9. Heavy-ion fragmentation studies in thick water absorbers

    NASA Technical Reports Server (NTRS)

    Shavers, M. R.; Miller, J.; Schimmerling, W.; Wilson, J. W.; Townsend, L. W.

    1993-01-01

    Proposed long-term space missions could expose crewmembers to significant fluxes of galactic cosmic radiation (GCR) particles and secondary particles created from nuclear collisions. An assessment of radiobiological risks is dependent upon an accurate description of the charged-particle radiation field inside the human body. As shield thickness increases and the incident ions are slowed, the production of secondary particles contributes an increasingly significant fraction of the total dose until eventually secondary particles become more important than the primary particles. The nuclear mean free path of the GCR ions (which usually have nuclear charge between 1 (protons) and 26 (iron), both inclusive) are comparable with thicknesses typical of spacecraft structures and the human body. Collisions in these media will create projectile and target fragments with charge less than that of the primary particle, and each interaction event can have a multiplicity of more than one emerging interaction product. Projectile fragments usually continue on with very nearly the velocity of the primary ion (the so-called straightahead approximation). Having sufficient energy, the fragments may collide with atomic nuclei in thick shields and create a second generation of fragments, and so on. Target fragments are emitted from a struck nucleus, usually with much lower energy than projectile fragments and nearly isotropically in the rest frame of the absorbing medium. The resulting spectrum of particles and their energy loss rates will be very different from that in the unshielded environment, will determine the radiobiological impact on exposed living tissues -- whether in space or in ground-based radiobiology experiments -- and will play an important role in radiation effects on microelectronics.

  10. Negative Ion CID Fragmentation of O-linked Oligosaccharide Aldoses—Charge Induced and Charge Remote Fragmentation

    NASA Astrophysics Data System (ADS)

    Doohan, Roisin A.; Hayes, Catherine A.; Harhen, Brendan; Karlsson, Niclas Göran

    2011-06-01

    Collision induced dissociation (CID) fragmentation was compared between reducing and reduced sulfated, sialylated, and neutral O-linked oligosaccharides. It was found that fragmentation of the [M - H]- ions of aldoses with acidic residues gave unique Z-fragmentation of the reducing end GalNAc containing the acidic C-6 branch, where the entire C-3 branch was lost. This fragmentation pathway, which is not seen in the alditols, showed that the process involved charge remote fragmentation catalyzed by a reducing end acidic anomeric proton. With structures containing sialic acid on both the C-3 and C-6 branch, the [M - H]- ions were dominated by the loss of sialic acid. This fragmentation pathway was also pronounced in the [M - 2H]2- ions revealing both the C-6 Z-fragment plus its complementary C-3 C-fragment in addition to glycosidic and cross ring fragmentation. This generation of the Z/C-fragment pairs from GalNAc showed that the charges were not participating in their generation. Fragmentation of neutral aldoses showed pronounced Z-fragmentation believed to be generated by proton migration from the C-6 branch to the negatively charged GalNAc residue followed by charge remote fragmentation similar to the acidic oligosaccharides. In addition, A-type fragments generated by charge induced fragmentation of neutral oligosaccharides were observed when the charge migrated from C-1 of the GalNAc to the GlcNAc residue followed by rearrangement to accommodate the 0,2A-fragmentation. LC-MS also showed that O-linked aldoses existed as interchangeable α/β pyranose anomers, in addition to a third isomer (25% of the total free aldose) believed to be the furanose form.

  11. Optical model calculations of heavy-ion target fragmentation

    NASA Technical Reports Server (NTRS)

    Townsend, L. W.; Wilson, J. W.; Cucinotta, F. A.; Norbury, J. W.

    1986-01-01

    The fragmentation of target nuclei by relativistic protons and heavy ions is described within the context of a simple abrasion-ablation-final-state interaction model. Abrasion is described by a quantum mechanical formalism utilizing an optical model potential approximation. Nuclear charge distributions of the excited prefragments are calculated by both a hypergeometric distribution and a method based upon the zero-point oscillations of the giant dipole resonance. Excitation energies are estimated from the excess surface energy resulting from the abrasion process and the additional energy deposited by frictional spectator interactions of the abraded nucleons. The ablation probabilities are obtained from the EVA-3 computer program. Isotope production cross sections for the spallation of copper targets by relativistic protons and for the fragmenting of carbon targets by relativistic carbon, neon, and iron projectiles are calculated and compared with available experimental data.

  12. A First Survey on the Abundance of Plastics Fragments and Particles on Two Sandy Beaches in Kuching, Sarawak, Malaysia

    NASA Astrophysics Data System (ADS)

    Noik, V. James; Mohd Tuah, P.

    2015-04-01

    Plastic fragments and particles as an emerging environmental contaminant and pollutant are gaining scientific attention in the recent decades due to the potential threats on biota. This study aims to elucidate the presence, abundance and temporal change of plastic fragments and particles from two selected beaches, namely Santubong and Trombol in Kuching on two sampling times. Morphological and polymer identification assessment on the recovered plastics was also conducted. Overall comparison statistical analysis revealed that the abundance of plastic fragments/debris on both of sampling stations were insignificantly different (p>0.05). Likewise, statistical analysis on the temporal changes on the abundance yielded no significant difference for most of the sampling sites on each respective station, except STB-S2. Morphological studies revealed physical features of plastic fragments and debris were diverse in shapes, sizes, colors and surface fatigues. FTIR fingerprinting analysis shows that polypropylene and polyethylene were the dominant plastic polymers debris on both beaches.

  13. Temporal Variability of Ion Acceleration and Abundances in Solar Flares

    NASA Technical Reports Server (NTRS)

    Shih, Albert

    2011-01-01

    Solar flares accelerate both ions and electrons to high energies, and their X-ray and gamma-ray signatures not only probe the relationship between their respective acceleration, but also allow for the measurement of accelerated and ambient abundances. RHESSI observations have shown a striking close linear correlation of gamma-ray line fluence from accelerated ions greater than approximately 20 MeV and bremsstrahlung emission from relativistic accelerated electrons greater than 300 keV, when integrated over complete flares, suggesting a common acceleration mechanism. SMM/GRS observations, however, show a weaker correlation, and this discrepancy might be associated with previously observed electron-rich episodes within flares and/or temporal variability of gamma-ray line fluxes over the course of flares. We use the latest RHESSI gamma-ray analysis techniques to study the temporal behavior of the RHESSI flares, and determine what changes can be attributed to an evolving acceleration mechanism or to evolving abundances. We also discuss possible explanations for changing abundances.

  14. Temporal Variability of Ion Acceleration and Abundances in Solar Flares

    NASA Technical Reports Server (NTRS)

    Shih, Albert Y.

    2012-01-01

    solar flares accelerate both ions and electrons to high energies, and their x-ray and gamma-ray signatures not only probe the relationship between their respective acceleration, but also allow for the measurement of accelerated and ambient abundances. RHESSI observations have shown a striking close linear correlation of gamma-ray line fluence from accelerated ions > approx 20 MeV and bremsstrahlung emission from relativistic accelerated electrons >300 kev, when integrated over complete flares, suggesting a common acceleration mechanism. SMM/GRS observations, however, show a weaker correlation, and this discrepancy might be associated with previously observed electron-rich episodes within flares and/or temporal variability of gamma-ray line fluxes over the course of flares. We use the latest RHESSI gamma-ray analysis techniques to study the temporal behavior of the RHESSI flares, and determine what changes can be attributed to an evolving acceleration mechanism or to evolving abundances. We also discuss possible explanations for changing abundances.

  15. Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation.

    PubMed

    Durbin, Kenneth R; Skinner, Owen S; Fellers, Ryan T; Kelleher, Neil L

    2015-05-01

    Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis. PMID:25716753

  16. Analyzing Internal Fragmentation of Electrosprayed Ubiquitin Ions During Beam-Type Collisional Dissociation

    NASA Astrophysics Data System (ADS)

    Durbin, Kenneth R.; Skinner, Owen S.; Fellers, Ryan T.; Kelleher, Neil L.

    2015-05-01

    Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis.

  17. Secondary Ion Mass Spectrometry of Zeolite Materials: Observation of Abundant Aluminosilicate Oligomers Using an Ion Trap

    SciTech Connect

    Groenewold, Gary Steven; Kessinger, Glen Frank; Scott, Jill Rennee; Gianotto, Anita Kay; Appelhans, Anthony David; Delmore, James Edward

    2000-12-01

    Oligomeric oxyanions were observed in the secondary ion mass spectra (SIMS) of zeolite materials. The oxyanions have the general composition AlmSinO2(m+n)H(m-1)- (m + n = 2 to 8) and are termed dehydrates. For a given mass, multiple elemental compositions are possible because (Al + H) is an isovalent and isobaric substitute for Si. Using 18 keV Ga+ as a projectile, oligomer abundances are low relative to the monomers. Oligomer abundance can be increased by using the polyatomic projectile ReO4- (~5 keV). Oligomer abundance can be further increased using an ion trap (IT-) SIMS; in this instrument, long ion lifetimes (tens of ms) and relatively high He pressure result in significant collisional stabilization and increased high-mass abundance. The dehydrates rapidly react with adventitious H2O present in the IT-SIMS to form mono-, di-, and trihydrates. The rapidity of the reaction and comparison to aluminum oxyanion hydration suggest that H2O adds to the aluminosilicate oxyanions in a dissociative fashion, forming covalently bound product ions. In addition to these findings, it was noted that production of abundant oligomeric aluminosilicates could be significantly increased by substituting the countercation (NH4+) with the larger alkali ions Rb+ and Cs+. This constitutes a useful tactic for generating large aluminosilicate oligomers for surface characterization and ion-molecule reactivity studies.

  18. Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

    2014-01-01

    To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

  19. Modeling the ion abundances in Saturn's inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Fleshman, B. L.; Bagenal, F.; Delamere, P. A.

    2011-12-01

    Water ejected from Enceladus's plumes provides much of the material that fills both the dense H2O torus centered on Enceladus's orbit, as well as Saturn's neutral clouds which extend at least four times farther from Saturn. Photo- and impact ionization transforms a few percent of these neutrals into the ions co-rotating with Saturn's magnetosphere, and charge exchange is responsible for a substantial redistribution among the hydrogen and water-group ions, though it does not alter the overall plasma density. In this paper, we explore ion abundances at Saturn with a chemistry model developed to include all of these processes. Building on our earlier attempts, we now include a source of neutrals from a neutral cloud model, so as to advance our description to include radial and latitudinal variations. At the same time, we now prescribe a radially-varying plasma diffusion coefficient to study the magnetosphere's inability to contain centrifigually-unstable plasma. We also are interested in the effect of hot electrons (102-103 eV) beamed along field lines into the equatorial region chiefly of interest. Our parameter study of radial diffusion and hot-electron flux is anchored to available Cassini CAPS water-group and proton abundances. Preliminary results suggest an injection of ~10 MW by hot electrons, and reveal promising radial trends in the water-group abundances that agree well with Sittler et al. (2008). We can also simulate an Enceladus torus dominated H3O+ -- a result not obtainable prior to coupling the chemistry and neutral cloud models.

  20. Ion-retarding lens improves the abundance sensitivity of tandem mass spectrometers

    NASA Technical Reports Server (NTRS)

    Kaiser, K. A.; Stevens, C. M.

    1969-01-01

    Ion-retarding lens which increases the abundance sensitivity of tandem magnetic-analyzer mass spectrometers measures isotopes of low abundance in mass positions adjacent to isotopes of high abundance. The lens increases the abundance sensitivity for isotopes lying farther from high abundance isotopes than the energy cutoff of the lens.

  1. A bent electrostatic ion beam trap for simultaneous measurements of fragmentation and ionization of cluster ions.

    PubMed

    Aviv, O; Toker, Y; Errit, M; Bhushan, K G; Pedersen, H B; Rappaport, M L; Heber, O; Schwalm, D; Zajfman, D

    2008-08-01

    We describe a bent electrostatic ion beam trap in which cluster ions of several keV kinetic energy can be stored on a V-shaped trajectory by means of an electrostatic deflector placed between two electrostatic mirrors. While maintaining all the advantages of its linear counterpart [Zajfman et al., Phys. Rev. A 55, R1577 (1997); Dahan et al., Rev. Sci. Instrum. 69, 76 (1998)], such as long storage times, straight segments, and a field-free region for merged or crossed beam experiments, the bent trap allows for simultaneous measurement of charged and neutral fragments and determination of the average kinetic energy released in the fragmentation. These unique properties of the bent trap are illustrated by first results concerning the competition between delayed fragmentation and ionization of Al(n) (-) clusters after irradiation by a short laser pulse. PMID:19044339

  2. A heavy ion spectrometer system for the measurement of projectile fragmentation of relativistic heavy ions

    NASA Astrophysics Data System (ADS)

    Engelage, J.; Crawford, H. J.; Albergo, S.; Kuo, C.; Caccia, Z.; Chen, C.-X.; Costa, S.; Cronqvist, M.; Flores, L.; Fonte, R.; Greiner, L.; Guzik, T. G.; Insolia, A.; Mitchell, J. W.

    1996-06-01

    The Heavy Ion Spectrometer System (HISS) at the LBL Bevalac provided a unique facility for measuring projectile fragmentation cross sections important in deconvolving the Galactic Cosmic Ray (GCR) source composition. The general characteristics of the apparatus specific to this application are described and the main features of the event reconstruction and analysis used in the TRANSPORT experiment are discussed.

  3. Habitat fragmentation and effects of herbivore (howler monkey) abundances on bird species richness.

    PubMed

    Feeley, Kenneth J; Terborgh, John W

    2006-01-01

    Habitat fragmentation can alter herbivore abundances, potentially causing changes in the plant community that can propagate through the food web and eventually influence other important taxonomic groups such as birds. Here we test the relationship between the density of red howler monkeys (Alouatta seniculus) and bird species richness on a large set of recently isolated land-bridge islands in Lago Guri, Venezuela (n = 29 islands). Several of these islands host relict populations of howler monkeys at densities up to more than 30 times greater than those on the mainland. These "hyperabundant" herbivores previously have been shown to have a strong positive influence on aboveground plant productivity. We predicted that this should lead to a positive, indirect effect of howler monkey density on bird species richness. After accounting for passive sampling (the tendency for species richness to be positively associated with island area, regardless of differences in habitat quality) we found a significant positive correlation between howler monkey density and bird species richness. A path analysis incorporating data on tree growth rates from a subset of islands (n = 9) supported the hypothesis that the effect of howler monkeys on the resident bird communities is indirect and is mediated through changes in plant productivity and habitat quality. These results highlight the potential for disparate taxonomic groups to be related through indirect interactions and trophic cascades. PMID:16634305

  4. Mechanism of fragmentation and atomization of molecular ions in gasdynamic transport cell

    NASA Astrophysics Data System (ADS)

    Bazhenov, A. N.; Bulovich, S. V.; Gall, L. N.; Kretinina, A. V.; Lapushkin, M. N.; Gall, N. R.

    2010-04-01

    The fragmentation of molecular ions formed upon the electrospraying of a sample and transported through the gasdynamic system of a mass spectrometer equipped with an IESAP (Ion Extraction from Solution at Atmospheric Pressure) source has been experimentally studied. It is established that ion fragmentation in a Kantorowicz-Gray type cell takes place in the immediate vicinity of a skimmer port, apparently, as a result of collisions between ions (accelerated in an electric field) and stagnant gas. Molecular mechanisms of fragmentation are considered and it is concluded that this process can take place in a single ion-molecule collision event.

  5. Studies of complex fragment emission in heavy ion reactions

    SciTech Connect

    Charity, R.J.; Sobotka, L.G.

    1992-01-01

    Our work involves the study of intermediate energy heavy-ion nuclear reactions. This work has two foci. On the one hand, we desire to learn about the properties of nuclear matter under abnormal conditions, in this energy domain, predominately low densities. This purpose runs abreast of the second, which is the study of the relevant reaction mechanisms. The two objectives are inexorably linked because our experimental laboratory for studying nuclear matter properties is a dynamic one. We are forced to ask how nuclear matter properties, such as phase transitions, are reflected in the dynamics of the reactions. It may be that irrefutable information about nuclear matter will not be extracted from the reaction work. Nevertheless, we are compelled to undertake this effort not only because it is the only game in town and as yet we do not know that information cannot be extracted, but also because of our second objective. The process leads to an understanding of the reaction mechanism themselves and therefore to the response characteristics of finite, perhaps non-equilibrium, strongly interacting systems. Our program has been: To study energy, mass, and angular momentum deposition by studying incomplete fusion reactions. To gain confidence that we understand how highly excited systems decompose by studying all emissions from the highly excited systems. To push these kinds of studies into the intermediate energy domain, with excitation function studies. And attempt to learn about the dynamics of the decays using particle-particle correlations. In the last effort, we have decided to focus on simple systems, where we believe, definitive statements are possible. These avenues of research share a common theme, large complex fragment production.

  6. Abundance and Source Population of Suprathermal Heavy Ions in Corotating Interaction Regions

    NASA Astrophysics Data System (ADS)

    Jensema, R. J.; Desai, M. I.; Broiles, T. W.; Dayeh, M. A.

    2015-12-01

    In this study we analyze the abundances of suprathermal heavy ions in 75 Corotating Interaction Region (CIR) events between January 1st 1995 and December 31st 2008. We correlate the heavy ion abundances in these CIRs with those measured in the solar wind and suprathermal populations upstream of these events. Our analysis reveals that the CIR suprathermal heavy ion abundances vary by nearly two orders of magnitude over the solar activity cycle, with higher abundances (e.g., Fe/O) occurring during solar maximum and depleted values occurring during solar minimum. The abundances are also energy dependent, with larger abundances at higher energies, particularly during solar maximum. Following the method used by Mason et al. 2008, we correlate the CIR abundances with the corresponding solar wind and suprathermal values measured during 6-hour intervals for upstream periods spanning 10 days prior to the start of each CIR event. This correlation reveals that suprathermal heavy ions are better correlated with upstream suprathermal abundances measured at the same energy compared with the solar wind heavy ion abundances. Using the 6-hour averaging method, we also identified timeframes of maximum correlation between the CIR and the upstream suprathermal abundances, and find that the time of maximum correlation depends on the energy of the suprathermal ions. We discuss the implications of these results in terms of previous studies of CIR and suprathermal particles, and CIR seed populations and acceleration mechanisms.

  7. Effects of Habitat Structure and Fragmentation on Diversity and Abundance of Primates in Tropical Deciduous Forests in Bolivia

    PubMed Central

    Büntge, Anna B. S.; Herzog, Sebastian K.; Kessler, Michael

    2010-01-01

    Habitat structure and anthropogenic disturbance are known to affect primate diversity and abundance. However, researchers have focused on lowland rain forests, whereas endangered deciduous forests have been neglected. We aimed to investigate the relationships between primate diversity and abundance and habitat parameters in 10 deciduous forest fragments southeast of Santa Cruz, Bolivia. We obtained primate data via line-transect surveys and visual and acoustic observations. In addition, we assessed the vegetation structure (canopy height, understory density), size, isolation time, and surrounding forest area of the fragments. We interpreted our results in the context of the historical distribution data for primates in the area before fragmentation and interviews with local people. We detected 5 of the 8 historically observed primate species: Alouatta caraya, Aotus azarae boliviensis, Callithrix melanura, Callicebus donacophilus, and Cebus libidinosus juruanus. Total species number and detection rates decreased with understory density. Detection rates also negatively correlated with forest areas in the surroundings of a fragment, which may be due to variables not assessed, i.e., fragment shape, distance to nearest town. Observations for Alouatta and Aotus were too few to conduct further statistics. Cebus and Callicebus were present in 90% and 70% of the sites, respectively, and their density did not correlate with any of the habitat variables assessed, signaling high ecological plasticity and adaptability to anthropogenic impact in these species. Detections of Callithrix were higher in areas with low forest strata. Our study provides baseline data for future fragmentation studies in Neotropical dry deciduous forests and sets a base for specific conservation measures. PMID:20949116

  8. An (e, 2e + ion) investigation of fragmentation of methane induced by low energy electrons

    NASA Astrophysics Data System (ADS)

    Xu, S.; Ma, X.; Ren, X.; Senftleben, A.; Pflüger, T.; Ullrich, J.; Yan, S.; Zhang, P.; Yang, J.; Dorn, A.

    2014-04-01

    An (e, 2e+ion) investigation of the ionization and dissociation of methane by 54 eV electron impact is performed using the advanced reaction microscope. By measuring two electrons and the ion in the final state in triple coincidence, the species of the ions are identified, and the energies deposited into the target are determined. The species and the kinetic energies of the fragmented ion show strong dependence on the intermediate states of the parent ion.

  9. Isotope Harvesting at Heavy-Ion Fragmentation Facilities

    NASA Astrophysics Data System (ADS)

    Mastren, Tara

    Isotope harvesting from heavy-ion fragmentation facilities is a potential source of isotopes of interest for applications research. With the upgrade of the National Superconducting Cyclotron Laboratory (NSCL) to the Facility for Rare Isotope Beams (FRIB) usable quantities of many isotopes of interest will be produced and available for harvest from an aqueous beam dump. If available, these isotopes would be of interest to a broad range of applications such as medicine, geology, and stockpile stewardship. Preliminary experiments were performed at the NSCL in order to determine the feasibility of isotope harvesting at (FRIB). A water target station that consisted of a 100 mL beam dump was designed and built to collect secondary beams at the NSCL. This target station could be controlled remotely from outside of the experimental vault allowing for multiple collections with minimal exposure to radioactivity. Three secondary beam collections were made with the water target station: a 24Na beam, an analyzed 67Cu beam, and an unanalyzed 67Cu beam. To test the durability of the target station, a 73% pure 85 MeV/u 24Na secondary beam was stopped and collected in the beam dump. Multiple collections were made with currents up to 2 x 106 particles per second without visible radiolytic damage to the target cell. The station operated without any observed release of radiolytic gases, spills, or loss of radioactive liquids. The water target station was then used collect a 77% pure 76 MeV/u 67Cu secondary beam. 67Cu was separated from the other secondary beam contaminants with an average recovery of 88 +/- 3 % and used to radiolabel an antibody. The radiochemical yield of 67Cu-NOTA-Bz-NCS-Trastuzumab was >95%. To better mimic the conditions that would be present in the beam dump at FRIB an unanalyzed beam was collected. This secondary beam was 2.6% pure and contained many contaminants most of which are located in period four of the periodic table. 67Cu was separated from the beam

  10. Effect of land cover, habitat fragmentation and ant colonies on the distribution and abundance of shrews in southern California

    USGS Publications Warehouse

    Laakkonen, J.; Fisher, R.N.; Case, T.J.

    2001-01-01

    1. Because effects of habitat fragmentation and anthropogenic disturbance on native animals have been relatively little studied in arid areas and in insectivores, we investigated the roles of different land covers, habitat fragmentation and ant colonies on the distribution and abundance of shrews, Notiosorex crawfordi and Sorex ornatus, in southern California. 2. Notiosorex crawfordi was the numerically dominant species (trap-success rate 0.52) occurring in 21 of the 22 study sites in 85% of the 286 pitfall arrays used in this study. Sorex ornatus was captured in 14 of the sites, in 52% of the arrays with a total trap-success rate of 0.2. Neither of the species was found in one of the sites. 3. The population dynamics of the two shrew species were relatively synchronous during the 4-5-year study; the peak densities usually occurred during the spring. Precipitation had a significant positive effect, and maximum temperature a significant negative effect on the trap-success rate of S. ornatus. 4. Occurrence and abundance of shrews varied significantly between sites and years but the size of the landscape or the study site had no effect on the abundance of shrews. The amount of urban edge had no significant effect on the captures of shrews but increased edge allows invasion of the Argentine ants, which had a highly significant negative impact on the abundance of N. crawfordi. 5. At the trap array level, the percentage of coastal sage scrub flora had a significant positive, and the percentage of other flora had a significant negative effect on the abundance of N. crawfordi. The mean canopy height and the abundance of N. crawfordi had a significant positive effect on the occurrence of S. ornatus. 6. Our study suggests that the loss of native coastal sage scrub flora and increasing presence of Argentine ant colonies may significantly effect the distribution and abundance of N. crawfordi. The very low overall population densities of both shrew species in most study sites

  11. Fragmentation of 1 GeV/nucleon iron ions in thick targets relevantfor space exploration

    SciTech Connect

    La Tessa, Chiara; Guetersloh, Stephen B.; Heilbronn Lawrence H.; Miller, Jack; Sihver, Lembit; Zeitlin, Cary

    2005-02-01

    We have measured charged nuclear fragments produced by 1GeV/nucleon 56Fe ions interacting with aluminium, polyethylene and lead. These materials are relevant for assessment of radiation risk for manned space flight. The data will be presented in a form suitable for comparison with models of nuclear fragmentation and transport, including linear energy transfer (LET) spectrum, fluence for iron and fragments, event-tack- and event-dose-averaged LET, total dose and iron contribution to dose.

  12. Travelling wave ion mobility and negative ion fragmentation for the structural determination of N-linked glycans.

    PubMed

    Harvey, David J; Scarff, Charlotte A; Edgeworth, Matthew; Crispin, Max; Scanlan, Christopher N; Sobott, Frank; Allman, Sarah; Baruah, Kavitha; Pritchard, Laura; Scrivens, James H

    2013-08-01

    Travelling wave ion mobility was investigated for its ability to separate N-glycans from other compounds and for resolution of isomers. Charged glycans, exemplified by sialylated complex N-glycans released from bovine fetuin and ionised by electrospray, could be separated from residual glycopeptides allowing the minor, more highly sialylated compounds to be detected where their ions were obscured by ions from other compounds in different charge states. This technique was also found to be excellent for extracting the N-glycan profiles from contaminated samples. Structural identification of the glycans was performed by negative ion CID fragmentation, a method that provides a wealth of structurally diagnostic ions. However, fragment ions can also appear in the glycan profiles where they can be mistaken for glycan molecular ions. Fragments and molecular ions were frequently shown to have different drift time profiles, allowing them to be differentiated. Some separation of isomers was found but only for the smallest compounds. Differentiation from conformers was achieved by plotting drift time profiles of the fragments; these profiles matched those of the precursor ions where conformers were present. The techniques were applied to investigations of N-glycans released from the fungus Piptoporus betulinus where the technique was used to separate different carbohydrate types present in biological extracts. PMID:23712623

  13. Fragmentation of positively-charged biological ions activated with a beam of high-energy cations.

    PubMed

    Chingin, Konstantin; Makarov, Alexander; Denisov, Eduard; Rebrov, Oleksii; Zubarev, Roman A

    2014-01-01

    First results are reported on the fragmentation of multiply protonated polypeptide ions produced in electrospray ionization mass spectrometry (ESI-MS) with a beam of high-energy cations as a source of activation. The ion beam is generated with a microwave plasma gun installed on a benchtop Q Exactive mass spectrometer. Precursor polypeptide ions are activated when trapped inside the collision cell of the instrument (HCD cell), and product species are detected in the Orbitrap analyzer. Upon exposure to the beam of air plasma cations (∼100 μA, 5 s), model precursor species such as multiply protonated angiotensin I and ubiquitin dissociated across a variety of pathways. Those pathways include the cleavages of C-CO, C-N as well as N-Cα backbone bonds, accordingly manifested as b/y, a, and c/z fragment ion series in tandem mass spectra. The fragmentation pattern observed includes characteristic fragments of collision-induced dissociation (CID) (b/y/a fragments) as well as electron capture/transfer dissociation (ECD, ETD) (c/z fragments), suggesting substantial contribution of both vibrational and electronic excitation in our experiments. Besides backbone cleavages, notable amounts of nondissociated precursor species were observed with reduced net charge, formed via electron or proton transfer between the colliding partners. Peaks corresponding to increased charge states of the precursor ions were also detected, which is the major distinctive feature of ion beam activation. PMID:24236851

  14. DNA Fragmentation and DSB correlation Induced in Human Fibroblasts by Accelerated 56Fe Ions of Differing Energies

    NASA Astrophysics Data System (ADS)

    Antonelli, F.; Belli, M.; Campa, A.; Dini, V.; Esposito, G.; Furusawa, Y.; Simone, G.; Sorrentino, E.; Tabocchini, M. A.

    HZE particles from space radiation raise an important protection concern during long-term astronauts travels Although these particles are less abundant than protons they are more effective in damaging biological systems It is thought that this is due to the frequent production of spatially correlated DNA damaged sites particularly double strand breaks DSB since this correlation can strongly affect the repair capability of the cells In this work we have studied the DNA fragmentation induced in human fibroblasts by accelerated 56 Fe ions of four different energies i e 115 MeV u 414 MeV u 1 GeV u and 5 GeV u and by gamma-rays used as reference radiation DNA fragmentation was studied in various size ranges varying from 1 to 5700 kbp using Pulsed or Constant Field Gel Electrophoresis The DSB yields have been derived from fragmentation in the overall range as well as in the two ranges 1-23 and 23-5700 kbp The overall DSB yield slightly increased with the ion energy maily due to the contribution of the 23-5700 kbp fragments while that of small fragments 1-23 kbp was almost constant Accordingly the relative biological effectiveness RBE for DSB induction increased with energy from about 1 3 at 115 MeV u to about 1 8 at about 5 GeV u i e less than the RBE for chromosome aberration and cell inactivation The degree of spatial correlation of DSB was evaluated through the departure from the randomness of the fragment distribution with a simple theoretical tool that we have recently introduced To this aim a parameter R was used

  15. Effects of Fragment and Vegetation Structure on the Population Abundance of Ateles hybridus, Alouatta seniculus and Cebus albifrons in Magdalena Valley, Colombia.

    PubMed

    Marsh, Christopher; Link, Andres; King-Bailey, Gillian; Donati, Giuseppe

    2016-01-01

    Many primate species currently subsist in fragmented and anthropogenically disturbed habitats. Different threats arise depending on the species' life history strategy, dietary requirements and habitat preference. Additionally, anthropogenic disturbance is far from uniform and may affect individual forest fragments in a single landscape in differing ways. We studied the effects of fragmentation on three species of diurnal primate, Cebus albifrons, Alouatta seniculus and Ateles hybridus, in Magdalena Valley, Colombia. We tested the assumption that generalist species are more resilient than specialist species to habitat degradation by examining the fragments' vegetation and spatial structure and how these affected primate presence and abundance patterns. We found C. albifrons, a generalist, to be the most abundant species in 9 of 10 forest fragments, regardless of the level of habitat disturbance. A. hybridus, a large-bodied primate with a specialist diet, was either absent or low in abundance in fragments that had experienced recent disturbances and was found only in higher-quality fragments, regardless of the fragment size. A. seniculus, a species considered to have a highly flexible diet and the ability to survive in degraded habitat, was found in intermediate abundances between those of Cebus spp. and Ateles spp., and was more frequently found in high-quality fragments. PMID:27093602

  16. Modeling of ion complexation and extraction using substructural molecular fragments

    PubMed

    Solov'ev; Varnek; Wipff

    2000-05-01

    A substructural molecular fragment (SMF) method has been developed to model the relationships between the structure of organic molecules and their thermodynamic parameters of complexation or extraction. The method is based on the splitting of a molecule into fragments, and on calculations of their contributions to a given property. It uses two types of fragments: atom/bond sequences and "augmented atoms" (atoms with their nearest neighbors). The SMF approach is tested on physical properties of C2-C9 alkanes (boiling point, molar volume, molar refraction, heat of vaporization, surface tension, melting point, critical temperature, and critical pressures) and on octanol/water partition coefficients. Then, it is applied to the assessment of (i) complexation stability constants of alkali cations with crown ethers and phosphoryl-containing podands, and of beta-cyclodextrins with mono- and 1,4-disubstituted benzenes, and (ii) solvent extraction constants for the complexes of uranyl cation by phosphoryl-containing ligands. PMID:10850791

  17. Fragmentation of water by ion impact: Kinetic energy release spectra

    SciTech Connect

    Rajput, Jyoti; Safvan, C. P.

    2011-11-15

    The fragmentation of isolated water molecules on collision with 450-keV Ar{sup 9+} has been studied using time-of-flight mass spectrometry employing multihit detection. The kinetic energy release spectrum for the dissociation of [H{sub 2}O]{sup 2+ White-Star} into (H{sup White-Star },H{sup +},O{sup +}) fragments has been measured where H{sup White-Star} is a neutral Rydberg hydrogen atom. Ab initio calculations are carried out for the lowest states of [H{sub 2}O]{sup q+} with q=2 and 3 to help interpret the kinetic energy release spectra.

  18. Small-angle fragmentation of carbon ions at 0.6 GeV/n: A comparison with models of ion-ion interactions

    DOE PAGESBeta

    Krutenkova, A. P.; Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; Bulychjov, S. A.; Dukhovskoy, I. A.; Khanov, A. I.; Kulikov, V. V.; Martemianov, M. A.; Mashnik, S. G.; et al

    2015-05-29

    Momentum distributions of hydrogen and helium isotopes from ¹²C fragmentation at 3.5° were measured at 0.6 GeV/nucleon in the FRAGM experiment at ITEP TWA heavy ion accelerator. The fragments were selected by correlated time of flight and dE/dx measurements with a magnetic spectrometer with scintillation counters. The main attention was drawn to the high momentum region where the fragment velocity exceeds the velocity of the projectile nucleus. The momentum spectra of fragments span the region of the fragmentation peak as well as the cumulative region. The differential cross sections cover six orders of magnitude. The distributions measured are compared tomore » the predictions of three ion-ion interaction models: BC, QMD and LAQGSM03.03. The kinetic energy spectra of fragments in the projectile rest frame have an exponential shape with two temperatures, being defined by their slope parameters.« less

  19. Small-angle fragmentation of carbon ions at 0.6 GeV/n. A comparison with models of ion-ion interactions

    DOE PAGESBeta

    Krutenkova, Anna P.; Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; Bulychjov, S. A.; Dukhovskoy, I. A.; Khanov, A. I.; Kulikov, V. V.; Martemianov, M. A.; Mashnik, Stepan Georgievich; et al

    2015-05-29

    The momentum distributions of hydrogen and helium isotopes from 12C fragmentation at 3.5° were measured at 0.6 GeV/nucleon in the FRAGM experiment at ITEP TWA heavy ion accelerator. The fragments were selected by correlated time of flight and dE/dx measurements with a magnetic spectrometer with scintillation counters. The main attention was drawn to the high momentum region where the fragment velocity exceeds the velocity of the projectile nucleus. The momentum spectra of fragments span the region of the fragmentation peak as well as the cumulative region. Moreover, the differential cross sections cover six orders of magnitude. The distributions measured aremore » compared to the predictions of three ion-ion interaction models: BC, QMD and LAQGSM03.03. The kinetic energy spectra of fragments in the projectile rest frame have an exponential shape with two temperatures, being defined by their slope parameters.« less

  20. Small-angle fragmentation of carbon ions at 0.6 GeV/n. A comparison with models of ion-ion interactions

    SciTech Connect

    Krutenkova, Anna P.; Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; Bulychjov, S. A.; Dukhovskoy, I. A.; Khanov, A. I.; Kulikov, V. V.; Martemianov, M. A.; Mashnik, Stepan Georgievich; Matsyuk, M. A.; Turdakina, E. N.

    2015-05-29

    The momentum distributions of hydrogen and helium isotopes from 12C fragmentation at 3.5° were measured at 0.6 GeV/nucleon in the FRAGM experiment at ITEP TWA heavy ion accelerator. The fragments were selected by correlated time of flight and dE/dx measurements with a magnetic spectrometer with scintillation counters. The main attention was drawn to the high momentum region where the fragment velocity exceeds the velocity of the projectile nucleus. The momentum spectra of fragments span the region of the fragmentation peak as well as the cumulative region. Moreover, the differential cross sections cover six orders of magnitude. The distributions measured are compared to the predictions of three ion-ion interaction models: BC, QMD and LAQGSM03.03. The kinetic energy spectra of fragments in the projectile rest frame have an exponential shape with two temperatures, being defined by their slope parameters.

  1. Small-angle fragmentation of carbon ions at 0.6 GeV/n: A comparison with models of ion-ion interactions

    SciTech Connect

    Krutenkova, A. P.; Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; Bulychjov, S. A.; Dukhovskoy, I. A.; Khanov, A. I.; Kulikov, V. V.; Martemianov, M. A.; Mashnik, S. G.; Matsyuk, M. A.; Turdakina, E. N.; Bravina, L.; Foka, Y.; Kabana, S.

    2015-05-29

    Momentum distributions of hydrogen and helium isotopes from ¹²C fragmentation at 3.5° were measured at 0.6 GeV/nucleon in the FRAGM experiment at ITEP TWA heavy ion accelerator. The fragments were selected by correlated time of flight and dE/dx measurements with a magnetic spectrometer with scintillation counters. The main attention was drawn to the high momentum region where the fragment velocity exceeds the velocity of the projectile nucleus. The momentum spectra of fragments span the region of the fragmentation peak as well as the cumulative region. The differential cross sections cover six orders of magnitude. The distributions measured are compared to the predictions of three ion-ion interaction models: BC, QMD and LAQGSM03.03. The kinetic energy spectra of fragments in the projectile rest frame have an exponential shape with two temperatures, being defined by their slope parameters.

  2. Ion appearance energies at electron-impact dissociative ionization of sulfur hexafluoride molecule and its fragments

    NASA Astrophysics Data System (ADS)

    Demesh, Shandor Sh.; Remeta, Eugene Yu.

    2015-07-01

    Theoretical analysis of appearance energies for SF{/k +} ( k = 0- n) ion fragments of SF6 molecule as well as F+ and F{2/+} ions at electron-impact dissociative ionization of SF n ( n = 1-6) molecules is presented. Theoretical methods of GAMESS software package were used to calculate the total energies of neutral and charged molecular and atomic fragments. The dissociative ionization process is concluded to occur via repulsive highly-excited electronic states of the SF6 molecule and its fragments, due to which the observed appearance energies exceed the theoretical values. The electron binding energies on the molecular orbitals in the SF6 molecule are compared with the ion fragment appearance energies.

  3. Isotope yield ratios of fragments from heavy-ion reactions

    SciTech Connect

    Deak, F.; Kiss, A. ); Seres, Z. ); Galonsky, A.; Heilbronn, L. )

    1991-05-01

    Isotope yield ratios produced in collisions of 35 MeV/nucleon {sup 14}N with targets of C, Ni, Ag, and Ho have an exponential dependence on total neutron-to-proton ratio. A statistical multifragmentation model including particle emission from excited fragments predicted such behavior for yield ratios measured earlier at the higher energy of 84 MeV/nucleon.

  4. On the fragment ion angular distributions arising from the tetrahedral molecule CH3I

    NASA Astrophysics Data System (ADS)

    Graham, P.; Ledingham, K. W. D.; Singhai, R. P.; Hankin, S. M.; McCanny, T.; Fang, X.; Kosmidis, C.; Tzallas, P.; Taday, P. F.; Langley, A. J.

    2001-10-01

    The mass spectra for both horizontal and vertical polarizations and the angular distributions of fragment ions arising from Coulomb explosion of tetrahedral methyl iodide (CH3I) ions, obtained at a laser intensity of 1016 W cm-2 are presented. All fragment ion distributions are peaked along the direction corresponding to collinearity of the laser electric field with the time-of-flight mass spectrometer axis. The In + ion (n≤7) angular distributions from the dissociation of the parent ions are all of similar widths, which would imply a geometric, as opposed to dynamic, alignment. Additionally, the lower-charged I ions have an isotropic component that decreases as the charge state increases. Measurements of the CHm+ (m≤3), Cp + (p≤4) and H+ ion distributions show that these are also maximal along the polarization direction. Furthermore, there is also a CH22+ ion peak present in the CHm group, which has a distribution similar to those measured for the other ions. This mass peak is the prominent multi-charged ion in this group. As the CH3I molecule is initially tetrahedral, these results suggest that the molecular structure undergoes a change such that the H-C and C-I bonds tend to lie along the field. Several authors have described work which first aligned CH3I molecules with a nanosecond laser and then photodissociated with a femtosecond laser, to produce fragment ion distributions. This is the first time that the angular distributions from a tetrahedral molecule have been presented using femtosecond laser pulses only and in the case of CH3I, for fragments other than CH3+ and I+. The fragment energetics from the single CH3I molecule have been compared with those from recent work dealing with the Coulomb explosion of CH3I clusters.

  5. The role of the environment in the ion induced fragmentation of uracil.

    PubMed

    Markush, Pal; Bolognesi, Paola; Cartoni, Antonella; Rousseau, Patrick; Maclot, Sylvain; Delaunay, Rudy; Domaracka, Alicja; Kocisek, Jaroslav; Castrovilli, Mattea C; Huber, Bernd A; Avaldi, Lorenzo

    2016-06-22

    The fragmentation of uracil molecules and pure and nano-hydrated uracil clusters by (12)C(4+) ion impact is investigated. This work focuses on the fragmentation behavior of complex systems and the effect of the environment. On the one hand, it is found that the environment in the form of surrounding uracil or water molecules has a significant influence on the fragmentation dynamics, providing an overall 'protective' effect, while on the other hand we observe the opening of specific fragmentation channels. In particular, we report on the first observation of a series of hydrated fragments. This indicates a strong interaction between uracil and water molecules, holding the water clusters bound to the observed molecular fragments. PMID:27271080

  6. Fragmentation cross-section of relativistic oxygen ions and determination of overlap parameter

    NASA Technical Reports Server (NTRS)

    Verma, S. D.

    1977-01-01

    Results are presented for measurements of total fragmentation cross sections of relativistic O-16 ions in CsI crystals, which were performed using a monochromatic bevatron ion beam at energies of 0.5 and 2.1 GeV/nucleon. The total fragmentation cross section at each energy is determined on the basis of detected changes in the charge of the incident ions, and the values obtained at both energies are found to be the same to within the experimental errors. Values of the O-16 nucleon radius and overlap parameter are derived simultaneously from the measured cross sections.

  7. Site-Specific Fragmentation of Polystyrene Molecule Using Size-Selected Ar Gas Cluster Ion Beam

    NASA Astrophysics Data System (ADS)

    Moritani, Kousuke; Mukai, Gen; Hashinokuchi, Michihiro; Mochiji, Kozo

    2009-04-01

    The secondary ion mass spectrum (SIMS) of a polystyrene thin film was investigated using a size-selected Ar gas cluster ion beam (GCIB). The fragmentation in the SIM spectrum varied by kinetic energy per atom (Eatom); the Eatom dependence of the secondary ion intensity of the fragment species of polystyrene can be essentially classified into three types based on the relationship between Eatom and the dissociation energy of a specific bonding site in the molecule. These results indicate that adjusting Eatom of size-selected GCIB may realize site-specific bond breaking within a molecule.

  8. Proton Mobility in b₂ Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides.

    PubMed

    Nelson, Carissa R; Abutokaikah, Maha T; Harrison, Alex G; Bythell, Benjamin J

    2016-03-01

    A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting. PMID:26602904

  9. Proton Mobility in b2 Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides

    NASA Astrophysics Data System (ADS)

    Nelson, Carissa R.; Abutokaikah, Maha T.; Harrison, Alex G.; Bythell, Benjamin J.

    2016-03-01

    A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting.

  10. Fragmentation of HCN in optically selected mass spectrometry: Nonthermal ion cooling in helium nanodroplets

    SciTech Connect

    Lewis, William K.; Bemish, Raymond J.; Miller, Roger E.

    2005-10-08

    A technique that combines infrared laser spectroscopy and helium nanodroplet mass spectrometry, which we refer to as optically selected mass spectrometry, is used to study the efficiency of ion cooling in helium. Electron-impact ionization is used to form He{sup +} ions within the droplets, which go on to transfer their charge to the HCN dopant molecules. Depending upon the droplet size, the newly formed ion either fragments or is cooled by the helium before fragmentation can occur. Comparisons with gas-phase fragmentation data suggest that the cooling provided by the helium is highly nonthermal. An 'explosive' model is proposed for the cooling process, given that the initially hot ion is embedded in such a cold solvent.

  11. Ion Mobility Mass Spectrometry for Ion Recovery and Clean-Up of MS and MS/MS Spectra Obtained from Low Abundance Viral Samples

    NASA Astrophysics Data System (ADS)

    Harvey, David J.; Crispin, Max; Bonomelli, Camille; Scrivens, Jim H.

    2015-07-01

    Many samples of complex mixtures of N-glycans released from small amounts of material, such as glycoproteins from viruses, present problems for mass spectrometric analysis because of the presence of contaminating material that is difficult to remove by conventional methods without involving sample loss. This study describes the use of ion mobility for extraction of glycan profiles from such samples and for obtaining clean CID spectra when targeted m/z values capture additional ions from those of the target compound. N-glycans were released enzymatically from within SDS-PAGE gels, from the representative recombinant glycoprotein, gp120 of the human immunodeficiency virus, and examined by direct infusion electrospray in negative mode followed by ion mobility with a Waters Synapt G2 mass spectrometer (Waters MS-Technologies, Manchester, UK). Clean profiles of singly, doubly, and triply charged N-glycans were obtained from samples in cases where the raw electrospray spectra displayed only a few glycan ions as the result of low sample concentration or the presence of contamination. Ion mobility also enabled uncontaminated CID spectra to be obtained from glycans when their molecular ions displayed coincidence with ions from fragments or multiply charged ions with similar m/z values. This technique proved to be invaluable for removing extraneous ions from many CID spectra. The presence of such ions often produces spectra that are difficult to interpret. Most CID spectra, even those from abundant glycan constituents, benefited from such clean-up, showing that the extra dimension provided by ion mobility was invaluable for studies of this type.

  12. Effects of ion abundances on electromagnetic ion cyclotron wave growth rate in the vicinity of the plasmapause

    SciTech Connect

    Henning, F. D. Mace, R. L.

    2014-04-15

    Electromagnetic ion cyclotron (EMIC) waves in multi-ion species plasmas propagate in branches. Except for the branch corresponding to the heaviest ion species, which has only a resonance at its gyrofrequency, these branches are bounded below by a cutoff frequency and above by a resonant gyrofrequency. The condition for wave growth is determined by the thermal anisotropies of each ion species, j, which sets an upper bound, ω{sub j}{sup ∗}, on the wave frequency below which that ion species contributes positively to the growth rate. It follows that the relative positions of the cutoffs and the critical frequencies ω{sub j}{sup ∗} play a crucial role in determining whether a particular wave branch will be unstable. The effect of the magnetospheric ion abundances on the growth rate of each branch of the EMIC instability in a model where all the ion species have kappa velocity distributions is investigated by appealing to the above ideas. Using the variation of the cutoff frequencies predicted by cold plasma theory as a guide, optimal ion abundances that maximise the EMIC instability growth rate are sought. When the ring current is comprised predominantly of H{sup +} ions, all branches of the EMIC wave are destabilised, with the proton branch having the maximum growth rate. When the O{sup +} ion abundance in the ring current is increased, a decrease in the growth rate of the proton branch and cyclotron damping of the helium branch are observed. The oxygen branch, on the other hand, experiences an increase in the maximum growth rate with an increase in the O{sup +} ion abundance. When the ring current is comprised predominantly of He{sup +} ions, only the helium and oxygen branches of the EMIC wave are destabilised, with the helium branch having the maximum growth rate.

  13. Doubly differential cross sections for galactic heavy-ion fragmentation

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Norbury, John W.; Khandelwal, Govind S.; Townsend, Lawrence W.

    1987-01-01

    An abrasion-ablation T-matrix formulation is applied to the calculation of double differential-cross sections in projectile fragmentation of 2.1 GeV/nucleon O-16 on Be-9 and 86 MeV/nucleon C-12 on C-12 and Ag-108. An exponential parameterization of the ablation T-matrix is used and the total width of the intermediate states is taken as a parameter. Fitted values of the total width to experimental results are used to predict the lifetime of the ablation stage and indicate a decay time on the order of 10 to the -19th power sec.

  14. Electromagnetic dissociation effects in galactic heavy-ion fragmentation

    NASA Technical Reports Server (NTRS)

    Norbury, J. W.; Townsend, L. W.

    1986-01-01

    Methods for calculating cross sections for the breakup of galactic heavy ions by the Coulomb fields of the interacting nuclei are presented. By using the Weizsacker-Williams method of virtual quanta, estimates of electromagnetic dissociation cross sections for a variety of reactions applicable to galactic cosmic ray shielding studies are presented and compared with other predictions and with available experimental data.

  15. Abundance of minor ion species at Mars: ASPERA-3 observations

    NASA Astrophysics Data System (ADS)

    Zhang, Yiteng; Nilsson, Hans; Barabash, Stas; Li, Lei

    2012-07-01

    The main species at Mars are O+, O2+, CO2+, while there are also some minor species. This article successfully separates minor species of O++, He+ and H2+ with about 12eV by integrating from two and a half years ASPERA-3 data on Mars Express and by integrating and taking some corrections and data processing. At the same time some space statistic Statistics of these Mars ions and estimating are taken place. The result indicates O++ ions density reduce quickly in the region without sunlight, and have moreis higher at subsolar than in the high alatitude place,. and reduces quickly in the region without sunlight. He+ and H2+ have similar distribution in space mainly above in the high altitude ionosphere, and relatively reduce sparse in the midnight space. O++ and He+ have a comparable volume density about 0.1% of O+, and H2+ is muchone order of magnitude lowerless for one order. Our results imply that O++ ions in the martian space are mainly the product of phtoionization in the ionosphere, while H2+ and He+ might also be originated in the planet.

  16. Ion-polycyclic aromatic hydrocarbon collisions: kinetic energy releases for specific fragmentation channels

    NASA Astrophysics Data System (ADS)

    Reitsma, G.; Zettergren, H.; Boschman, L.; Bodewits, E.; Hoekstra, R.; Schlathölter, T.

    2013-12-01

    We report on 30 keV He2 + collisions with naphthalene (C10H8) molecules, which leads to very extensive fragmentation. To unravel such complex fragmentation patterns, we designed and constructed an experimental setup, which allows for the determination of the full momentum vector by measuring charged collision products in coincidence in a recoil ion momentum spectrometer type of detection scheme. The determination of fragment kinetic energies is found to be considerably more accurate than for the case of mere coincidence time-of-flight spectrometers. In fission reactions involving two cationic fragments, typically kinetic energy releases of 2-3 eV are observed. The results are interpreted by means of density functional theory calculations of the reverse barriers. It is concluded that naphthalene fragmentation by collisions with keV ions clearly is much more violent than the corresponding photofragmentation with energetic photons. The ion-induced naphthalene fragmentation provides a feedstock of various small hydrocarbonic species of different charge states and kinetic energy, which could influence several molecule formation processes in the cold interstellar medium and facilitates growth of small hydrocarbon species on pre-existing polycyclic aromatic hydrocarbons.

  17. Protons from carbon ion fragmentation at 0.3–2.0 GeV/nucleon: Comparison with models of ion-ion interactions

    SciTech Connect

    Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; Bulychjov, S. A.; Dukhovskoy, I. A.; Krutenkova, A. P.; Kulikov, V. V. Martemianov, M. A.; Matsyuk, M. A.; Mashnik, S. G.; Turdakina, E. N.; Khanov, A. I.

    2015-05-15

    Yields of protons at 3.5° from carbon ion fragmentation at energies of T{sub 0} = 0.3, 0.6, 0.95, and 2.0 GeV/nucleon on a Be target were measured in the FRAGM experiment at TWA-ITEP heavy-ion facility. Proton momentum spectra cover both the region of the fragmentation maximum and the cumulative region. The differential cross sections span six orders of its magnitude. The spectra are compared with the predictions of four models of ion-ion interactions: LAQGSM03.03, SHIELD-HIT, QMD, and BC.

  18. Fragmentation of amino acids induced by collisions with low-energy highly charged ions

    NASA Astrophysics Data System (ADS)

    Piekarski, D. G.; Maclot, S.; Domaracka, A.; Adoui, L.; Alcamí, M.; Rousseau, P.; Díaz-Tendero, S.; Huber, B. A.; Martín, F.

    2014-04-01

    Fragmentation of amino acids NH2-(CH2)n-COOH (n=1 glycine; n=2 β-alanine and n=3 γ-aminobutyric acid GABA) following collisions with slow highly charged ions has been studied in the gas phase by a combined experimental and theoretical approach. In the experiments, a multi-coincidence detection method was used to deduce the charge state of the molecules before fragmentation. Quantum chemistry calculations have been carried out in the basis of the density functional theory and ab initio molecular dynamics. The combination of both methodologies is essential to unambiguously unravel the different fragmentation pathways.

  19. Ion Mobility Mass Spectrometry Direct Isotope Abundance Analysis

    SciTech Connect

    Manuel J. Manard, Stephan Weeks, Kevin Kyle

    2010-05-27

    The nuclear forensics community is currently engaged in the analysis of illicit nuclear or radioactive material for the purposes of non-proliferations and attribution. One technique commonly employed for gathering nuclear forensics information is isotope analysis. At present, the state-of-the-art methodology for obtaining isotopic distributions is thermal ionization mass spectrometry (TIMS). Although TIMS is highly accurate at determining isotope distributions, the technique requires an elementally pure sample to perform the measurement. The required radiochemical separations give rise to sample preparation times that can be in excess of one to two weeks. Clearly, the nuclear forensics community is in need of instrumentation and methods that can expedite their decision making process in the event of a radiological release or nuclear detonation. Accordingly, we are developing instrumentation that couples a high resolution IM drift cell to the front end of a MS. The IM cell provides a means of separating ions based upon their collision cross-section and mass-to-charge ratio (m/z). Two analytes with the same m/z, but with different collision cross-sections (shapes) would exit the cell at different times, essentially enabling the cell to function in a similar manner to a gas chromatography (GC) column. Thus, molecular and atomic isobaric interferences can be effectively removed from the ion beam. The mobility selected chemical species could then be introduced to a MS for high-resolution mass analysis to generate isotopic distributions of the target analytes. The outcome would be an IM/MS system capable of accurately measuring isotopic distributions while concurrently eliminating isobaric interferences and laboratory radiochemical sample preparation. The overall objective of this project is developing instrumentation and methods to produce near real-time isotope distributions with a modular mass spectrometric system that performs the required gas-phase chemistry and

  20. Fragmentation of DNA components by hyperthermal heavy ion (Ar+ and Xe+) impact in the condensed phase

    NASA Astrophysics Data System (ADS)

    Sarabipour, Sarvenaz; Sarvenaz Sarabipour, Ms; Michaud, Marc; Deng, Zongwu; Huels, Michael A.

    The overriding environmental factor that presently limits human endeavors in space is exposure to heavy ion radiation. While knowledge of its damage to living tissue is essential for radiation protection and risk estimates for astronauts, very little data exists at the molecular level regarding the nascent DNA damage by the primary particle track, or by secondary species during subsequent reaction cascades. This persistent lack of a basic understanding of nascent damage induced by such low dose, high LET radiation, introduces unacceptable errors in radiation risk estimates (based mainly on extrapolation from high dose, low LET radiation), particularly for long term exposure. Mutagenic effects induced by heavy ion radiation to cells are largely due to DNA damage by secondary transient species, i.e. secondary ballistic ions, electrons and radicals generated along the ion tracks; the secondary ions have hyperthermal energies up to several 100 eV, which they will deposit within a few nm in the surrounding medium; thus their LET is very high, and yields lethal clustered DNA lesions. We present measurements of molecular damage induced in films of DNA components by ions with precisely such low energies (1-100 eV) and compare results to conventional electron impact measurements. Experiments are conducted in UHV using a mass selected low energy ion source, and a high-resolution quadrupole MS to monitor ion yields desorbing from molecular films. Among the major fragments, NH4 + is identified in the desorption mass spectra of irradiated films of Adenine, Guanine, Cytosine, indicating efficient deamination; in cells this results in pre-mutagenic lesions. Experiments with 5-amino-Uracil, and comparison to previous results on uracil and thymine show that deamination is a key step in the NH4 + fragment formation. For Adenine, we also observe formation of amine aducts in the films, viz. amination of Adenine, and global fragmentation in all ion impact mass spectra, attributed

  1. The anatomy of a cluster IDP. Part 1: Carbon abundance, bulk chemistry, and mineralogy of fragments from L2008#5

    NASA Technical Reports Server (NTRS)

    Thomas, K. L.; Keller, L. P.; Klock, W.; Warren, J.; Blanford, G. E.; Mckay, David S.

    1994-01-01

    The objective of this study was to determine whether or not cluster particles are sufficiently homogeneous to enable observations from one fragment of the cluster to be extrapolated to the entire cluster. We report on the results of a consortium study of the fragments of a large cluster particle. Multiple fragments from one large cluster were distributed to several research groups and were subjected to a variety of mineralogical and chemical analyses including: SEM, TEM, ion probe, SXRF, noble gas measurements, and microprobe laser mass spectrometry of individual fragments.

  2. Modulation of Phosphopeptide Fragmentation via Dual Spray Ion/Ion Reactions Using a Sulfonate-Incorporating Reagent.

    PubMed

    Cotham, Victoria C; McGee, William M; Brodbelt, Jennifer S

    2016-08-16

    The labile nature of phosphoryl groups has presented a long-standing challenge for the characterization of protein phosphorylation via conventional mass spectrometry-based bottom-up proteomics methods. Collision-induced dissociation (CID) causes preferential cleavage of the phospho-ester bond of peptides, particularly under conditions of low proton mobility, and results in the suppression of sequence-informative fragmentation that often prohibits phosphosite determination. In the present study, the fragmentation patterns of phosphopeptides are improved through ion/ion-mediated peptide derivatization with 4-formyl-1,3-benezenedisulfonic acid (FBDSA) anions using a dual spray reactor. This approach exploits the strong electrostatic interactions between the sulfonate moieties of FBDSA and basic sites to facilitate gas-phase bioconjugation and to reduce charge sequestration and increase the yield of phosphate-retaining sequence ions upon CID. Moreover, comparative CID fragmentation analysis between unmodified phosphopeptides and those modified online with FBDSA or in solution via carbamylation and 4-sulfophenyl isothiocyanate (SPITC) provided evidence for sulfonate interference with charge-directed mechanisms that result in preferential phosphate elimination. Our results indicate the prominence of charge-directed neighboring group participation reactions involved in phosphate neutral loss, and the implementation of ion/ion reactions in a dual spray reactor setup provides a means to disrupt the interactions by competing hydrogen-bonding interactions between sulfonate groups and the side chains of basic residues. PMID:27467576

  3. Michigan state upgrade to produce intense radioactive ion beams by fragmentation technique

    SciTech Connect

    Lubkin, G.B.

    1997-05-01

    This article describes the planned upgrading of accelerator facilities to produce intense radioactive ion beams, by a fragmentation technique, for experimental simulation of nucleosynthesis in novas and supernovas. (AIP) {ital 1997 American Institute of Physics.} {copyright} {ital 1997} {ital American Institute of Physics}

  4. Carbon ion fragmentation effects on the nanometric level behind the Bragg peak depth.

    PubMed

    Francis, Z; Seif, E; Incerti, S; Champion, C; Karamitros, M; Bernal, M A; Ivanchenko, V N; Mantero, A; Tran, H N; El Bitar, Z

    2014-12-21

    In this study, fragmentation yields of carbon therapy beams are estimated using the Geant4 simulation toolkit version 9.5. Simulations are carried out in a step-by-step mode using the Geant4-DNA processes for each of the major contributing fragments. The energy of the initial beam is taken 400 MeV amu(-1) as this is the highest energy, which is used for medical accelerators and this would show the integral role of secondary contributions in radiotherapy irradiations. The obtained results showed that 64% of the global dose deposition is initiated by carbon ions, while up to 36% is initiated by the produced fragments including all their isotopes. The energy deposition clustering yields of each of the simulated fragments are then estimated using the DBSCAN clustering algorithm and they are compared to the yields of the incident primary beam. PMID:25415376

  5. DNA fragmentation induced by fe ions in human cells: shielding influence on spatially correlated damage

    SciTech Connect

    Antonelli, F.; Belli, M.; Campa, A.; Chatterjee, A.; Dini, V.; Esposito, G.; Rydberg, B.; Simone, G.; Tabocchini, M.A.

    2003-11-19

    Outside the magnetic field of the Earth, high energy heavy ions constitute a relevant part of the biologically significant dose to astronauts during the very long travels through space. The typical pattern of energy deposition in the matter by heavy ions on the microscopic scale is believed to produce spatially correlated damage in the DNA which is critical for radiobiological effects. We have investigated the influence of a lucite shielding on the initial production of very small DNA fragments in human fibroblasts irradiated with 1 GeV/u iron (Fe) ions. We also used small gamma, Greek-rays as reference radiation. Our results show: (1) a lower effect per incident ion when the shielding is used; (2) an higher DNA Double Strand Breaks (DSB) induction by Fe ions than by small gamma, Greek-rays in the size range 123 kbp; (3) a non-random DNA DSB induction by Fe ions.

  6. DNA fragmentation induced by Fe ions in human cells: shielding influence on spatially correlated damage

    NASA Technical Reports Server (NTRS)

    Antonelli, F.; Belli, M.; Campa, A.; Chatterjee, A.; Dini, V.; Esposito, G.; Rydberg, B.; Simone, G.; Tabocchini, M. A.

    2004-01-01

    Outside the magnetic field of the Earth, high energy heavy ions constitute a relevant part of the biologically significant dose to astronauts during the very long travels through space. The typical pattern of energy deposition in the matter by heavy ions on the microscopic scale is believed to produce spatially correlated damage in the DNA which is critical for radiobiological effects. We have investigated the influence of a lucite shielding on the initial production of very small DNA fragments in human fibroblasts irradiated with 1 GeV/u iron (Fe) ions. We also used gamma rays as reference radiation. Our results show: (1) a lower effect per incident ion when the shielding is used; (2) an higher DNA Double Strand Breaks (DSB) induction by Fe ions than by gamma rays in the size range 1-23 kbp; (3) a non-random DNA DSB induction by Fe ions. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

  7. Electron emission and molecular fragmentation during hydrogen and deuterium ion impact on carbon surfaces

    NASA Astrophysics Data System (ADS)

    Qayyum, A.; Schustereder, W.; Mair, C.; Scheier, P.; Märk, T. D.; Cernusca, S.; Winter, HP.; Aumayr, F.

    2003-03-01

    Molecular fragmentation and electron emission during hydrogen ion impact on graphite surfaces has been investigated in the eV to keV impact energy region typical for fusion edge plasma conditions. As a target surface graphite tiles for the Tokamak experiment Tore Supra in CEA-Cadarache/France and highly oriented pyrolytic graphite (HOPG) have been used. For both surfaces studied, the experimentally observed threshold for electron emission is at about 50 eV/amu impact energy. Electron emission from the high conductivity side of the carbon tile is 15-20% less as compared to its low conductivity side, whereas results for HOPG are generally between these two cases. Deuterium and hydrogen ions are almost equally effective in liberating electrons from graphite when comparing results for the same impact velocity. Surface-induced dissociation of deuterium ions D 3+ upon impact on Tore Supra graphite tiles, in the collision energy range of 20-100 eV, produced only atomic fragment ions D +. The other possible fragment ion D 2+ could not be observed.

  8. Observations of solar wind stream with high abundance of heavy ions and relation with coronal conditions

    NASA Astrophysics Data System (ADS)

    Zastenker, G. N.; Yermolaev, Yu. I.

    1981-11-01

    Long intervals, during which heavy ions were detected in the high energy tail of the energy spectra of solar wind ions, were recorded by the plasma spectrometer SCS onboard the Prognoz-7 satellite. In particular, such a region with unusual features - low velocity, high density, low temperature of protons and, especially, low temperature of alpha-particles - was observed during 10-13 December 1978. The time dependence of these parameters makes it possible to recognize this event as 'noncompressive density enhancement'. In this region heavy ions such as O(6+), O(7+), Si(7+), Si(8+), Si(9+) and a group of iron from Fe(6+) to Fe(13+) were identified by the electrostatic analyzer. The abundance of these ions relative to protons was about ten times higher than had previously been observed. The coronal temperature, estimated from the ratios of the ion fluxes with different ionization states, is higher than that estimated earlier for the oxygen ions.

  9. Interplay between compound and fragments aspects of nuclear fission and heavy-ion reaction

    SciTech Connect

    Moller, Peter; Iwamoto, A; Ichikawa, I

    2010-09-10

    The scission point in nuclear fission plays a special role where one-body system changes to two-body system. Inverse of this situation is realized in heavy-ion fusion reaction where two-body system changes to one body system. Among several peculiar phenomena expected to occur during this change, we focus our attention to the behavior of compound and fragments shell effects. Some aspects of the interplay between compound and fragments shell effect are discussed related to the topics of the fission valleys in the potential energy surface of actinide nuclei and the fusion-like trajectory found in the cold fusion reaction leading to superheavy nuclei.

  10. Sputtered metal and silicon cluster ions: collision-induced fragmentation and neutralization

    NASA Astrophysics Data System (ADS)

    Begemann, W.; Hector, R.; Liu, Y. Y.; Tiggesbäumker, J.; Meiwes-Broer, K. H.; Lutz, H. O.

    1989-03-01

    Mass separated metal and silicon cluster ion beams M{/n +, -} are produced by sputtering and undergo fragmenting and/or neutralizing collisions at different kinetic energies (100 1800 eV) in Ar and SF6. Fragment patterns induced by rare gas collisions open a way to determine ionization potentials and electron affinities of clusters. These values are compared to known experimental and theoretical data. For negatively charged clusters the absorption in gas targets is mainly due to neutralization, the cross sections varying with cluster material, number of atoms and collision partner from 10 Å2 to about 50 Å2.

  11. Collision-Induced Dissociation of Fatty Acid [M - 2H + Na]- Ions: Charge-Directed Fragmentation and Assignment of Double Bond Position

    NASA Astrophysics Data System (ADS)

    Thomas, Michael C.; Altvater, Jens; Gallagher, Thomas J.; Nette, Geoffrey W.

    2014-08-01

    The collision-induced dissociation (CID) of cationic fatty acid-metal ion complexes has been extensively studied and, in general, provides rich structural information. In particular, charge-remote fragmentation processes are commonly observed allowing the assignment of double bond position. In a previous manuscript, we presented two methods to doubly deprotonate polyunsaturated fatty acids to form anionic fatty acid-sodium ion complexes, referred to as [M - 2H + Na] - ions. In the current manuscript, the CID behavior of these [M - 2H + Na] - ions is investigated for the first time. Significantly, we also present a deuterium-labeling experiment, which excludes the possibility that deprotonation occurs predominately at the α-carbon in the formation of fatty acid [M - H + NaF]- ions. This supports our original proposal where deprotonation occurs at the bis-allylic positions of polyunsaturated fatty acids. CID spectra of polyunsaturated fatty acid [M - 2H + Na]- ions display abundant product ions arising from acyl chain cleavages. Through the examination of fatty acid isomers, it is demonstrated that double bond position may be unequivocally determined for methylene-interrupted polyunsaturated fatty acids with three or more carbon-carbon double bonds. In addition, CID of [M - 2H + Na]- ions was applied to 18:3 isomers of Nannochloropsis oculata and three isomers were tentatively identified: ∆9,12,1518:3, ∆6,9,1218:3, and ∆5,8,1118:3. We propose that structurally-informative product ions are formed via charge-driven fragmentation processes at the site of the resonance-stabilized carbanion as opposed to charge-remote fragmentation processes, which could be inferred if deprotonation occurred predominately at the α-carbon.

  12. Measurements of 12 C ion fragmentation on thin carbon target from the FIRST collaboration at GSI

    NASA Astrophysics Data System (ADS)

    Toppi, M.; FIRST Collaboration

    2015-04-01

    The FIRST (Fragmentation of Ions Relevant for Space and Therapy) experiment at GSI laboratory took data in summer 2011, studying the collisions of a 12C ion beam with Carbon and Au thin targets. The experiment main purpose is the double differential cross section measurement of the carbon ion fragmentation at energies that are relevant both for tumor therapy and space radiation protection applications (100-1000 MeV/u). The FIRST dataset contains carbon ions collisions on a 3.43 g·Cin-2 carbon target (about 24 M events) and on a 0.96 g·cm-2 Au target (about 4.5 M events). The SIS (heavy ion synchrotron) was used to accelerate the 12C ions at the energy of 400 MeV/u. The preliminary results of differential cross sections measurements as a function of angle and energy for carbon target, in the small angle region (θ ≤ 5°), are presented.

  13. Coincidence measurements between fragment ions and the number of emitted electrons in heavy ion collisions with polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Murai, T.; Majima, T.; Kishimoto, T.; Tsuchida, H.; Itoh, A.

    2012-11-01

    We have studied multiple ionization and multifragmentation of a chlorofluorocarbon molecule, CH2FCF3, induced by collisions of 580-keV C+ ions. Coincidence measurements of product ions and the number of emitted electrons from CH2FCF3 were performed under charge-changing conditions of C+ → Cq+ (q = 0, 2, 3). A fully inclusive measurement regardless of outgoing projectile charge state was also performed by making coincidence with a pulsed ion beam. Mass distributions of fragment ions and number distributions of emitted electrons were both found to change greatly according to charge-changing conditions. Highly multiple ionization emitting up to about 10 electrons was observed in electron loss collisions.

  14. A T-matrix theory of galactic heavy-ion fragmentation

    NASA Technical Reports Server (NTRS)

    Norbury, J. W.; Townsend, L. W.; Deutchman, P. A.

    1985-01-01

    The theory of galactic heavy ion fragmentation is furthered by incorporating a T matrix approach into the description of the three step process of abrasion, ablation, and final state interations. The connection between this T matrix and the interaction potential is derived. For resonant states, the substitution of complex energies for real energies in the transition rate is formerly justified for up to third order processes. The previously developed abrasion-ablation fragmentation theory is rederived from first principles and is shown to result from time ordering, classical probability, and zero width resonance approximations. Improvements in the accuracy of the total fragmentation cross sections require an alternative to the latter two approximations. A Lorentz invariant differential abrasion-ablation cross section is derived which explicitly includes the previously derived abrasion total cross sections. It is demonstrated that spectral and angular distributions can be obtained from the general Lorentz invariant form.

  15. The source charge and isotopic abundances of cosmic rays with Z = 9-16 - A study using new fragmentation cross sections

    SciTech Connect

    Webber, W.R.; Gupta, M.; Soutoul, A.; Ferrando, P. CEA, Service d'Astrophysique, Gif-sur-Yvette )

    1990-01-01

    The cosmic ray source charge and isotopic abundances for charges with Z = 9-16 are reexamined using newly measured fragmentation cross sections in a standard Galactic propagation model. Compared with earlier studies, the cosmic-ray data are now consistent with no excess of Si-29 and Si-30 in the source relative to the solar coronal abundances. The excess of Mg-25 and Mg-26 is now about 1 sigma or less relative to solar coronal isotopic abundances, leaving Ne-22 as the only clearly established neutron-rich isotopic excess in the cosmic ray source. Better estimates of the source abundances of elements obtained using the new cross sections permit the conclusion that high first ionization potential (FIP) elements have a wide spread of compositional differences in the cosmic-ray source relative to solar coronal abundances, whereas elements with a low FIP have a composition similar to the solar corona. 28 refs.

  16. The source charge and isotopic abundances of cosmic rays with Z = 9-16 - A study using new fragmentation cross sections

    NASA Technical Reports Server (NTRS)

    Webber, W. R.; Gupta, M.; Soutoul, A.; Ferrando, P.

    1990-01-01

    The cosmic ray source charge and isotopic abundances for charges with Z = 9-16 are reexamined using newly measured fragmentation cross sections in a standard Galactic propagation model. Compared with earlier studies, the cosmic-ray data are now consistent with no excess of Si-29 and Si-30 in the source relative to the solar coronal abundances. The excess of Mg-25 and Mg-26 is now about 1 sigma or less relative to solar coronal isotopic abundances, leaving Ne-22 as the only clearly established neutron-rich isotopic excess in the cosmic ray source. Better estimates of the source abundances of elements obtained using the new cross sections permit the conclusion that high first ionization potential (FIP) elements have a wide spread of compositional differences in the cosmic-ray source relative to solar coronal abundances, whereas elements with a low FIP have a composition similar to the solar corona.

  17. Deduction of compound nucleus formation probability from the fragment angular distributions in heavy-ion reactions

    NASA Astrophysics Data System (ADS)

    Yadav, C.; Thomas, R. G.; Mohanty, A. K.; Kapoor, S. S.

    2015-07-01

    The presence of various fissionlike reactions in heavy-ion induced reactions is a major hurdle in the path to laboratory synthesis of heavy and super-heavy nuclei. It is known that the cross section of forming a heavy evaporation residue in fusion reactions depends on the three factors—the capture cross section, probability of compound nucleus formation PCN, and the survival probability of the compound nucleus against fission. As the probability of compound nucleus formation, PCN is difficult to theoretically estimate because of its complex dependence on several parameters; attempts have been made in the past to deduce it from the fission fragment anisotropy data. In the present work, the fragment anisotropy data for a number of heavy-ion reactions are analyzed and it is found that deduction of PCN from the anisotropy data also requires the knowledge of the ratio of relaxation time of the K degree of freedom to pre-equilibrium fission time.

  18. Differentiation of metal ion-induced transitions of prothrombin fragment 1.

    PubMed

    Prendergast, F G; Mann, K G

    1977-02-10

    The intrinsic fluorescence of human and bovine prothrombin fragment 1 is quenched (approximately -35%) when calcium ions are bound. The intrinsic fluorescence of prothrombin is also quenched by the binding of Ca2+ but to a lesser extent (total change is approximately -6%). The prothrombin fragment 1 fluorescence transition is also effected by the binding of Mg2+, Mn2+, Gd3+, and Tb3+. With all ions the fluorescence quenching is readily reversed by titration with EDTA. Titration with any of the above ions results in a sigmoidal titration curve. The fluorescence transition midpoints (expressed as Tm) occur at the following concentrations of ions: Ca2+, 0.22 (0.35) mM; Mg2+, 0.22 (0.45) mM; Mn2+, 12.6 (12.6) muM; and Gd3+, 3.6 (5.3) muM (the values in parentheses indicate the concentration of the respective ions bound to bovine prothrombin fragment 1). The presence of phospholipid steepens the Ca2+ titration curve, significantly more so for the bovine system than for the human. Tm values for Ca2+ binding in the presence of phospholipid are 0.21 mM and 0.22 mM for binding to human and bovine prothrombin fragment 1, respectively. Sedimentation equilibrium and velocity studies indicate that prothrombin fragment 1 which is monomeric in the presence of EDTA undergoes concentration-dependent association in the presence of Ca2+. A plot of fraction monomer versus Ca2+ concentration is sigmoidal, with a Tm of approximately 1 mM Ca2+. Mg2+ is only marginally effective in promoting the dimerization, and Mn2+ and Gd3+ are even less effective. However, sedimentation studies performed in the presence of 1 mM Mg2+ at varying Ca2+ concentrations shifted the apparent dimerization transition markedly to the left, the midpoint of the transition occurring at 0.25 mM. Kinetic studies reveal that while Mg2+ by itself does not promote prothrombin activation to thrombin, Mg2+ will partially substitute for Ca2+ in prothrombin activation. In the presence of 1 mM Mg2+ maximal activation rates

  19. Hydrophobic derivatization of N-linked glycans for increased ion abundance in electrospray ionization mass spectrometry.

    PubMed

    Walker, S Hunter; Lilley, Laura M; Enamorado, Monica F; Comins, Daniel L; Muddiman, David C

    2011-08-01

    A library of neutral, hydrophobic reagents was synthesized for use as derivatizing agents in order to increase the ion abundance of N-linked glycans in electrospray ionization mass spectrometry (ESI MS). The glycans are derivatized via hydrazone formation and are shown to increase the ion abundance of a glycan standard more than 4-fold. Additionally, the data show that the systematic addition of hydrophobic surface area to the reagent increases the glycan ion abundance, a property that can be further exploited in the analysis of glycans. The results of this study will direct the future synthesis of hydrophobic reagents for glycan analysis using the correlation between hydrophobicity and theoretical non-polar surface area calculation to facilitate the development of an optimum tag for glycan derivatization. The compatibility and advantages of this method are demonstrated by cleaving and derivatizing N-linked glycans from human plasma proteins. The ESI-MS signal for the tagged glycans are shown to be significantly more abundant, and the detection of negatively charged sialylated glycans is enhanced. PMID:21953184

  20. Hydrophobic Derivatization of N-linked Glycans for Increased Ion Abundance in Electrospray Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Walker, S. Hunter; Lilley, Laura M.; Enamorado, Monica F.; Comins, Daniel L.; Muddiman, David C.

    2011-08-01

    A library of neutral, hydrophobic reagents was synthesized for use as derivatizing agents in order to increase the ion abundance of N-linked glycans in electrospray ionization mass spectrometry (ESI MS). The glycans are derivatized via hydrazone formation and are shown to increase the ion abundance of a glycan standard more than 4-fold. Additionally, the data show that the systematic addition of hydrophobic surface area to the reagent increases the glycan ion abundance, a property that can be further exploited in the analysis of glycans. The results of this study will direct the future synthesis of hydrophobic reagents for glycan analysis using the correlation between hydrophobicity and theoretical non-polar surface area calculation to facilitate the development of an optimum tag for glycan derivatization. The compatibility and advantages of this method are demonstrated by cleaving and derivatizing N-linked glycans from human plasma proteins. The ESI-MS signal for the tagged glycans are shown to be significantly more abundant, and the detection of negatively charged sialylated glycans is enhanced.

  1. Molecular formula analysis of fragment ions by isotope-selective collision-induced dissociation tandem mass spectrometry of pharmacologically active compounds.

    PubMed

    Bianco, Giuliana; Buchicchio, Alessandro; Lelario, Filomena; Cataldi, Tommaso R I

    2014-12-01

    The purpose of this work is to explore the mass fragment characterization of commonly used drugs through a novel approach, which involves isotope-selective tandem mass spectrometry (MS/MS). Collision-induced dissociation (CID) was performed with a low-resolution linear ion trap mass spectrometer in positive electrospray ionization. Three pharmacologically active ingredients, i.e. omeprazole, meloxicam and brinzolamide, selected as model compounds in their own formulation, were investigated as a sodiated adduct [C17 H19 N3 O3 S + Na](+) (omeprazole) and as protonated adducts, [C14 H13 N3 O4 S2  + H](+) and [C12 H21 N3 O5 S3  + H](+) , meloxicam and brinzolamide, respectively. Selecting a narrow window of ±0.5 m/z units, precursor ion fragmentation by CID-MS/MS of isotopologues A + 0, A + 1 and A + 2 was found very useful to confirm the chemical formula of product ions, thus aiding the establishment of characteristic fragmentation pathways of all three examined compounds. The correctness of putative molecular formula of product ions was easily demonstrated by exploiting the isotope peak abundance ratios (i.e. IF+0 /IF+1 and IF+0 /IF+2 ) as simple constraints in low-resolution MS instrumentations. PMID:25476951

  2. Relative abundance of heavy ions in the inner zone of the radiation belts of the earth

    SciTech Connect

    Panasyuk, M.I.

    1986-03-01

    The energy dependences of the relative abundances of energetic (E > 1 MeV/nucleon) H, He, and O ions in the radiation belts are analyzed on the basis of experimental results obtained from measurement of their spectral characteristics on several satellites: Molniya-2, Kosmos-900, Prognoz-5, Explorer-45, ISEE-1, and OV1-19. It is shown that the formation of the energy dependence of He/H and O/H can be explained with a model providing for ion diffusion into the interior of the radiation belts with Coulomb losses taken into account under thecondition that the total-energy spectra at the boundary are more rigid for the heavy ions and are determined by such parameters of the quiet solar wind as the relative concentrations of the individual ion components and their charge states. It is shown that the fluxes of O and Fe ions with E > 1 MeV/nucleon measured on the orbital stations Salyut-6 and Skylab have an energy dependence of the relative abundances not inconsistent with above-noted mechanism for the formation of energetic ions of the inner radiation belt.

  3. Fragmentation of deuteronated aromatic derivatives: The role of ion-neutral complexes

    NASA Astrophysics Data System (ADS)

    Harrison, Alex G.; Wang, Jian-Yao

    1997-01-01

    The low-energy collision-induced dissociation reactions of the MD+ ions of a number of alkyl phenyl ethers, alkylbenzenes, acetophenones and benzaldehyde have been studied as a function of collision energy to establish qualitatively the dependence of the fragmentation reactions observed on internal energy. Deuteronated alkyl phenyl ethers (ROC6H5·D+, R = C3H7, C4H9) fragment at low collision energies to form C6H5OHD+ + (R-H), the thermochemically favoured products; with increasing collision energy (and, hence, internal energy) formation of the alkyl ion R+ increases significantly in importance. Deuteronated alkylbenzenes (RC6H5, RC6H4R', R = C2H5, C3H7) similarly form the deuteronated benzene (the thermochemically favoured product) at low collision energies with formation of the alkyl ion R+ being observed at higher collision energies. The results for both systems are consistent with a fragmentation mechanism involving initial formation of an R+/aromatic ion/neutral complex. At low internal energies proton transfer occurs within this complex to form an ion/neutral complex consisting of the deuteronated aromatic and a neutral olefin; this complex fragments to the thermochemically favoured products. Since the transition state leading to these products is a "tight" transition state involving loss of rotational degrees of freedom, the proton transfer reaction is unfavourable entropically with respect to simple dissociation of the R+/aromatic complex to R+ + ArD. Consequently, these products increase in importance as the internal energy is increased. The fragmentation of deuteronated aromatic carbonyl compounds can also be rationalized by similar mechanisms involving the intermediacy of ion/neutral complexes. Deuteronated acetophenone forms only CH3CO+ at all collision energies; this is both the thermochemically and entropically favoured product. However, deuteronated p-aminoacetophenone forms deuteronated aniline, the thermochemically favoured product at low collision

  4. Kinetic energy distributions in ion-induced CO fragmentation: Signature of shallow states in multiply charged CO

    NASA Astrophysics Data System (ADS)

    Rajput, Jyoti; Safvan, C. P.

    2007-06-01

    Ion-induced molecular fragmentation of CO has been studied using time-of-flight mass spectroscopy with position sensitive detectors in multihit coincidence mode. Ar8+ ions having a velocity of 1.1 a.u. were used as projectiles. The features observed in the kinetic energy release (KER) spectra for all the detected fragmentation channels are discussed in light of the existing and calculated ab initio potential energy curves. The preference of the symmetric breakup over the asymmetric one is clearly observed. For fragmentation channels originating from the same parent molecular ion, it is observed that the most probable KER value is higher for the dissociation channel having a higher charge on the oxygen ion. Occurrence of sharp peaks in KER spectra of some of the fragmentation channels hints towards the existence of shallow (possibly metastable) excited states of COq+ (q=4,5) molecular ions and calls for further theoretical investigations.

  5. Fragmentation of molecular adsorbates by electron and ion bombardment: methoxy chemistry on Al(111)

    SciTech Connect

    Basu, P.; Chen, J.G.; Ng, L.; Colaianni, M.L.; Yates, J.T.

    1988-08-15

    High-resolution electron-energy-loss spectroscopy (HR)EELS has been used successfully to provide direct spectroscopic evidence regarding details of the molecular fragmentation of methoxy (CH3O) on Al(lll) caused by energetic electron and ion beams. Chemisorbed methoxy on Al(lll) is produced by heating of absorbed CH3OH. Irradiation of CH3O(a) by either energetic (approx 300 eV) electrons or Ar+ ions results in C-O and C-H bond scission with simultaneous formation of Al-O and Al-C bonds. During electron stimulated desorption the CH3O(a) species undergo sequential fragmentation first to CHx groups that are captured by the surface and in the final decay process to adsorbed carbon. C-O bonds in CH3O9a) are depleted preferentially compared to C-H bonds in CHx(a) species. The electron-induced sequential fragmentation of the patent CH3 group (from methoxy) to resultant CHx(a) occurs with an efficiency approx. 3 orders of magnitude greater than the subsequent process of CHx(a)=C(a). Cross sections for various bond scission processes in electron and ion bombardment have been estimated.

  6. Abundances of Suprathermal Heavy Ions in CIRs During the Minimum of Solar Cycle 23

    NASA Astrophysics Data System (ADS)

    Bučík, R.; Mall, U.; Korth, A.; Mason, G. M.

    2012-11-01

    In this paper we examine the elemental composition of the 0.1 - 1 MeV nucleon-1 interplanetary heavy ions from H to Fe in corotating interaction regions (CIRs) measured by the SIT ( Suprathermal Ion Telescope) instrument. We use observations taken on board the STEREO spacecraft from January 2007 through December 2010, which included the unusually long solar minimum following Solar Cycle 23. During this period instruments on STEREO observed more than 50 CIR events making it possible to investigate CIR ion abundances during solar minimum conditions with unprecedented high statistics. The observations reveal annual variations of relative ion abundances in the CIRs during the 2007 - 2008 period as indicated by the He/H, He/O and Fe/O elemental ratios. We discuss possible causes of the variability in terms of the helium focusing cone passage and heliolatitude dependence. The year 2009 was very quiet in CIR-event activity. In 2010 the elemental composition in CIRs were influenced by sporadic solar energetic particle (SEP) events. The 2010 He/H and He/O abundance ratios in CIRs show large event-to-event variations with values resembling the SEP-like composition. This finding suggests that the suprathermal SEPs could be the source population for CIR acceleration.

  7. On the differences in element abundances of energetic ions from corotating events and from large solar events

    NASA Technical Reports Server (NTRS)

    Reames, D. V.; Richardson, I. G.; Barbier, L. M.

    1991-01-01

    The abundances of energetic ions accelerated from high-speed solar wind streams by shock waves formed at corotating interaction regions (CIRs) where high-speed streams overtake the lower-speed solar wind are examined. The observed element abundances appear to represent those of the high-speed solar wind, unmodified by the shock acceleration. These abundances, relative to those in the solar photosphere, are organized by the first ionization potential (FIP) of the ions in a way that is different from the FIP effect commonly used to describe differences between abundances in the solar photosphere and those in the solar corona, solar energetic particles (SEPs), and the low-speed solar wind. In contrast, the FIP effect of the ion abundances in the CIR events is characterized by a smaller amplitude of the differences between high-FIP and low-FIP ions and by elevated abundances of He, C, and S.

  8. Ion acceleration and abundance enhancements in coronal heating and during impulsive flares

    NASA Astrophysics Data System (ADS)

    Drake, J. F.; Swisdak, M. M.; Liu, Y.

    2012-12-01

    Particle-in-cell simulations and modeling results are presented of ion heating during guide-field reconnection of large-scale current layers with multiple species. We focus on the reconnection exhaust where most of the magnetic energy is released. We show that the classical MHD description of the exhaust in which rotational discontinuities (RDs) switch off the reconnecting field and slow shocks then heat the plasma fails because of strong ion heating at the RD. We have shown that the heating at the RD depends critically on the mass-to-charge of the particles. Ions with mi/Z_im_p>√ {β pr}, where β pr=8π pp/B_r2 is based on the proton pressure and reconnecting magnetic field Br just upstream of the exhaust, behave like "pickup" particles and are strongly heated. As reconnection in wide current layers begins, Br is initially very small and there is essentially no heating of any ion species. As reconnection proceeds, ions with progressively higher values of mi/Z_im_p are heated with most of the energy going to the perpendicular component with T⊥ ˜ micAr2. Thus, high-mass-to-charge ions are heated first and gain the most energy, producing a simple, direct mechanism for producing the abundance enhancements seen in impulsive flares. For typical coronal parameters ions reach temperatures of several keV/nucleon. During flares further energy gain can take place as ions interact with multiple magnetic islands.

  9. Novel Fragmentation Pathways of Anionic Adducts of Steroids Formed by Electrospray Anion Attachment Involving Regioselective Attachment, Regiospecific Decompositions, Charge-Induced Pathways, and Ion-Dipole Complex Intermediates

    NASA Astrophysics Data System (ADS)

    Rannulu, Nalaka S.; Cole, Richard B.

    2012-09-01

    The analysis of several bifunctional neutral steroids, 5-α-pregnane diol (5-α-pregnane-3α-20βdiol), estradiol (3,17α-dihydroxy-1,3,5(10)-estratriene), progesterone (4-pregnene-3,20-dione), lupeol (3β-hydroxy-20(29)-lupene), pregnenolone (5-pregnen-3β-ol-20-one), and pregnenolone acetate (5-pregnen-3β-ol-20-one acetate) was accomplished by negative ion electrospray mass spectrometry (ESI-MS) employing adduct formation with various anions: fluoride, bicarbonate, acetate, and chloride. Fluoride yielded higher abundances of anionic adducts and more substantial abundances of deprotonated molecules compared with other investigated anions. Collision-induced dissociation (CID) of precursor [M + anion]- adducts of these steroids revealed that fluoride adduct [M + F]- precursors first lose HF to produce [M - H]- and then undergo consecutive decompositions to yield higher abundances of structurally-informative product ions than the other tested anions. In addition to charge-remote fragmentations, the majority of CID pathways of estradiol are deduced to occur via charge-induced fragmentation. Most interestingly, certain anions exhibit preferential attachment to a specific site on these bifunctional steroid molecules, which we are calling "regioselective anion attachment." Regioselective anion attachment is evidenced by subsequent regiospecific decomposition. Regioselective attachment of fluoride (and acetate) anions to low (and moderate) acidity functional groups of pregnenolone, respectively, is demonstrated using deuterated compounds. Moreover, the formation of unique intermediate ion-dipole complexes leading to novel fragmentation pathways of fluoride adducts of pregnenolone acetate, and bicarbonate adducts of d4-pregnenolone, are also discussed.

  10. Atomic Data for Nebular Abundance Determinations: Photoionization and Recombination Properties of Xenon Ions

    NASA Astrophysics Data System (ADS)

    Sterling, Nicholas C.; Kerlin, Austin B.

    2016-01-01

    We present preliminary results of a study of the photoionization (PI) and recombination properties of low-charge Xe ions. The abundances of neutron(n)-capture elements (atomic number Z > 30) are of interest in planetary nebulae (PNe) since they can be enriched by slow n-capture nucleosynthesis (the ``s-process'') in the progenitor asymptotic giant branch (AGB) stars. Xe is particularly valuable, because it is the most widely-observed ``heavy-s'' species (Z > 40) in PNe. Its abundance relative to lighter n-capture elements can be used to determine s-process neutron exposures, and constrain s-process enrichment patterns as a function of progenitor metallicity. Using the atomic structure code AUTOSTRUCTURE (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections and radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for neutral through six-times ionized Xe, data which are critically needed for accurate Xe abundance determinations in ionized nebulae. We find good agreement between our computed direct PI cross sections and experimental measurements. Internal uncertainties are estimated for our calculations by using three different configuration interaction expansions for each ion, and by testing the sensitivity of our results to the radial orbital scaling parameters. As found for other n-capture elements (Sterling & Witthoeft 2011, A&A, 529, A147; Sterling 2011, A&A, 533, A62), DR is the dominant recombination mechanism for Xe ions at nebular temperatures (~104 K). Following Sterling et al. (2015, ApJS, 218, 25), these data will be added to nebular modeling codes to compute ionization correction factors for unobserved Xe ions in PNe, which will enable elemental Xe abundances to be determined with much higher accuracy than is currently possible. This work is supported by NSF award AST-1412928.

  11. Nuclear fragmentation of GCR-like ions: comparisons between data and PHITS

    NASA Astrophysics Data System (ADS)

    Zeitlin, Cary; Guetersloh, Stephen; Heilbronn, Lawrence; Miller, Jack; Sihver, Lembit; Mancusi, Davide; Fukumura, Aki; Iwata, Yoshi; Murakami, Takeshi

    We present a summary of results from recent work in which we have compared nuclear fragmentation cross section data to predictions of the PHITS Monte Carlo simulation. The studies used beams of 12 C, 35 Cl, 40 Ar, 48 Ti, and 56 Fe at energies ranging from 290 MeV/nucleon to 1000 MeV/nucleon. Some of the data were obtained at the Brookhaven National Laboratory, others at the National Institute of Radiological Sciences in Japan. These energies and ion species are representative of the heavy ion component of the Galactic Cosmic Rays (GCR), which contribute significantly to the dose and dose equivalent that will be received by astronauts on deep-space missions. A critical need for NASA is the ability to accurately model the transport of GCR heavy ions through matter, including spacecraft walls, equipment racks, and other shielding materials, as well as through tissue. Nuclear interaction cross sections are of primary importance in the GCR transport problem. These interactions generally cause the incoming ion to break up (fragment) into one or more lighter ions, which continue approximately along the initial trajectory and with approximately the same velocity the incoming ion had prior to the interaction. Since the radiation dose delivered by a particle is proportional to the square of the quantity (charge/velocity), i.e., to (Z/β)2 , fragmentation reduces the dose (and, typically, dose equivalent) delivered by incident ions. The other mechanism by which dose can be reduced is ionization energy loss, which can lead to some particles stopping in the shielding. This is the conventional notion of shielding, but it is not applicable to human spaceflight, since the particles in the GCR tend to be highly energetic and because shielding must be relatively thin in order to keep overall mass as low as possible, keeping launch costs within reason. To support these goals, our group has systematically measured a large number of nuclear cross sections, intended to be used as either

  12. Dependence of simulated positron emitter yields in ion beam cancer therapy on modeling nuclear fragmentation.

    PubMed

    Lühr, Armin; Priegnitz, Marlen; Fiedler, Fine; Sobolevsky, Nikolai; Bassler, Niels

    2014-01-01

    In ion beam cancer therapy, range verification in patients using positron emission tomography (PET) requires the comparison of measured with simulated positron emitter yields. We found that (1) changes in modeling nuclear interactions strongly affected the positron emitter yields and that (2) Monte Carlo simulations with SHIELD-HIT10Areasonably matched the most abundant PET isotopes (11)C and (15)O. We observed an ion-energy (i.e., depth) dependence of the agreement between SHIELD-HIT10Aand measurement. Improved modeling requires more accurate measurements of cross-section values. PMID:23352823

  13. SOLAR CYCLE ABUNDANCE VARIATIONS IN COROTATING INTERACTION REGIONS: EVIDENCE FOR A SUPRATHERMAL ION SEED POPULATION

    SciTech Connect

    Mason, G. M.; Desai, M. I.; Li, G.

    2012-04-01

    We have surveyed the heavy ion composition of corotating interaction regions (CIRs) over the recent solar minimum and combined this with our earlier survey to cover the 1998-2011 period encompassing a full solar cycle and onset of the new cycle. We find that the solar minimum CIR intensities and spectral forms are similar to those in active periods, indicating that the basic acceleration mechanism does not vary with solar activity for energies below a few MeV nucleon{sup -1}. However, the heavy ion abundances show a clear correlation with sunspot number, where heavy ions are more enhanced during active periods. Over the mass range He-Fe, the enhancement is organized by a power law in Q/M with exponent -1.9, with Fe/O varying by a factor of {approx}6. During solar minimum CIR Fe/O was {approx}0.05, well below the corresponding solar wind ratio. Previous studies have shown that rare ions (He{sup +}, {sup 3}He) enhanced in CIRs come from the suprathermal ion pool. The observations presented here extend this evidence, indicating that in addition to rare He{sup +} and {sup 3}He the CIR major heavy ion species are accelerated out of the suprathermal ion pool, not the bulk solar wind.

  14. Measurement of fragmentation cross sections of 12C ions on a thin gold target with the FIRST apparatus

    NASA Astrophysics Data System (ADS)

    Toppi, M.; Abou-Haidar, Z.; Agodi, C.; Alvarez, M. A. G.; Aumann, T.; Balestra, F.; Battistoni, G.; Bocci, A.; Böhlen, T. T.; Boudard, A.; Brunetti, A.; Carpinelli, M.; Cirio, R.; Cirrone, G. A. P.; Cortes-Giraldo, M. A.; Cuttone, G.; de Napoli, M.; Durante, M.; Fernández-García, J. P.; Finck, Ch.; Golosio, B.; Iarocci, E.; Iazzi, F.; Ickert, G.; Introzzi, R.; Juliani, D.; Krimmer, J.; Kummali, A. H.; Kurz, N.; Labalme, M.; Leifels, Y.; Le Fèvre, A.; Leray, S.; Marchetto, F.; Monaco, V.; Morone, M. C.; Nicolosi, D.; Oliva, P.; Paoloni, A.; Piersanti, L.; Pleskac, R.; Randazzo, N.; Rescigno, R.; Romano, F.; Rossi, D.; Rosso, V.; Rousseau, M.; Sacchi, R.; Sala, P.; Salvador, S.; Sarti, A.; Scheidenberger, C.; Schuy, C.; Sciubba, A.; Sfienti, C.; Simon, H.; Sipala, V.; Spiriti, E.; Tropea, S.; Vanstalle, M.; Younis, H.; Patera, V.; FIRST Collaboration

    2016-06-01

    A detailed knowledge of the light ions interaction processes with matter is of great interest in basic and applied physics. As an example, particle therapy and space radioprotection require highly accurate fragmentation cross-section measurements to develop shielding materials and estimate acute and late health risks for manned missions in space and for treatment planning in particle therapy. The Fragmentation of Ions Relevant for Space and Therapy experiment at the Helmholtz Center for Heavy Ion research (GSI) was designed and built by an international collaboration from France, Germany, Italy, and Spain for studying the collisions of a 12C ion beam with thin targets. The collaboration's main purpose is to provide the double-differential cross-section measurement of carbon-ion fragmentation at energies that are relevant for both tumor therapy and space radiation protection applications. Fragmentation cross sections of light ions impinging on a wide range of thin targets are also essential to validate the nuclear models implemented in MC simulations that, in such an energy range, fail to reproduce the data with the required accuracy. This paper presents the single differential carbon-ion fragmentation cross sections on a thin gold target, measured as a function of the fragment angle and kinetic energy in the forward angular region (θ ≲6° ), aiming to provide useful data for the benchmarking of the simulation softwares used in light ions fragmentation applications. The 12C ions used in the measurement were accelerated at the energy of 400 MeV/nucleon by the SIS (heavy ion synchrotron) GSI facility.

  15. Modelization of DNA fragmentation induced in human fibroblasts by Fe-56 ions

    NASA Astrophysics Data System (ADS)

    Ballarini, F.; Belli, M.; Campa, A.; Esposito, G.; Friedland, W.; Ottolenghi, A.; Paretzke, H.

    DNA double-strand breaks DSB are widely recognized as cellular critical lesions in the pathways leading from initial energy deposition by radiation to the formation of relevant biological endpoints such as gene mutations chromosome aberrations and cell death Chromatin conformation and radiation track structure are expected to have a strong influence on the spatial modulation of DSB induction at the scale of the nucleosome i e 100 base pairs bp and of the low-level chromatin fiber organization i e 1 kbp At larger scales the DNA fragmentation pattern induced by sparsely ionizing radiation approaches a scenario resulting from a random distribution of DSB However the pattern induced by high-LET irradiation can lead to deviation from randomness also at these scales This feature can have important biological consequences since spatial correlation of DSB is thought to affect their reparability Therefore studies on fragment size distributions induced by radiations of various qualities can help to link the physical characteristics of radiation with the cellular endpoints This is an important issue for understanding the main mechanisms of cell damage induced by HZE particles In this work we have compared the pattern of DNA fragmentation in the range 1-5700 kbp induced in human fibroblasts by gamma -rays with that induced by high-energy Fe-ions which have biological significance for radiation protection issues during long term astronauts travels The study has taken into account the comparison of the experimental fragmentation spectra

  16. Novel apparatus to measure hyperthermal heavy ion damage to DNA: Strand breaks, base loss, and fragmentation

    SciTech Connect

    Sellami, L.; Lacombe, S.; Hunting, D.; Wagner, R. J.; Huels, M. A.

    2007-08-15

    We have developed a novel apparatus that allows us to irradiate nonvolatile organic films of high mass (1-100 {mu}g range) spread out over a large surface area (42 cm{sup 2}) with low energy (kT-100 eV) heavy ions and to quantitatively analyze the film substance via standard biochemical techniques afterwards. Here we discuss the details of the apparatus and method and show that it allows us to measure substantial damage to double stranded DNA molecules (plasmids) and its fundamental subunits induced by heavy ions with unprecedented low energies, i.e., 2.5 eV/amu; these energies correspond to track end energies of stopping ions or secondary ions created along primary ion tracks. We find that hyperthermal Ar{sup +} ions interacting with plasmid DNA will lead to the formation of single and double strand breaks, as well as fragmentation of nucleosides, which also involve chemical modifications and site specific rupture along the N1-C1 glycosidic bond, resulting in base release. In cells, such localized clustered damage will enhance the severity of DNA strand lesions, thus making them harder to repair.

  17. Optical model methods of predicting nuclide production cross sections from heavy ion fragmentation

    NASA Technical Reports Server (NTRS)

    Townsend, L. W.; Ramsey, C. R.; Tripathi, R. K.; Cucinotta, F. A.; Norbury, J. W.; Wilson, J. W. (Principal Investigator)

    1999-01-01

    Quantum mechanical optical potential methods for calculating inclusive isotope and element production cross sections from the fragmenting of heavy nuclei by intermediate- and high-energy protons and heavy ions are presented based upon a modified abrasion-ablation-FSI (frictional spectator interaction) collision model. The abrasion stage is treated as a quantum mechanical knockout process that leaves the residual prefragment in an excited state. Prefragment excitation energies are estimated using a combined liquid drop and FSI method. In ablation the prefragment deexcites by particle and photon emission to produce the final fragment. Contributions from electromagnetic dissociation to single nucleon removal cross sections are incorporated using a Weiszacker-Williams theory that includes electric dipole and electric quadrupole interactions. Estimates of elemental and isotopic production cross sections are in good agreement with published cross section measurements for a variety of projectile-target-beam energy combinations.

  18. A modular solid state detector for measuring high energy heavy ion fragmentation near the beam axis

    NASA Technical Reports Server (NTRS)

    Zeitlin, C. J.; Frankel, K. A.; Gong, W.; Heilbronn, L.; Lampo, E. J.; Leres, R.; Miller, J.; Schimmerling, W.

    1994-01-01

    A multi-element solid state detector has been designed to measure fluences of fragments produced near the beam axis by high energy heavy ion beams in thick targets. The detector is compact and modular, so as to be readily reconfigured according to the range of fragment charges and energies to be measured. Preamplifier gain settings and detector calibrations are adjustable remotely under computer control. We describe the central detector, its associated detectors and electronics, triggering scheme, data acquisition and particle identification techniques, illustrated by data taken with 600 MeV/u 56Fe beams and thick polyethylene targets at the LBL Bevalac. The applications of this work to space radiation protection are discussed.

  19. Atomic Data for Nebular Abundance Determinations: Photoionization, Recombination, and Collisional Excitation of Rubidium and Bromine Ions

    NASA Astrophysics Data System (ADS)

    Kerlin, Austin; Macaluso, David A.; Bautista, Manuel; Bilodeau, Rene C.; Aguilar, Alejandro; Kilcoyne, A. L. David; Dumitriu, Ileana; Sterling, Nicholas C.

    2016-01-01

    We present results of an investigation into the photoionization (PI), recombination, and electron-impact excitation properties of low-charge Br and Rb ions. Br and Rb are among the relatively few neutron(n)-capture elements (atomic number Z > 30) that have been detected in planetary nebulae (PNe). Their abundances can reveal unique information regarding nucleosynthesis in asymptotic giant branch (AGB) stars, including slow n-capture (s-process) neutron densities and the dominant neutron source in more massive AGB stars (4-8 solar masses). However, the requisite atomic data needed for accurate Rb and Rb nebular abundance determinations are unknown. Our work addresses this need, via a synthesis of theoretical and experimental methods. Using the AUTOSTRUCTURE atomic structure code (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections, and rate coefficients for radiative recombination (RR) and dielectronic recombination (DR) for neutral through six-times ionized Br and Rb. To benchmark our calculations, we have measured absolute PI cross sections of Br+-Br4+ and Rb+-Rb5+ at the Advanced Light Source synchrotron radiation facility in Berkeley, CA. Breit-Pauli R-matrix calculations are in progress to facilitate analysis of the experimental data, including resonance identifications and determining the metastable populations of the primary ion beams. Finally, we are performing R-matrix calculations of effective collision strengths for electron-impact excitation of astrophysically detected Br and Rb ions. Our Rb3+ effective collision strength results have been applied to two PNe, with excellent agreement found for ionic abundances determined from different [Rb IV] lines. The combination of these atomic data will dramatically improve the accuracy of Br and Rb abundance determinations in astrophysical nebulae, providing new insight into heavy element nucleosynthesis in low- and intermediate-mass stars

  20. Nuclear fragmentation energy and momentum transfer distributions in relativistic heavy-ion collisions

    NASA Technical Reports Server (NTRS)

    Khandelwal, Govind S.; Khan, Ferdous

    1989-01-01

    An optical model description of energy and momentum transfer in relativistic heavy-ion collisions, based upon composite particle multiple scattering theory, is presented. Transverse and longitudinal momentum transfers to the projectile are shown to arise from the real and absorptive part of the optical potential, respectively. Comparisons of fragment momentum distribution observables with experiments are made and trends outlined based on our knowledge of the underlying nucleon-nucleon interaction. Corrections to the above calculations are discussed. Finally, use of the model as a tool for estimating collision impact parameters is indicated.

  1. Warm target recoil ion momentum spectroscopy for fragmentation of molecular hydrogen by ultrashort laser pulses.

    PubMed

    Liu, Jia; Wu, Jian; Czasch, Achim; Zeng, Heping

    2009-07-20

    We demonstrate warm target recoil ion momentum spectroscopy for the fragmentation dynamics of the warm hydrogen molecules at room temperature. The thermal movement effect of the warm molecule is removed by using a correction algorithm in the momentum space. Based on the reconstructed three-dimensional momentum vectors as well as the kinetic energy release spectra, different vibrational states of the H(2)(+) ground state are clearly visible and the internuclear separation for charge resonance enhanced ionization of the second electron is identified. The results show adequate accordance with the former experiments using other techniques. PMID:19654636

  2. Sulfur abundances in the solar wind measured by SWICS on Ulysses. [Solar Wind Ion Composition Spectrometer

    NASA Technical Reports Server (NTRS)

    Shafer, C. M.; Gloeckler, G.; Galvin, A. B.; Ipavich, F. M.; Geiss, J.; Von Steiger, R.; Ogilvie, K.

    1993-01-01

    One of the nine experiments on Ulysses (launched October, 1990), the Solar Wind Ion Composition Spectrometer, utilizes an energy per charge deflection system along with time of flight technology to uniquely determine the mass and mass per charge of solar wind particles. Thus the composition of various solar wind types can be analyzed. Using the SWICS data accumulated during the in-ecliptic phase of the mission, we have determined the sulfur abundance, relative to silicon, in two different types of solar wind: transient and coronal hole associated flows. Sulfur is of extreme interest because it is one of the few elements that lies in the transitional region of the FIP-dependent relative abundance enrichment function, observed for solar energetic particles and some types of solar wind flows.

  3. A recoil ion momentum spectrometer for molecular and atomic fragmentation studies.

    PubMed

    Khan, Arnab; Tribedi, Lokesh C; Misra, Deepankar

    2015-04-01

    We report the development and performance studies of a newly built recoil ion momentum spectrometer for the study of atomic and molecular fragmentation dynamics in gas phase upon the impact of charged particles and photons. The present design is a two-stage Wiley-McLaren type spectrometer which satisfies both time and velocity focusing conditions and is capable of measuring singly charged ionic fragments up-to 13 eV in all directions. An electrostatic lens has been introduced in order to achieve velocity imaging. Effects of the lens on time-of-flight as well as on the position have been investigated in detail, both, by simulation and in experiment. We have used 120 keV proton beam on molecular nitrogen gas target. Complete momentum distributions and kinetic energy release distributions have been derived from the measured position and time-of-flight spectra. Along with this, the kinetic energy release spectra of fragmentation of doubly ionized nitrogen molecule upon various projectile impacts are presented. PMID:25933839

  4. A recoil ion momentum spectrometer for molecular and atomic fragmentation studies

    SciTech Connect

    Khan, Arnab; Tribedi, Lokesh C.; Misra, Deepankar

    2015-04-15

    We report the development and performance studies of a newly built recoil ion momentum spectrometer for the study of atomic and molecular fragmentation dynamics in gas phase upon the impact of charged particles and photons. The present design is a two-stage Wiley-McLaren type spectrometer which satisfies both time and velocity focusing conditions and is capable of measuring singly charged ionic fragments up-to 13 eV in all directions. An electrostatic lens has been introduced in order to achieve velocity imaging. Effects of the lens on time-of-flight as well as on the position have been investigated in detail, both, by simulation and in experiment. We have used 120 keV proton beam on molecular nitrogen gas target. Complete momentum distributions and kinetic energy release distributions have been derived from the measured position and time-of-flight spectra. Along with this, the kinetic energy release spectra of fragmentation of doubly ionized nitrogen molecule upon various projectile impacts are presented.

  5. An abrasion-ablation model description of galactic heavy-ion fragmentation

    NASA Technical Reports Server (NTRS)

    Townsend, L. W.; Wilson, J. W.; Norbury, J. W.; Bidasaria, H. B.

    1984-01-01

    The fragmentation of high-energy galactic heavy ions by nuclear interactions with arbitrary target nuclei is described within the context of a simple abrasion-ablation fragmentation model. The abrasion part of the theory utilizes a quantum-mechanical formalism based upon an optical model potential approximation to the exact nucleus-nucleus multiple-scattering series. Nuclear charge distributions of the excited prefragments are calculated using either a hypergeometric distribution or a method based upon the zero-point oscillations of the giant dipole resonance. The excitation energy of the prefragment is estimated from the geometric clean-cut abrasion-ablation model. The decay probabilities for the various particle emission channels, in the ablation stage of the fragmentation, are obtained from the EVAP-4 Monte Carlo computer program. Elemental production cross sections for 1.88-GeV/nucleon iron colliding with carbon, silver, and lead targets are calculated and compared with experimental data and with the predictions from the semiempirical relations of Silberberg and Tsao.

  6. Ultraviolet laser desorption/ionization mass spectrometry of single-core and multi-core polyaromatic hydrocarbons under variable conditions of collisional cooling: insights into the generation of molecular ions, fragments and oligomers.

    PubMed

    Gámez, Francisco; Hortal, Ana R; Martínez-Haya, Bruno; Soltwisch, Jens; Dreisewerd, Klaus

    2014-11-01

    The ultraviolet laser desorption/ionization of polyaromatic hydrocarbons (PAHs) has been investigated under different background pressures of an inert gas (up to 1.2 mbar of N2) in the ion source of a hybrid, orthogonal-extracting time-of-flight mass spectrometer (oTOF-MS). The study includes an ensemble of six model PAHs with isolated single polyaromatic cores and four ones with multiple cross-linked aromatic and polyaromatic cores. In combination with a weak ion extraction field, the variation of the buffer gas pressure allowed to control the degree of collisional cooling of the desorbed PAHs and, thus, to modulate their decomposition into fragments. The dominant fragmentation channels observed are related to dehydrogenation of the PAHs, in most cases through the cleavage of even numbers of C-H bonds. Breakage of C-C bonds leading to the fragmentation of rings, side chains and core linkages is also observed, in particular, at low buffer gas pressures. The precise patterns of the combined fragmentation processes vary significantly between the PAHs. The highest abundances of molecular PAH ions and cleanest mass spectra were consistently obtained at the highest buffer gas pressure of 1.2 mbar. The effective quenching of the fragmentation pathways at this elevated pressure improves the sensitivity and data interpretation for analytical applications, although the fragmentation of side chains and of bonds between (poly)aromatic cores is not completely suppressed in all cases. Moreover, these results suggest that the detected fragments are generated through thermal equilibrium processes rather than as a result of rapid photolysis. This assumption is further corroborated by a laser desorption/ionization post-source decay analysis using an axial time-of-flight MS. In line with these findings, covalent oligomers of the PAHs, which are presumably formed by association of two or more dehydrogenated fragments, are detected with higher abundances at the lower buffer gas

  7. The angular distributions of fragment ions from labelled and unlabelled N2O in intense laser fields

    NASA Astrophysics Data System (ADS)

    Graham, P.; Ledingham, K. W. D.; Singhal, R. P.; McCanny, T.; Hankin, S. M.; Fang, X.; Tzallas, P.; Kosmidis, C.; Taday, P. F.; Langley, A. J.

    2000-09-01

    The mass spectra and angular distributions of fragment ions arising from a Coulomb explosion of highly charged parent nitrous oxide ions, obtained in the femtosecond regime (~1016 W cm-2), are investigated. The N ion angular distributions from 14N2O show maxima when the laser polarization is parallel and orthogonal to the time-of-flight axis. Measurements with labelled molecules (15N-14N = 16O) indicate that the maxima arise from the peripheral and central N atoms in the molecular structure. The anisotropic distributions may be explained by assuming increased ionization and fragmentation when the molecular axis is parallel to the laser field. The bond angle prior to explosion is determined to be ~140°, irrespective of the charge state of the precursor, and calculations of the kinetic energies imparted to the fragment ions suggest that dissociation occurs at the equilibrium internuclear distance of the neutral molecule.

  8. Why do the Abundances of Ions Generated by MALDI Look Thermally Determined?

    NASA Astrophysics Data System (ADS)

    Bae, Yong Jin; Choe, Joong Chul; Moon, Jeong Hee; Kim, Myung Soo

    2013-11-01

    In a previous study ( J. Mass Spectrom. 48, 299-305, 2013), we observed that the abundance of each ion in a matrix-assisted laser desorption ionization (MALDI) spectrum looked thermally determined. To find out the explanation for the phenomenon, we estimated the ionization efficiency and the reaction quotient (QA) for the autoprotolysis of matrix, M + M → [M + H]+ + [M - H]-, from the temperature-controlled laser desorption ionization spectra of α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB). We also evaluated the equilibrium constants (KA) for the autoprotolysis at various temperatures by quantum chemical calculation. Primary ion formation via various thermal models followed by autoprotolysis-recombination was compatible with the observations. The upper limit of the effective temperature of the plume where autoprotolysis-recombination occurs was estimated by equating QA with the calculated equilibrium constant. [Figure not available: see fulltext.

  9. Peptide Fragmentation and Surface Structural Analysis by Means of ToF-SIMS Using Large Cluster Ion Sources.

    PubMed

    Yokoyama, Yuta; Aoyagi, Satoka; Fujii, Makiko; Matsuo, Jiro; Fletcher, John S; Lockyer, Nicholas P; Vickerman, John C; Passarelli, Melissa K; Havelund, Rasmus; Seah, Martin P

    2016-04-01

    Peptide or protein structural analysis is crucial for the evaluation of biochips and biodevices, therefore an analytical technique with the ability to detect and identify protein and peptide species directly from surfaces with high lateral resolution is required. In this report, the efficacy of ToF-SIMS to analyze and identify proteins directly from surfaces is evaluated. Although the physics governing the SIMS bombardment process precludes the ability for researchers to detect intact protein or larger peptides of greater than a few thousand mass unit directly, it is possible to obtain information on the partial structures of peptides or proteins using low energy per atom argon cluster ion beams. Large cluster ion beams, such as Ar clusters and C60 ion beams, produce spectra similar to those generated by tandem MS. The SIMS bombardment process also produces peptide fragment ions not detected by conventional MS/MS techniques. In order to clarify appropriate measurement conditions for peptide structural analysis, peptide fragmentation dependency on the energy of a primary ion beam and ToF-SIMS specific fragment ions are evaluated. It was found that the energy range approximately 6 ≤ E/n ≤ 10 eV/atom is most effective for peptide analysis based on peptide fragments and [M + H] ions. We also observed the cleaving of side chain moieties at extremely low-energy E/n ≤ 4 eV/atom. PMID:26916620

  10. Relative abundance of the light ions in the winter nighttime topside ionosphere

    NASA Technical Reports Server (NTRS)

    Sanatani, S.; Breig, E. L.

    1984-01-01

    Ion concentration measurements with the retarding potential analyzer onboard OGO 6 satellite have served as basis for investigation of the distribution of the light ions, H(+) and He(+), relative to that of O(+) in the 500- to 800-km height range in the winter nighttime ionosphere. This concentration ratio exhibits distinct large-scale horizontal variations, with a relative depression in the ratio observed over a broad region about -45 deg longitude northward of approximately 40 deg dip latitude. The lower ratios are associated primarily with well-defined relative increases in the abundance of O(+), and occur in the same longitude sector that has been characterized in an earlier study by both an observed concurrent relative enhancement in ion temperature and the presence of large fluxes of energetic electrons. Comparisons are presented for the altitude distributions of the concentration ratio between regions representing extremes of the horizontal variation. A simple diffusive-equilibrium model demonstrates that the effects of ion temperature on the O(+) vertical distribution are a significant factor leading to the observed variation of the concentration ratio.

  11. Formation and Fragmentation of Unsaturated Fatty Acid [M - 2H + Na]- Ions: Stabilized Carbanions for Charge-Directed Fragmentation

    NASA Astrophysics Data System (ADS)

    Thomas, Michael C.; Kirk, Benjamin B.; Altvater, Jens; Blanksby, Stephen J.; Nette, Geoffrey W.

    2013-12-01

    Fatty acids are long-chain carboxylic acids that readily produce [M - H]- ions upon negative ion electrospray ionization (ESI) and cationic complexes with alkali, alkaline earth, and transition metals in positive ion ESI. In contrast, only one anionic monomeric fatty acid-metal ion complex has been reported in the literature, namely [M - 2H + FeIICl]-. In this manuscript, we present two methods to form anionic unsaturated fatty acid-sodium ion complexes (i.e., [M - 2H + Na]-). We find that these ions may be generated efficiently by two distinct methods: (1) negative ion ESI of a methanolic solution containing the fatty acid and sodium fluoride forming an [M - H + NaF]- ion. Subsequent collision-induced dissociation (CID) results in the desired [M - 2H + Na]- ion via the neutral loss of HF. (2) Direct formation of the [M - 2H + Na]- ion by negative ion ESI of a methanolic solution containing the fatty acid and sodium hydroxide or bicarbonate. In addition to deprotonation of the carboxylic acid moiety, formation of [M - 2H + Na]- ions requires the removal of a proton from the fatty acid acyl chain. We propose that this deprotonation occurs at the bis-allylic position(s) of polyunsaturated fatty acids resulting in the formation of a resonance-stabilized carbanion. This proposal is supported by ab initio calculations, which reveal that removal of a proton from the bis-allylic position, followed by neutral loss of HX (where X = F- and -OH), is the lowest energy dissociation pathway.

  12. Effects of landscape composition and wetland fragmentation on frog and toad abundance and species richness in Iowa and Wisconsin, USA [abstract

    USGS Publications Warehouse

    Knutson, M.G.; Sauer, J.R.; Olsen, D.A.; Mossman, M.J.; Hemesath, L.M.; Lannoo, M.J.

    1998-01-01

    We examined the relationships between anuran diversity and landscape features in the Upper Midwestern United States. Anuran relative abundance and species richness were measured using data collected by Wisconsin and Iowa state calling surveys conducted from 1990-1995. Landscape features surrounding survey points were determined using National Wetland Inventory and Wisconsin Wetland Inventory maps. We tested several hypotheses suggested by the literature. We hypothesized that the relative abundance and species richness of anurans that breed in ephemeral wetlands is positively correlated with the surrounding area of temporary wetlands and emergent wetlands. We hypothesized that the relative abundance and species richness of anurans is positively correlated with patch diversity and wetland edges, in the absence of local fragmentation effects. We hypothesized that the relative abundance and species richness of anurans is positively associated with forests but negatively associated with agriculture and urban areas. Our results show that the interspersion of different wetland types and the concomitant increase in wetland edge habitats were generally positive for frogs and toads and anuran abundance and diversity were generally higher in association with forests, especially forested wetlands. The presence of agriculture did not always depress frog and toad populations or diversity; some species were associated with agricultural landscapes. The two states differed in how anurans were associated with landscape features like lakes and permanent wetlands. We found that frog and toad relative abundance and diversity were lower when urban areas were present. Managers can use models like ours, generated from landscape analyses, along with range maps and population trend analyses to get a comprehensive picture of the health of individual species and groups of species. Our models could be applied to the landscape as a whole, and used to predict species relative abundance and

  13. The detection of fast neutral fragments following the photodissociation of krypton cluster ions

    NASA Astrophysics Data System (ADS)

    Smith, J. A.; Winkel, J. F.; Jones, A. B.; Stace, A. J.; Whitaker, B. J.

    1994-05-01

    Mass and kinetic energy resolved krypton cluster ions, Kr+n, have been photodissociated in the entrance to a time-of-flight (TOF) device of variable length. The subsequent deflection of all ions allowed for time resolved measurements to be undertaken on the neutral photofragments. Following the absorption of a photon (hν=2.33 eV), all cluster ions up to Kr+25 were found to eject one or, possibly, two neutral atoms with relatively high kinetic energies. An analysis of the laser polarization dependence of this event showed that the atoms are ejected on a time scale which is short compared with the rotational period of a cluster (10-100 ps). Remaining internal energy within the cluster ions is dissipated through the further loss of neutral atoms, but with low kinetic energies. The latter process is found to be isotropic with respect to the angle of polarization of the laser radiation. Kinetic energy releases calculated from the TOF spectra exhibit a gradual decline as a function of cluster size out as far as Kr+13 and, thereafter, maintain a constant value. This pattern of behavior is significantly different from that observed previously [Smith et al., J. Chem. Phys. 97, 397 (1992)] for argon cluster ions, Ar+n. A careful analysis of the kinetic energy data for Kr+3 photodissociation reveals that, in at least one of the reaction paths, the Kr+ fragment can only be formed in the ground spin-orbit state. This observation implies that photofragmentation proceeds via a 1(1/2)g←1(1/2)u transition. The implications of this result for the analogous Ar+3 photofragmentation are discussed.

  14. On the Benefits of Acquiring Peptide Fragment Ions at High Measured Mass Accuracy

    PubMed Central

    Scherl, Alexander; Shaffer, Scott A.; Taylor, Gregory K.; Hernandez, Patricia; Appel, Ron D.; Binz, Pierre-Alain; Goodlett, David R.

    2008-01-01

    The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap – Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the “C-trap” in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated with this data acquisition mode. It is therefore concluded that acquisition of tandem mass spectral data with high measured mass accuracy and resolution is a competitive alternative to “classical” data acquisition strategies, especially in situations of complex searches from large databases, searches for modified peptides, or for peptides resulting from unspecific cleavages. PMID:18417358

  15. The FRS Ion Catcher - A facility for high-precision experiments with stopped projectile and fission fragments

    NASA Astrophysics Data System (ADS)

    Plaß, W. R.; Dickel, T.; Purushothaman, S.; Dendooven, P.; Geissel, H.; Ebert, J.; Haettner, E.; Jesch, C.; Ranjan, M.; Reiter, M. P.; Weick, H.; Amjad, F.; Ayet, S.; Diwisch, M.; Estrade, A.; Farinon, F.; Greiner, F.; Kalantar-Nayestanaki, N.; Knöbel, R.; Kurcewicz, J.; Lang, J.; Moore, I.; Mukha, I.; Nociforo, C.; Petrick, M.; Pfützner, M.; Pietri, S.; Prochazka, A.; Rink, A.-K.; Rinta-Antila, S.; Schäfer, D.; Scheidenberger, C.; Takechi, M.; Tanaka, Y. K.; Winfield, J. S.; Yavor, M. I.

    2013-12-01

    At the FRS Ion Catcher at GSI, projectile and fission fragments are produced at relativistic energies, separated in-flight, range-focused, slowed down and thermalized in a cryogenic stopping cell. A multiple-reflection time-of-flight mass spectrometer (MR-TOF-MS) is used to perform direct mass measurements and to provide an isobarically clean beam for further experiments, such as mass-selected decay spectroscopy. A versatile RF quadrupole transport and diagnostics unit guides the ions from the stopping cell to the MR-TOF-MS, provides differential pumping, ion identification and includes reference ion sources. The FRS Ion Catcher serves as a test facility for the Low-Energy Branch of the Super-FRS at the Facility for Antiproton and Ion Research (FAIR), where the cryogenic stopping cell and the MR-TOF-MS will be key devices for the research with stopped projectile and fission fragments that will be performed with the experiments MATS and LaSpec. Off-line tests of the stopping cell yield a combined ion survival and extraction efficiency for 219Rn ions of about 30% and an extraction time of about 25 ms. The stopping cell and the MR-TOF-MS were commissioned on-line as part of the FRS Ion Catcher. For the first time, a stopping cell for exotic nuclei was operated on-line at cryogenic temperatures. Using a gas density almost two times higher than ever reached before for a stopping cell with RF ion repelling structures, various 238U projectile fragments were thermalized and extracted with very high efficiency. Direct mass measurements of projectile fragments were performed with the MR-TOF-MS, among them the nuclide 213Rn with a half-life of 19.5 ms only.

  16. Structure Fragmentation in a Subsurface Nickel Titanium Layer Caused by its Irradiation with Pulsed Silicon ion Fluxes

    NASA Astrophysics Data System (ADS)

    Meisner, S. N.

    2014-07-01

    Using the methods of electron backscatter diffraction, an investigation of variations in microstructure of the subsurface nickel titanium layer after its irradiation with pulsed, medium-energy silicon ion fluxes is performed. It is shown that following this ion-beam irradiation of the specimen surfaces, the subsurface-layer structure changes and undergoes fragmentation down to as deep as 5-15 μm, which is smaller than the average grain size of the initial alloy. It is found out that the fragmented-structure layer is characterized by the presence of a martensitic В19' phase and a high concentration of interfaces and grain boundaries; the linear dimensions of the fragments exceed 1 μm, the structure refinement in the layer below the irradiated surface is nonuniform and depends on crystallographic orientation of the initial grain. A reason for intensive fragmentation of individual grains of the initial B2 phase after ion-beam treatment is assumed to be the proximity of the orientation axes of the principal slip planes to that of the incident ion beam flux. This might have resulted in an earlier, compared to other grains, onset of plastic deformation in these grains and, as a result, partial fragmentation of their structure.

  17. Femtosecond probing of sodium cluster ion Na sub n sup + fragmentation

    SciTech Connect

    Baumert, T.; Roettgermann, C.; Rothenfusser, C.; Thalweiser, R.; Weiss, V.; Gerber, G. )

    1992-09-07

    We report on the first femtosecond time-resolved experiments in cluster physics. The photofragmentation dynamics of small sodium cluster ions Na{sub {ital n}}{sup +} have been studied with pump-probe techniques. Ultrashort laser pulses of 60-fs duration are employed to photoionize the sodium clusters and to probe the photofragments. We find that the ejection of neutral dimer Na{sub 2} and, observed for the first time, neutral trimer Na{sub 3} photofragments occur on ultrashort time scales of 2.5 and 0.4 ps, respectively. This and the absence of cluster heating reveals that direct photoinduced fragmentation processes are important at short times rather than the statistical unimolecular decay.

  18. Fragmentation of Electrospray-Produced Deprotonated Ions of Oligodeoxyribonucleotides Containing an Alkylated or Oxidized Thymidine

    NASA Astrophysics Data System (ADS)

    Wang, Pengcheng; Williams, Renee T.; Guerrero, Candace R.; Ji, Debin; Wang, Yinsheng

    2014-07-01

    Alkylation and oxidation constitute major routes of DNA damage induced by endogenous and exogenous genotoxic agents. Understanding the biological consequences of DNA lesions often necessitates the availability of oligodeoxyribonucleotide (ODN) substrates harboring these lesions, and sensitive and robust methods for validating the identities of these ODNs. Tandem mass spectrometry is well suited for meeting these latter analytical needs. In the present study, we evaluated how the incorporation of an ethyl group to different positions (i.e., O 2, N3, and O 4) of thymine and the oxidation of its 5-methyl carbon impact collisionally activated dissociation (CAD) pathways of electrospray-produced deprotonated ions of ODNs harboring these thymine modifications. Unlike an unmodified thymine, which often manifests poor cleavage of the C3'-O3' bond, the incorporation of an alkyl group to the O 2 position and, to a much lesser extent, the O 4 position, but not the N3 position of thymine, led to facile cleavage of the C3'-O3' bond on the 3' side of the modified thymine. Similar efficient chain cleavage was observed when thymine was oxidized to 5-formyluracil or 5-carboxyluracil, but not 5-hydroxymethyluracil. Additionally, with the support of computational modeling, we revealed that proton affinity and acidity of the modified nucleobases govern the fragmentation of ODNs containing the alkylated and oxidized thymidine derivatives, respectively. These results provided important insights into the effects of thymine modifications on ODN fragmentation.

  19. Seasonal Blowfly Distribution and Abundance in Fragmented Landscapes. Is It Useful in Forensic Inference about Where a Corpse Has Been Decaying?

    PubMed Central

    Zabala, Jabi; Díaz, Beatriz; Saloña-Bordas, Marta I.

    2014-01-01

    Blowflies are insects of forensic interest as they may indicate characteristics of the environment where a body has been laying prior to the discovery. In order to estimate changes in community related to landscape and to assess if blowfly species can be used as indicators of the landscape where a corpse has been decaying, we studied the blowfly community and how it is affected by landscape in a 7,000 km2 region during a whole year. Using baited traps deployed monthly we collected 28,507 individuals of 10 calliphorid species, 7 of them well represented and distributed in the study area. Multiple Analysis of Variance found changes in abundance between seasons in the 7 analyzed species, and changes related to land use in 4 of them (Calliphora vomitoria, Lucilia ampullacea, L. caesar and L. illustris). Generalised Linear Model analyses of abundance of these species compared with landscape descriptors at different scales found only a clear significant relationship between summer abundance of C. vomitoria and distance to urban areas and degree of urbanisation. This relationship explained more deviance when considering the landscape composition at larger geographical scales (up to 2,500 m around sampling site). For the other species, no clear relationship between land uses and abundance was found, and therefore observed changes in their abundance patterns could be the result of other variables, probably small changes in temperature. Our results suggest that blowfly community composition cannot be used to infer in what kind of landscape a corpse has decayed, at least in highly fragmented habitats, the only exception being the summer abundance of C. vomitoria. PMID:24918607

  20. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    PubMed Central

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2016-01-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contributes to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), that enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the following iterations. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. PMID:26419769

  1. reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

    PubMed

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W; Moritz, Robert L

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ. PMID:26419769

  2. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    NASA Astrophysics Data System (ADS)

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

  3. Infrared Ion-Gain Spectroscopy and Fractional Abundance Measurements of Conformer Populations

    NASA Astrophysics Data System (ADS)

    Buchanan, Evan G.; Dean, Jacob C.; Marsh, Brett M.; Zwier, Timothy S.

    2011-06-01

    Studies of the single-conformation spectroscopy of large, flexible molecules has as one of its goals providing incisive tests of the predictions of calculations on the isolated molecules, whether ab initio or semi-empirical in nature. An important aspect of this comparison that is often lacking is quantitative data on the fractional abundances of the conformations. Previous studies from our group have provided such data using mass-resolved infrared population transfer (IRPT) spectroscopy. In this talk, we present an alternative method that in certain circumstances has advantages over IRPT, especially in ease of implementation. The method, infrared ion-gain (IRIG) spectroscopy, was first introduced by Fujii and co-workers on molecules without conformational isomers. Here we extend the method to conformationally flexible molecules, and test whether it can be used to provide fractional abundances by comparing with IRPT results^a on jet-cooled Ac-γ2-hPhe-NHMe, using thermal methods for vaporization of the molecule. The comparison provides some confidence that IRIG can be used for this purpose, but also points out conditions where it must be used with care. Analogous fractional abundance measurements on a prototypical lignin monomer will also be described, this time brought into the gas phase by laser desorption. Details of the laser desorption scheme used will also be provided. W. H. James III, C. W. Muller, E. G. Buchanan, M. G. D. Nix, L. Guo, L. Roskop, M. S. Gordon, L. V. Slipchenko, S. H. Gellman and T. S. Zwier J. Am. Chem. Soc. 131, (14243-14245), 2009. S. Ishiuchi, H. Shitomi, K. Takazawa and M. Fujii Chem. Phys. Lett. 283, (243-250), 1998.

  4. Ion abundances and implications for photochemistry in Comets Halley (1986 III) and Bradfield (1987 XXIX)

    NASA Astrophysics Data System (ADS)

    Lutz, B. L.; Womack, M.; Wagner, R. M.

    1993-04-01

    The Ohio State University Image Dissector Scanner on the Perkins 1.8-m telescope at the Lowell Observatory was used to record spectra of the plasma tails of Comets P/Halley (1986 III) and P/Bradfield (1987 XXIX, also 1987s). The ionic species CO(+), N2(+), CH(+), and H2O(+) were identified in these spectra, and column densities for them were calculated from measured fluxes. The observed N2(+)/H2O(+) ratios are at least an order of magnitude lower and the observed CH(+)/H2O(+) ratios are a factor of 100 higher than theoretical results. The abundance ratio N2/CO was derived in the plasma tail of Bradfield from N2(+) and CO(+) data, and found to be an order of magnitude higher than a value measured in Halley. The relative ion abundances of CH(+), N2(+), CO(+), and H2O(+) in Halley are consistent with in situ measurements obtained from the Giotto spacecraft.

  5. Ion abundances and implications for photochemistry in Comets Halley (1986 III) and Bradfield (1987 XXIX)

    NASA Technical Reports Server (NTRS)

    Lutz, Barry L.; Womack, Maria; Wagner, R. M.

    1993-01-01

    The Ohio State University Image Dissector Scanner on the Perkins 1.8-m telescope at the Lowell Observatory was used to record spectra of the plasma tails of Comets P/Halley (1986 III) and P/Bradfield (1987 XXIX, also 1987s). The ionic species CO(+), N2(+), CH(+), and H2O(+) were identified in these spectra, and column densities for them were calculated from measured fluxes. The observed N2(+)/H2O(+) ratios are at least an order of magnitude lower and the observed CH(+)/H2O(+) ratios are a factor of 100 higher than theoretical results. The abundance ratio N2/CO was derived in the plasma tail of Bradfield from N2(+) and CO(+) data, and found to be an order of magnitude higher than a value measured in Halley. The relative ion abundances of CH(+), N2(+), CO(+), and H2O(+) in Halley are consistent with in situ measurements obtained from the Giotto spacecraft.

  6. Abundances and charge states in quiet-time low-energy ion fluxes at 1 AU

    NASA Astrophysics Data System (ADS)

    Kecskemety, Karoly; Zeldovich, Mariya; Klecker, Berndt; Logachev, Yurii

    Abundances of C and Fe ions with energies 0.04-1.28 MeV/nuc in the 23rd solar activity cycle are examined in the quiet-time fluxes using ACE, SOHO and STEREO data. They are com-bined with charge state measurement data from SEPICA (ACE, 0.18-0.43 MeV/nuc). Quiet periods of solar activity were selected using the criteria a) Jp < 2x10-4 protons/(cm2 s sr MeV) for 4-8 MeV protons (from EPHIN/SOHO) and b) the ratio H/He < 10 at these energies. The values of C/O and Fe/O were determined over the solar cycle and the following was found. In about 50% of the time intervals during high activity they both were near the average values observed in the solar corona, whereas at solar minimum in more than 90% of the periods the ratios were around the solar wind values. Most of the quiet time periods around maximum, which have sufficient statistics show high average Fe charge states (>15), consistent with im-pulsive solar event origin. During the SC minima the abundances in almost all cases correspond to solar wind values. The results obtained suggest that the active structures on the Sun arising at low solar activity are mostly responsible for background particle fluxes at these energies. There may be microflares, disappearing of ribbons, soft X-ray bright points etc.

  7. An Ion Microprobe Study of a Unique Oldhamite-Pyroxenite Fragment from the Bustee Aubrite

    NASA Astrophysics Data System (ADS)

    Kurat, G.; Zinner, E.; Brandstatter, F.

    1992-07-01

    While it is widely believed that the minerals in aubrite breccias are of igneous origin (e.g., 1) bulk trace element abundances (e.g., 2) and the distribution of trace elements between phases (e.g., 3-5) are incompatible with an igneous genesis and strongly suggest a nebular origin (e.g., 6). Here we report trace element data on mineral phases in a unique rock fragment from the Bustee meteorite as well as with the N and Ti isotope compositions in osbornite. In the first characterization of Bustee, Story-Maskelyne (7) described a rock fragment consisting of oldhamite, enstatite, augite, and plagioclase in which he also first dicovered osbornite. The rock consists of large (2-3 mm) rounded oldhamite embedded in granular pyroxene (pictures given by 7 and 8). Osbornite is commonly included in oldhamite. Some metal (Si- and Cr-bearing) and a few grains of heideite and other rare sulfides are present. The REE abundances in selected minerals are shown in the figure. Surprisingly, all patterns are nearly flat. The oldhamite is strongly enriched in REE (see also 3-5) and has a positive Eu anomaly. Osbornite shows a slightly fractionated pattern with La>Lu and REE abundances of 0.5-9 x CI. Pyroxenes have the lowest REE contents at 0.2-0.3 x CI (pigeonite) and 0.03-0.08 x CI (enstatite). Isotopic compositions of Ti and N in osbornite and of Ca in oldhamite are indistinguishable from terrestrial. The distribution of REE beween mineral phases does not correspond to experimentally determined distribution coefficients (9). This and the primitive (not crystal-chemically controlled) REE abundances in all phases make it very likely that the minerals of the oldhamite-pyroxenite from Bustee were formed by condensation. The condensation sequence must have been osbornite-oldhamite- pigeonite-enstatite. As the first major phase to condense, oldhamite apparently scavenged most of the REE present in the gas. It must have been formed well below 1380 K (10) and from a slightly fractionated

  8. Changes in the molecular ion yield and fragmentation of peptides under various primary ions in ToF-SIMS and matrix-enhanced ToF-SIMS.

    PubMed

    Körsgen, Martin; Tyler, Bonnie J; Pelster, Andreas; Lipinsky, Dieter; Dreisewerd, Klaus; Arlinghaus, Heinrich F

    2016-06-01

    Time of flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique for the nanoanalysis of biological samples, but improvements in sensitivity are needed in order to detect large biomolecules, such as peptides, on the individual cell level at physiological concentrations. Two promising options to improve the sensitivity of SIMS to large peptides are the use of cluster primary ions to increase desorption of intact molecules or the use of matrix-assisted laser desorption/ionization (MALDI) matrices to increase the ionization probability. In this paper, the authors have combined these two approaches in order to improve understanding of the interaction between ionization and fragmentation processes. The peptides bradykinin and melittin were prepared as neat monolayers on silicon, in a Dextran-40 matrix and in two common MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxy cinnamic acid (HCCA). ToF-SIMS spectra of these samples were collected using a range of small Bi cluster primary ions and large Ar cluster primary ions. The trends observed in the molecular ion yield and the [M+H](+)/C4H8N(+) ratio with primary ion cluster size were sample system dependent. The molecular ion yield of the bradykinin was maximized by using 30 keV Bi3 (+) primary ions in a DHB matrix but in the HCCA matrix, the maximum molecular ion yield was obtained by using 30 keV Bi7 (+) primary ions. In contrast, the molecular ion yield for melittin in both matrices was greatest using 20 keV Ar2000 (+) primary ions. Improvements in the molecular ion yield were only loosely correlated with a decrease in small fragment ions. The data indicate a complex interplay between desorption processes and ion formation processes which mean that the optimal analytical conditions depend on both the target analyte and the matrix. PMID:26829968

  9. High Spatial Resolution Isotopic Abundance Measurements by Secondary Ion Mass Spectrometry: Status and Prospects

    NASA Astrophysics Data System (ADS)

    McKeegan, K. D.

    2007-12-01

    Secondary Ion Mass Spectrometry, SIMS or ion microprobe analysis, has become an important tool for geochemistry because of its ability study the distributions of elemental and isotopic abundances in situ on polished samples with high (typically a few microns to sub-micron) spatial resolution. In addition, SIMS exhibits high sensitivity for a wide range of elements (H to Pu) so that isotope analyses can sometimes be performed for elements that comprise only trace quantities of some mineral phase (e.g., Pb in zircon) or on major and/or minor elements in very small samples (e.g., presolar dust grains). Offsetting these positive attributes are analytical difficulties due to the complexity of the sputtering source of analyte ions: (1) relatively efficient production of molecular ion species (especially from a complex matrix such as most natural minerals) that cause interferences at the same nominal mass as atomic ions of interest, and (2) quantitation problems caused by variations in the ionization efficiencies of different elements and/or isotopes depending upon the chemical state of the sample surface during sputtering--the so-called "matrix effects". Despite the availability of high mass resolution instruments (e.g., SHRIMP II/RG, CAMECA 1270/1280/NanoSIMS), the molecular ion interferences effectively limit the region of the mass table that can be investigated in most samples to isotope systems at Ni or lighter or at Os or heavier. The matrix effects and the sensitivity of instrumental mass discrimination to the physical state of the sample surface can hamper reproducibility and have contributed to a view that SIMS analyses, especially for so- called stable isotopes, are most appropriate for extraterrestrial samples which are often small, rare, and can exhibit large magnitude isotopic effects. Recent improvements in instrumentation and technique have extended the scope of SIMS isotopic analyses and applications now range from geochronology to paleoclimatology to

  10. Effects of landscape composition and wetland fragmentation on frog and toad abundance and species richness in Iowa and Wisconsin, USA

    USGS Publications Warehouse

    Knutson, M.G.; Sauer, J.R.; Olsen, D.A.; Mossman, M.J.; Hemesath, L.M.; Lannoo, M.J.

    1999-01-01

    Management of amphibian populations to reverse recent declines will require defining high-quality habitat for individual species or groups of species, followed by efforts to retain or restore these habitats on the landscape. We examined landscape-level habitat relationships for frogs and toads by measuring associations between relative abundance and species richness based on survey data derived from anuran calls and features of land-cover maps for Iowa and Wisconsin. The most consistent result across all anuran guilds was a negative association with the presence of urban land. Upland and wetland forests and emergent wetlands tended to be positively associated with anurans. Landscape metrics that represent edges and patch diversity also had generally positive associations, indicating that anurans benefit from a complex of habitats that include wetlands. In Iowa the most significant associations with relative abundance were the length of the edge between wetland and forest (positive) and the presence of urban land (negative). In Wisconsin the two most significant associations with relative abundance were forest area and agricultural area (both positive). Anurans had positive associations with agriculture in Wisconsin but not in Iowa. Remnant forest patches in agricultural landscapes may be providing refuges for some anuran species. Differences in anuran associations with deep water and permanent wetlands between the two states suggest opportunities for management action. Large-scale maps can contribute to predictive models of amphibian habitat use, but water quality and vegetation information collected from individual wetlands will likely be needed to strengthen those predictions. Landscape habitat analyses provide a framework for future experimental and intensive research on specific factors affecting the health of anurans.

  11. Development of Diagnostic Fragment Ion Library for Glycated Peptides of Human Serum Albumin: Targeted Quantification in Prediabetic, Diabetic, and Microalbuminuria Plasma by Parallel Reaction Monitoring, SWATH, and MSE.

    PubMed

    Korwar, Arvind M; Vannuruswamy, Garikapati; Jagadeeshaprasad, Mashanipalya G; Jayaramaiah, Ramesha H; Bhat, Shweta; Regin, Bhaskaran S; Ramaswamy, Sureshkumar; Giri, Ashok P; Mohan, Viswanathan; Balasubramanyam, Muthuswamy; Kulkarni, Mahesh J

    2015-08-01

    Human serum albumin is one of the most abundant plasma proteins that readily undergoes glycation, thus glycated albumin has been suggested as an additional marker for monitoring glycemic status. Hitherto, only Amadori-modified peptides of albumin were quantified. In this study, we report the construction of fragment ion library for Amadori-modified lysine (AML), N(ε)-(carboxymethyl)lysine (CML)-, and N(ε)-(carboxyethyl)lysine (CEL)-modified peptides of the corresponding synthetically modified albumin using high resolution accurate mass spectrometry (HR/AM). The glycated peptides were manually inspected and validated for their modification. Further, the fragment ion library was used for quantification of glycated peptides of albumin in the context of diabetes. Targeted Sequential Window Acquisition of all THeoretical Mass Spectra (SWATH) analysis in pooled plasma samples of control, prediabetes, diabetes, and microalbuminuria, has led to identification and quantification of 13 glycated peptides comprised of four AML, seven CML, and two CEL modifications, representing nine lysine sites of albumin. Five lysine sites namely K549, K438, K490, K88, and K375, were observed to be highly sensitive for glycation modification as their respective m/z showed maximum fold change and had both AML and CML modifications. Thus, peptides involving these lysine sites could be potential novel markers to assess the degree of glycation in diabetes. PMID:26023067

  12. Mercury-induced fragmentation of n-decane and n-undecane in positive mode ion mobility spectrometry.

    PubMed

    Gunzer, F

    2015-09-21

    Ion mobility spectrometry is a well-known technique for trace gas analysis. Using soft ionization techniques, fragmentation of analytes is normally not observed, with the consequence that analyte spectra of single substances are quite simple, i.e. showing in general only one peak. If the concentration is high enough, an extra cluster peak involving two analyte molecules can often be observed. When investigating n-alkanes, different results regarding the number of peaks in the spectra have been obtained in the past using this spectrometric technique. Here we present results obtained when analyzing n-alkanes (n-hexane to n-undecane) with a pulsed electron source, which show no fragmentation or clustering at all. However, when investigating a mixture of mercury and an n-alkane, a situation quite typical in the oil and gas industry, a strong fragmentation and cluster formation involving these fragments has been observed exclusively for n-decane and n-undecane. PMID:26247063

  13. Low-energy mass-selected ion beam production of fragments produced from hexamethyldisilane for SiC film formation

    NASA Astrophysics Data System (ADS)

    Yoshimura, Satoru; Sugimoto, Satoshi; Kiuchi, Masato

    2016-03-01

    We have proposed an experimental methodology which makes it possible to deposit silicon carbide (SiC) films on Si substrates with a low-energy mass-selected ion beam system using hexamethyldisilane (HMD) as a gas source. In this study, one of the fragment ions produced from HMD, SiCH4+, was mass-selected. The ion energy was approximately 100 eV. Then, the SiCH4+ ions were irradiated to a Si(100) substrate. When the temperature of the Si substrate was set at 800 °C during the ion irradiation, the X-ray diffraction and Raman spectroscopy of the substrate following the completion of ion irradiation experiment demonstrated the occurrence of 3C-SiC deposition.

  14. Dynamics of fragments and associated phenomena in heavy-ion collisions using a modified secondary algorithm

    NASA Astrophysics Data System (ADS)

    Kumar, Rohit

    2016-05-01

    We discuss the stability of fragments identified by secondary algorithms used to construct fragments within quantum molecular dynamics model. For this purpose we employ three different algorithms for fragment identification. 1) The conventional minimum spanning tree (MST) method based on the spatial correlations, 2) an improved version of MST with additional binding energy constraints of cold nuclear matter, 3) and that of hot matter. We find significant role of thermal binding energies over cold matter binding energies. Significant role is observed for fragment multiplicities and stopping of fragments. Whereas insignificant effect is observed on fragment's flow.

  15. Statistical Examination of the a and a + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions

    NASA Astrophysics Data System (ADS)

    Morrison, Lindsay J.; Rosenberg, Jake A.; Singleton, Jonathan P.; Brodbelt, Jennifer S.

    2016-05-01

    Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue.

  16. Statistical Examination of the a and a + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions

    NASA Astrophysics Data System (ADS)

    Morrison, Lindsay J.; Rosenberg, Jake A.; Singleton, Jonathan P.; Brodbelt, Jennifer S.

    2016-09-01

    Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue.

  17. High-resolution (e, 2e + ion) study of electron-impact ionization and fragmentation of methane

    SciTech Connect

    Ren, Xueguang Pflüger, Thomas; Weyland, Marvin; Baek, Woon Yong; Rabus, Hans; Ullrich, Joachim; Dorn, Alexander

    2015-05-07

    The ionization and fragmentation of methane induced by low-energy (E{sub 0} = 66 eV) electron-impact is investigated using a reaction microscope. The momentum vectors of all three charged final state particles, two outgoing electrons, and one fragment ion, are detected in coincidence. Compared to the earlier study [Xu et al., J. Chem. Phys. 138, 134307 (2013)], considerable improvements to the instrumental mass and energy resolutions have been achieved. The fragment products CH{sub 4}{sup +}, CH{sub 3}{sup +}, CH{sub 2}{sup +}, CH{sup +}, and C{sup +} are clearly resolved. The binding energy resolution of ΔE = 2.0 eV is a factor of three better than in the earlier measurements. The fragmentation channels are investigated by measuring the ion kinetic energy distributions and the binding energy spectra. While being mostly in consistence with existing photoionization studies the results show differences including missing fragmentation channels and previously unseen channels.

  18. Fragmentation of molecular ions in differential mobility spectrometry as a method for identification of chemical warfare agents.

    PubMed

    Maziejuk, M; Puton, J; Szyposzyńska, M; Witkiewicz, Z

    2015-11-01

    The subject of the work is the use of differential mobility spectrometry (DMS) for the detection of chemical warfare agents (CWA). Studies were performed for mustard gas, i.e., bis(2-chloroethyl)sulfide (HD), sarin, i.e., O-isopropyl methylphosphonofluoridate (GB) and methyl salicylate (MS) used as test compounds. Measurements were conducted with two ceramic DMS analyzers of different constructions allowing the generation of an electric field with an intensity of more than 120 Td. Detector signals were measured for positive and negative modes of operation in a temperature range from 0 to 80 °C. Fragmentations of ions containing analyte molecules were observed for all tested compounds. The effective temperatures of fragmentation estimated on the basis of dispersion plots were equal from about 148 °C for GB to 178 °C for MS. It was found that values of separation voltage (SV) and compensation voltage (CV) at which the fragmentation of sample ions is observed may be the parameters improving the certainty of detection for different analytes. The DMS analyzers enabling the observation of ion fragmentation can be successfully used for effective CWA detection. PMID:26452948

  19. Fragmented carbon nanotube macrofilms as adhesive conductors for lithium-ion batteries.

    PubMed

    Cao, Zeyuan; Wei, Bingqing

    2014-03-25

    Polymer binders such as poly(vinylidene fluoride) (PVDF) and conductive additives such as carbon black (CB) are indispensable components for manufacturing battery electrodes in addition to active materials. The concept of adhesive conductors employing fragmented carbon nanotube macrofilms (FCNTs) is demonstrated by constructing composite electrodes with a typical active material, LiMn2O4. The adhesive FCNT conductors provide not only a high electrical conductivity but also a strong adhesive force, functioning simultaneously as both the conductive additives and the binder materials for lithium-ion batteries. Such composite electrodes exhibit superior high-rate and retention capabilities compared to the electrodes using a conventional binder (PVDF) and a conductive additive (CB). An in situ tribology method combining wear track imaging and force measurement is employed to evaluate the adhesion strength of the adhesive FCNT conductors. The adhesive FCNT conductors exhibit higher adhesion strength than PVDF. It has further been confirmed that the adhesive FCNT conductor can be used in both cathodes and anodes and is proved to be a competent substitute for polymer binders to maintain mechanical integrity and at the same time to provide electrical connectivity of active materials in the composite electrodes. The organic-solvent-free electrode manufacturing offers a promising strategy for the battery industry. PMID:24564355

  20. Mechanical Design of a Heavy Ion Beam Dump for the RIA Fragmentation Line

    SciTech Connect

    Stein, W; Ahle, L E; Conner, D L

    2005-04-28

    The RIA fragmentation line requires a beam stop for the primary beam downstream of the first dipole magnet. The beam may consist of U, Ca, Sn, Kr, or O ions. with a variety of power densities. The configuration with highest power density is for the U beam, with a spot size of 3 cm x 3 cm and a total power of up to 300 kW. The mechanical design of the dump that meets these criteria consists of a 70 cm diameter aluminum wheel with water coolant channels. A hollow drive shaft supplies the coolant water and connects the wheel to an electrical motor located in an adjacent air space. The beam strikes the wheel along the outer perimeter and passes through a thin window of aluminum where 15% of its power is absorbed and the remainder of the beam is absorbed in flowing water behind the window. Rotation of the wheel at 400 RPM results in maximum aluminum temperatures below 100 C and acceptably low thermal stresses of 3 ksi. Rotating the wheel also results in low radiation damage levels by spreading the damage out over the whole perimeter of the wheel. For some of the other beams, a stationary dump consisting of a thin aluminum window with water acting as a coolant and absorber appears to be feasible.

  1. Fragmentation of doubly-protonated peptide ion populations labeled by H/D exchange with CD3OD

    NASA Astrophysics Data System (ADS)

    Herrmann, Kristin A.; Kuppannan, Krishna; Wysocki, Vicki H.

    2006-03-01

    Doubly-protonated bradykinin (RPPGFSPFR) and an angiotensin III analogue (RVYIFPF) were subjected to hydrogen/deuterium (H/D) exchange with CD3OD in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. A bimodal distribution of deuterium incorporation was present for bradykinin after H/D exchange for 90 s at a CD3OD pressure of 4 × 10-7 Torr, indicating the existence of at least two distinct populations. Bradykinin ion populations corresponding to 0-2 and 5-11 deuteriums (i.e., D0, D1, D2, D5, D6, D7, D8, D9, D10, and D11) were each monoisotopically selected and fragmented via sustained off-resonance irradiation (SORI) collision-induced dissociation (CID). The D0-D2 ion populations, which correspond to the slower exchanging population, consistently require lower SORI amplitude to achieve a similar precursor ion survival yield as the faster-reacting (D5-D11) populations. These results demonstrate that conformation/protonation motif has an effect on fragmentation efficiency for bradykinin. Also, the partitioning of the deuterium atoms into fragment ions suggests that the C-terminal arginine residue exchanges more rapidly than the N-terminal arginine. Total deuterium incorporation in the b1/y8 and b2/y7 ion pairs matches very closely the theoretical values for all ion populations studied, indicating that the ions of a complementary pair are likely formed during the same fragmentation event, or that no scrambling occurs upon SORI. Deuterium incorporation into the y1/a8 pseudo-ion pair does not closely match the expected theoretical values. The other peptide, doubly-protonated RVYIFPF, has a trimodal distribution of deuterium incorporation upon H/D exchange with CD3OD at a pressure of 1 × 10-7 Torr for 600 s, indicating at least three distinct ion populations. After 90 s of H/D exchange where at least two distinct populations are detected, the D0-D7 ion populations were monoisotopically selected and fragmented via SORI-CID over a range of SORI

  2. Two-dimensional ion-imaging of fragment angular distributions after photolysis of state-selected and oriented triatomic molecules

    SciTech Connect

    Teule, J.M.; Hilgeman, M.H.; Janssen, M.H.; Chandler, D.W.; Taatjes, C.A.; Stolte, S.

    1997-01-01

    Photodissociation experiments of state-selected and oriented triatomics are presented. Selective ionization using REMPI in combination with two-dimensional ion-imaging allows us to measure both the internal energy and angular distribution of the fragments. The dissociation of N{sub 2}O is studied using one laser around 204 nm for both the dissociation of the molecule and the ionization of the fragments. The angular distributions of O({sup 1}D) and N{sub 2}(J) are presented and implications of these results on the dissociation dynamics are discussed. {copyright} {ital 1997 American Institute of Physics.}

  3. Two-dimensional ion-imaging of fragment angular distributions after photolysis of state-selected and oriented triatomic molecules

    SciTech Connect

    Teule, J. M.; Hilgeman, M. H.; Janssen, M. H. M.; Chandler, D. W.; Taatjes, C. A.; Stolte, S.

    1997-01-15

    Photodissociation experiments of state-selected and oriented triatomics are presented. Selective ionization using REMPI in combination with two-dimensional ion-imaging allows us to measure both the internal energy and angular distribution of the fragments. The dissociation of N{sub 2}O is studied using one laser around 204 nm for both the dissociation of the molecule and the ionization of the fragments. The angular distributions of O({sup 1}D) and N{sub 2}(J) are presented and implications of these results on the dissociation dynamics are discussed.

  4. Constraining the pickup ion abundance and temperature through the multifluid reconstruction of the Voyager 2 termination shock crossing

    NASA Astrophysics Data System (ADS)

    Zieger, Bertalan; Opher, Merav; Tóth, Gábor; Decker, Robert B.; Richardson, John D.

    2015-09-01

    Voyager 2 observations revealed that the hot solar wind ions (the so-called pickup ions) play a dominant role in the thermodynamics of the termination shock and the heliosheath. The number density and temperature of this hot population, however, have remained unknown, since the plasma instrument on board Voyager 2 can only detect the colder thermal ion component. Here we show that due to the multifluid nature of the plasma, the fast magnetosonic mode splits into a low-frequency fast mode and a high-frequency fast mode. The coupling between the two fast modes results in a quasi-stationary nonlinear wave mode, the "oscilliton," which creates a large-amplitude trailing wave train downstream of the thermal ion shock. By fitting multifluid shock wave solutions to the shock structure observed by Voyager 2, we are able to constrain both the abundance and the temperature of the undetected pickup ions. In our three-fluid model, we take into account the nonnegligible partial pressure of suprathermal energetic electrons (0.022-1.5 MeV) observed by the Low-Energy Charged Particle Experiment instrument on board Voyager 2. The best fitting simulation suggests a pickup ion abundance of 20 ± 3%, an upstream pickup ion temperature of 13.4 ± 2 MK, and a hot electron population with an apparent temperature of ~0.83 MK. We conclude that the actual shock transition is a subcritical dispersive shock wave with low Mach number and high plasma β.

  5. Distribution and abundance of anadromous Sea Lamprey Spawners in a fragmented stream: Current status and potential range expansion following barrier removal

    USGS Publications Warehouse

    Zydlewski, Joseph; Gardner, Cory; Coghlan Jr., Stephen M.

    2012-01-01

    Dams fragment watersheds and prevent anadromous fishes from reaching historic spawning habitat. Sedgeunkedunk Stream, a small tributary to the Penobscot River (Maine), has been the focus of efforts to reestablish marine-freshwater connectivity and restore anadromous fishes via the removal of two barriers to fish migration. Currently, Petromyzon marinus (Sea Lamprey) is the only anadromous fish known to spawn successfully in the stream downstream of the lowermost dam. Here, we describe the distribution and abundance of a spawning population of Sea Lamprey in Sedgeunkedunk Stream, prior to and in anticipation of habitat increase after the completion of one barrier removal. In 2008, we estimated the abundance of Sea Lamprey and its nests using daily stream surveys and an open-population mark-recapture model. We captured 47 Sea Lamprey and implanted each with a PIT tag so that we could track movements and nest associations of individual fish. The spawning migration began on 18 June, and the last living individual was observed on 27 June. We located 31 nests, distributed from head-of-tide to the lowermost dam; no spawners or nests were observed in the tidally influenced zone or upstream of this dam. Mean longevity in the stream and the number of nests attended were correlated with arrival date; early migrants were alive longer and attended more nests than later migrants. Males were more likely to be observed away from a nest, or attending three or more nests, than were females, which attended usually one or two nests. We observed a negative association between nest abundance and substrate cover by fine sediment. Based on their observed movements in the system, and the extent of their habitat use, we anticipate that spawning Sea Lamprey will recolonize formerly inaccessible habitat after dam removals.

  6. Probing Temperature from Intermediate Mass Fragment by Isobaric Yield Ratio in Heavy-Ion Collisions

    NASA Astrophysics Data System (ADS)

    Yu, Mian; Wei, Hui-Ling; Ma, Chun-Wang

    2015-12-01

    A probe to extract the temperature (TIYR) from intermediate-mass fragment has been proposed using the isobaric yield ratio (IYR) difference based on the modified Fisher model. By analyzing the isobaric cross section in the measured 140A MeV 40,48Ca+9Be reactions, the TIYR can well fit the IYR difference for the large mass fragments. Because of the fragments are produced in different colliding regions, it is also suggested to select the fragments according to different mechanisms when using TIYR. Supported by Program for Science & Technology Innovation Talents in Universities of Henan Province under Grant No. 13HASTIT046

  7. Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Ren, Jianhua; Tian, Yuan; Hossain, Ekram; Connolly, Michael D.

    2016-04-01

    Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

  8. Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation.

    PubMed

    Ren, Jianhua; Tian, Yuan; Hossain, Ekram; Connolly, Michael D

    2016-04-01

    Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry. Graphical Abstract ᅟ. PMID:26832347

  9. Parallel Accumulation-Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device.

    PubMed

    Meier, Florian; Beck, Scarlet; Grassl, Niklas; Lubeck, Markus; Park, Melvin A; Raether, Oliver; Mann, Matthias

    2015-12-01

    In liquid chromatography-mass spectrometry (LC-MS)-based proteomics, many precursors elute from the column simultaneously. In data-dependent analyses, these precursors are fragmented one at a time, whereas the others are discarded entirely. Here we employ trapped ion mobility spectrometry (TIMS) on an orthogonal quadrupole time-of-flight (QTOF) mass spectrometer to remove this limitation. In TIMS, all precursor ions are accumulated in parallel and released sequentially as a function of their ion mobility. Instead of selecting a single precursor mass with the quadrupole mass filter, we here implement synchronized scans in which the quadrupole is mass positioned with sub-millisecond switching times at the m/z values of appropriate precursors, such as those derived from a topN precursor list. We demonstrate serial selection and fragmentation of multiple precursors in single 50 ms TIMS scans. Parallel accumulation-serial fragmentation (PASEF) enables hundreds of MS/MS events per second at full sensitivity. Modeling the effect of such synchronized scans for shotgun proteomics, we estimate that about a 10-fold gain in sequencing speed should be achievable by PASEF without a decrease in sensitivity. PMID:26538118

  10. Key Role for the 12-Hydroxy Group in the Negative Ion Fragmentation of Unconjugated C24 Bile Acids.

    PubMed

    Lan, Ke; Su, Mingming; Xie, Guoxiang; Ferslew, Brian C; Brouwer, Kim L R; Rajani, Cynthia; Liu, Changxiao; Jia, Wei

    2016-07-19

    Host-gut microbial interactions contribute to human health and disease states and an important manifestation resulting from this cometabolism is a vast diversity of bile acids (BAs). There is increasing interest in using BAs as biomarkers to assess the health status of individuals and, therefore, an increased need for their accurate separation and identification. In this study, the negative ion fragmentation behaviors of C24 BAs were investigated by UPLC-ESI-QTOF-MS. The step-by-step fragmentation analysis revealed a distinct fragmentation mechanism for the unconjugated BAs containing a 12-hydroxyl group. The unconjugated BAs lacking 12-hydroxylation fragmented via dehydration and dehydrogenation. In contrast, the 12-hydroxylated ones, such as deoxycholic acid (DCA) and cholic acid (CA), employed dissociation routes including dehydration, loss of carbon monoxide or carbon dioxide, and dehydrogenation. All fragmentations of the 12-hydroxylated unconjugated BAs, characterized by means of stable isotope labeled standards, were associated with the rotation of the carboxylate side chain and the subsequent rearrangements accompanied by proton transfer between 12-hydroxyl and 24-carboxyl groups. Compared to DCA, CA underwent further cleavages of the steroid skeleton. Accordingly, the effects of stereochemistry on the fragmentation pattern of CA were investigated using its stereoisomers. Based on the knowledge gained from the fragmentation analysis, a novel BA, 3β,7β,12α-trihydroxy-5β-cholanic acid, was identified in the postprandial urine samples of patients with nonalcoholic steatohepatitis. The analyses used in this study may contribute to a better understanding of the chemical diversity of BAs and the molecular basis of human liver diseases that involve BA synthesis, transport, and metabolism. PMID:27322813

  11. Ion microprobe U-Pb dating and REE abundance of biogenic apatite

    NASA Astrophysics Data System (ADS)

    Sano, Y.; Terada, K.; Ueki, S.

    2001-12-01

    If the direct U-Pb dating of a fossil itself is possible, the method could have great impact on stratigraphic studies in establishing the absolute chronology of sedimentary sequences. Micro fossil ?conodont? are candidates for this purpose since they consist of apatite (Ca2(PO5)3 (F,Cl,OH)), which would uptake U, Th and Pb after sedimentation no longer than a few million years and is supposed to remain closed to U and Pb under relatively low effective closure temperature. We report here results of direct ion microprobe U-Th-Pb dating of two conodonts; Trichognathus from Kinderhookian stage of Mississippian sedimentary sequence from Illinois Basin region in North America and Panderodus from a Llandoverian sedimentary sequence on Langkawi Island, northern Malaysia. Secondary purpose of the study is to indicate in situ analysis of all REE on the same spots of U-Pb measurements. Samples were cast into epoxy resin discs with a few grains of standard apatite, PRAP, derived from an alkaline rock of Prairie Lake circular complex in the Canadian Shield and polished until they were exposed through their mid-sections. U, Th and REE abundances, and Pb isotopic compositions were measured by using SHRIMP installed at Hiroshima University. Thirteen spots on Trichognathus yield a 238U/206Pb isochron age of 323+/-36 Ma, which is consistent with the depositional and early diagenetic ages. Fifteen spots on Panderodus give 232Th/208Pb isochron age of 429+/-50 Ma, which is again comparable to an early Silurian. Shale-normalized REE of Trichognathus shows a broadly flat pattern from light to middle REE and a decrease from middle to heavy REE with negative anomalies of Ce and Eu. In contrast Panderodus indicates a concave-shape pattern with middle REE enrichment. These characteristics are probably due to a different formation environment as suggested by other workers.

  12. Analysis of angular distribution of fragments in relativistic heavy-ion collisions by quantum molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ogawa, Tatsuhiko; Sato, Tatsuhiko; Hashimoto, Shintaro; Niita, Koji

    2016-05-01

    To predict angular distribution of fragments produced in nucleusnucleus collisions, JAERI quantum molecular dynamics model (JQMD) was improved. Because JQMD underestimated fragments in the forward angle, which were mainly produced by peripheral collisions, JQMD was revised so as to simulate peripheral collisions accurately. Density-dependent in-medium effect and relativistic effect on nucleonnucleon interactions were incorporated for this purpose. The revised version of JQMD coupled with a statistical decay model was used to calculate differential fragment production cross sections measured in earlier studies. Comparison of the measured data and calculation by the revised and old JQMD showed that the revised JQMD can predict fragment angular distribution better than old JQMD. Particularly, agreement of fragment yield in the forward angle is substantially improved.

  13. Fragment emission studies in low energy light heavy-ion reactions

    NASA Astrophysics Data System (ADS)

    Rana, T. K.; Bhattacharya, C.; Manna, S.; Srivastava, V.; Banerjee, K.; Kundu, S.; Roy, P.; Pandey, R.; Chaudhuri, A.; Roy, T.; Ghosh, T. K.; Mukherjee, G.; Bhattacharya, S.; Meena, J. K.; Pandit, S. K.; Mahata, K.; Patale, P.; Shrivastava, A.; Nanal, V.

    2015-01-01

    Fragment emission mechanisms have been studied in 12C on 12C and 13C on 12C reactions at same excitation energy. The inclusive energy distributions of the complex fragments (3≤ Z ≤ 5) emitted from the composite system have been measured in the angular range 14° to 36°. The present experiments have been performed with the motivation to study the isotopic dependence of fragment yields in these two reactions. From the preliminary analysis, it has been observed that fragments are emitted from a completely equilibrated and long lived composite system for both 12C + 12C and 13C + 12C reactions. It has also been observed that the emission of neutron-rich fragments are more in 13C + 12C compared to 12C + 12C reaction.

  14. An investigation of the angular distributions of fragment ions arising from the linear CS2 and CO2 molecules

    NASA Astrophysics Data System (ADS)

    Graham, P.; Ledingham, K. W. D.; Singhal, R. P.; McCanny, T.; Hankin, S. M.; Fang, X.; Smith, D. J.; Kosmidis, C.; Tzallas, P.; Langley, A. J.; Taday, P. F.

    1999-12-01

    The nonlinear interaction of the triatomic molecules CS2 and CO2 with the intense field of a linearly polarized laser beam of femtosecond (fs) pulse duration, was used to study the ionization and dissociation of the parent molecule. The fragment ion angular distributions arising from the Coulomb explosion of the parent ions were also measured. For CS2, the angular distributions of CS2+, CS22+, CS23+, CS+, CS2+, Sn+ (nicons/Journals/Common/le" ALT="le" ALIGN="TOP"/>6) and Cm+ (micons/Journals/Common/le" ALT="le" ALIGN="TOP"/>4) ions are presented for a laser intensity of 1 × 1016 W cm-2 at a wavelength of 790 nm and pulse duration of 50 fs. The angular distributions of the parent molecular ions are all isotropic. The Sn+ fragments are peaked along the time-of-flight (TOF) axis, whereas the Cm+ fragments explode perpendicularly to this. Similar results for CO2 are also presented for comparison. The S ion distributions do not narrow as their ionic charge increases, and it is argued that the angular distributions for CS2 are due mainly to the angular dependence of the ionization probability. On the other hand, the distributions from the lighter CO2 molecule are thought to be at least partly due to alignment via dipole moments induced by the laser, as in this case the On+ angular distributions are seen to narrow as their charge increases. The conclusion of these results is that the laser pulse may be too short for the CS2 molecule to align in the pulse. Angular distributions are also presented for varying laser pulse durations, in the range of 50 fs to 300 ps. The dynamics of the ionization/dissociation mechanism are discussed in the context of the TOF mass spectra and angular distributions recorded for CS2.

  15. Structural elucidation of monoterpene oxidation products by ion trap fragmentation using on-line atmospheric pressure chemical ionisation mass spectrometry in the negative ion mode.

    PubMed

    Warscheid, B; Hoffmann, T

    2001-01-01

    Based on ion trap mass spectrometry, an on-line method is described which provides valuable information on the molecular composition of structurally complex organic aerosols. The investigated aerosols were generated from the gas-phase ozonolysis of various C(10)H(16)-terpenes (alpha-pinene, beta-pinene, 3-carene, sabinene, limonene), and directly introduced into the ion source of the mass spectrometer. Negative ion chemical ionisation at atmospheric pressure (APCI(-)) enabled the detection of multifunctional carboxylic acid products by combining inherent sensitivity and molecular weight information. Sequential low-energy collision-induced product ion fragmentation experiments (MS(n)) were performed in order to elucidate characteristic decomposition pathways of the compounds. Dicarboxylic acids, oxocarboxylic acids and hydroxyketocarboxylic acid products could be clearly distinguished by multistage on-line MS. Furthermore, sabinonic acid and two C(9)-ether compounds were tentatively identified for the first time by applying on-line APCI(-)-MS(n). PMID:11746892

  16. Possible isomers in ligand protected Ag11 cluster ions identified by ion mobility mass spectrometry and fragmented by surface induced dissociation.

    PubMed

    Baksi, Ananya; Harvey, Sophie R; Natarajan, Ganapati; Wysocki, Vicki H; Pradeep, Thalappil

    2016-03-01

    This communication reports the identification of gas phase isomers in monolayer-protected silver clusters. Two different isomers of Ag11(SG)7(-) (SG-gulathione thiolate) with different drift times have been detected using combined electrospray ionization (ESI) and ion mobility (IM) mass spectrometry (MS). Surface induced dissociation (SID) of the 3(-) charge state of such clusters shows charge stripping to give the 1(-) charged ion with some sodium attachment, in addition to fragmentation. SID and collision induced dissociation (CID) for Ag11(SG)7(-) suggest different pathways being accessed with each method. SID was introduced for the first time for the study of monolayer-protected clusters. PMID:26864967

  17. Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS.

    PubMed

    Bilbao, Aivett; Zhang, Ying; Varesio, Emmanuel; Luban, Jeremy; Strambio-De-Castillia, Caterina; Lisacek, Frédérique; Hopfgartner, Gérard

    2015-11-01

    Data-independent acquisition LC-MS/MS techniques complement supervised methods for peptide quantification. However, due to the wide precursor isolation windows, these techniques are prone to interference at the fragment ion level, which, in turn, is detrimental for accurate quantification. The nonoutlier fragment ion (NOFI) ranking algorithm has been developed to assign low priority to fragment ions affected by interference. By using the optimal subset of high-priority fragment ions, these interfered fragment ions are effectively excluded from quantification. NOFI represents each fragment ion as a vector of four dimensions related to chromatographic and MS fragmentation attributes and applies multivariate outlier detection techniques. Benchmarking conducted on a well-defined quantitative data set (i.e., the SWATH Gold Standard) indicates that NOFI on average is able to accurately quantify 11-25% more peptides than the commonly used Top-N library intensity ranking method. The sum of the area of the Top3-5 NOFIs produces similar coefficients of variation as compared to that with the library intensity method but with more accurate quantification results. On a biologically relevant human dendritic cell digest data set, NOFI properly assigns low-priority ranks to 85% of annotated interferences, resulting in sensitivity values between 0.92 and 0.80, against 0.76 for the Spectronaut interference detection algorithm. PMID:26412574

  18. Measurement of large angle fragments induced by 400 MeV n-1 carbon ion beams

    NASA Astrophysics Data System (ADS)

    Aleksandrov, Andrey; Consiglio, Lucia; De Lellis, Giovanni; Di Crescenzo, Antonia; Lauria, Adele; Montesi, Maria Cristina; Patera, Vincenzo; Sirignano, Chiara; Tioukov, Valeri

    2015-09-01

    The use of carbon ion beams in radiotherapy presents significant advantages when compared to traditional x-ray. In fact, carbon ions deposit their energy inside the human body at the end of their range, the Bragg peak. Unlike x-ray beams, where the energy deposition decreases exponentially inside the irradiated volume, the shape of carbon beams is sharp and focused. Advantages are an increased energy released in the cancer volume while minimizing the irradiation to healthy tissues. Currently, the use of carbon beams is limited by the poor knowledge we have about the effects of the secondary fragments on the irradiated tissues. The secondary particles produced and their angular distribution is crucial to determine the global dose deposition. The knowledge of the flux of secondary particles plays a key role in the real time monitoring of the dose profile in hadron therapy. We present a detector based on nuclear emulsions for fragmentation measurements that performs a sub-micrometric tridimensional spatial resolution, excellent multi-particle separation and large angle track recognition. Nuclear emulsions are assembled in order to realize a hybrid detector (emulsion cloud chamber (ECC)) made of 300 μm nuclear emulsion films alternated with lead as passive material. Data reported here have been obtained by exposing two ECC detectors to the fragments produced by a 400 MeV n-1 12C beam on a composite target at the GSI laboratory in Germany. The ECC was exposed inside a more complex detector, named FIRST, in order to collect fragments with a continuous angular distribution in the range 47°-81° with respect to the beam axis. Results on the angular distribution of fragments as well as their momentum estimations are reported here.

  19. EVIDENCE FOR ANOMALOUS NUCLEI AMONG RELATIVISTIC PROJECTILE FRAGMENTS FROM HEAVY ION COLLISIONS AT BEVALAC ENERGIES

    SciTech Connect

    Friedlander, E.M.; Gimpel, R.W.; Heckman, H.H.; Karant, Y.J.; Judek, B.; Ganssauge, E.

    1980-06-01

    Two independent emulsion experiments using Bevalac beams of {sup 16}O and {sup 56}Fe at {approx}2 GeV/nucleon find with > 99.7% confidence that the reaction mean-free paths of projectile fragments, 3 {approx}< Z {approx}< 26, are shorter for a few centimeters after their emission than at larger distances, or than predicted from experiments on beam nuclei. This effect, which is enhanced in later generations of fragments, can be interpreted by the relatively rare occurrence of fragments that interact with an unexpectedly large cross section.

  20. Liquid chromatography, in combination with a quadrupole time-of-flight instrument (LC QTOF), with sequential window acquisition of all theoretical fragment-ion spectra (SWATH) acquisition: systematic studies on its use for screenings in clinical and forensic toxicology and comparison with information-dependent acquisition (IDA).

    PubMed

    Roemmelt, Andreas T; Steuer, Andrea E; Poetzsch, Michael; Kraemer, Thomas

    2014-12-01

    Forensic and clinical toxicological screening procedures are employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques with information-dependent acquisition (IDA) approaches more and more often. It is known that the complexity of a sample and the IDA settings might prevent important compounds from being triggered. Therefore, data-independent acquisition (DIA) methods should be more suitable for systematic toxicological analysis (STA). The DIA method sequential window acquisition of all theoretical fragment-ion spectra (SWATH), which uses Q1 windows of 20-35 Da for data-independent fragmentation, was systematically investigated for its suitability for STA. Quality of SWATH-generated mass spectra were evaluated with regard to mass error, relative abundance of the fragments, and library hits. With the Q1 window set to 20-25 Da, several precursors pass Q1 at the same time and are fragmented, thus impairing the library search algorithms to a different extent: forward fit was less affected than reverse fit and purity fit. Mass error was not affected. The relative abundance of the fragments was concentration dependent for some analytes and was influenced by cofragmentation, especially of deuterated analogues. Also, the detection rate of IDA compared to SWATH was investigated in a forced coelution experiment (up to 20 analytes coeluting). Even using several different IDA settings, it was observed that IDA failed to trigger relevant compounds. Screening results of 382 authentic forensic cases revealed that SWATH's detection rate was superior to IDA, which failed to trigger ∼10% of the analytes. PMID:25329363

  1. Characteristic Fragmentation of Polysiloxane Monolayer Films by Bombardment with Monatomic and Polyatomic Primary Ions in TOF-SIMS

    NASA Astrophysics Data System (ADS)

    Moon, Hye Kyoung; Wells, David D.; Gardella, Joseph A.

    2012-01-01

    This study reports the characteristic fragmentation patterns from two polysiloxane polymers that form ordered overlayer on silver substrates. Results are compared for the bombardment of various monatomic and polyatomic projectiles of Cs+, C{60/+} (10 keV), Bi{1/+}, and Bi{3/+} (25 keV) in the high mass range time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra. Results are reported from sub-monolayer (solution cast) coverages of poly(dimethylsiloxane)s with the number average molecular weights (Mn) of 2200 and 6140 Da, respectively, and Langmuir-Blodgett monolayers of poly(methylphenylsiloxane) with molecular weights (MW) from 600 and 1000 Da. For each film, Bi projectiles resulted in the emission of positive silver cluster ions from the substrate under the polymer overlayer and peaks corresponding to silver cluster ions with larger mass were observed by impact of polyatomic 25 keV Bi{3/+} projectiles. In addition, depending on the change of energy of Bi{3/+}, a different pattern of fragments was observed. With Cs+ and C{60/+} impact, however, the emission of silver cluster ions was not detected. In the case of C{60/+} impact for PDMS-6140, peaks corresponding to silver-cationized intact oligomers were not observed. In this paper, these results are explained by the possible bombardment mechanism for each projectile, based on its mass, energy, and split trajectories of the component atoms under the polyatomic impact.

  2. The influence of dose, dose-rate and particle fragmentation on cataract induction by energetic iron ions

    NASA Technical Reports Server (NTRS)

    Medvedovsky, C.; Worgul, B. V.; Huang, Y.; Brenner, D. J.; Tao, F.; Miller, J.; Zeitlin, C.; Ainsworth, E. J.

    1994-01-01

    Because activities in space necessarily involve chronic exposure to a heterogeneous charged particle radiation field it is important to assess the influence of dose-rate and the possible modulating role of heavy particle fragmentation on biological systems. Using the well-studied cataract model, mice were exposed to plateau 600 MeV/amu Fe-56 ions either as acute or fractionated exposures at total doses of 5-504 cGy. Additional groups of mice received 20, 360 and 504 cGy behind 50 mm of polyethylene, which simulates body shielding. The reference radiation consisted of Co-60 gamma radiation. The animals were examined by slit lamp biomicroscopy over their three year life spans. In accordance with our previous observations with heavy particles, the cataractogenic potential of the 600 MeV/amu Fe-56 ions was greater than for low-Linear Energy Transfer (LET) radiation and increased with decreasing dose relative to gamma rays. Fractionation of a given dose of Fe-56 ions did not reduce the cataractogenicity of the radiation compared to the acute regimen. Fragmentation of the beam in the polyethylene did not alter the cataractotoxicity of the ions, either when administered singly or in fractions.

  3. The influence of dose, dose-rate and particle fragmentation on cataract induction by energetic iron ions

    NASA Astrophysics Data System (ADS)

    Medvedovsky, C.; Worgul, B. V.; Huang, Y.; Brenner, D. J.; Tao, F.; Miller, J.; Zeitlin, C.; Ainsworth, E. J.

    1994-10-01

    Because activities in space necessarily involve chronic exposure to a heterogeneous charged particle radiation field it is important to assess the influence of dose-rate and the possible modulating role of heavy particle fragmentation on biological systems. Using the well-studied cataract model, mice were exposed to plateau 600 MeV/amu 56Fe ions either as acute or fractionated exposures at total doses of 5 - 504 cGy. Additional groups of mice received 20, 360 and 504 cGy behind 50 mm of polyethylene, which simulates body shielding. The reference radiation consisted of 60Co γ radiation. The animals were examined by slit lamp biomicroscopy over their three year life spans. In accordance with our previous observations with heavy particles, the cataractogenic potential of the 600 MeV/amu 56Fe ions was greater than for low-LET radiation and increased with decreasing dose relative to γ-rays. Fractionation of a given dose of 56Fe ions did not reduce the cataractogenicity of the radiation compared to the acute regimen. Fragmentation of the beam in the polyethylene did not alter the cataractotoxicity of the ions, either when administered singly or in fractions.

  4. Radiation induced redox reactions and fragmentation of constituent ions in ionic liquids II. Imidazolium cations.

    SciTech Connect

    Shkrob, I. A.; Marin, T. W.; Chemerisov, S. D.; Hatcher, J.; Wishart, J.

    2011-04-14

    In part 1 of this study, radiolytic degradation of constituent anions in ionic liquids (ILs) was examined. The present study continues the themes addressed in part 1 and examines the radiation chemistry of 1,3-dialkyl substituted imidazolium cations, which currently comprise the most practically important and versatile class of ionic liquid cations. For comparison, we also examined 1,3-dimethoxy- and 2-methyl-substituted imidazolium and 1-butyl-4-methylpyridinium cations. In addition to identification of radicals using electron paramagnetic resonance spectroscopy (EPR) and selective deuterium substitution, we analyzed stable radiolytic products using {sup 1}H and {sup 13}C nuclear magnetic resonance (NMR) and tandem electrospray ionization mass spectrometry (ESMS). Our EPR studies reveal rich chemistry initiated through 'ionization of the ions': oxidation and the formation of radical dications in the aliphatic arms of the parent cations (leading to deprotonation and the formation of alkyl radicals in these arms) and reduction of the parent cation, yielding 2-imidazolyl radicals. The subsequent reactions of these radicals depend on the nature of the IL. If the cation is 2-substituted, the resulting 2-imidazolyl radical is relatively stable. If there is no substitution at C(2), the radical then either is protonated or reacts with the parent cation forming a C(2)-C(2) {sigma}{sigma}*-bound dimer radical cation. In addition to these reactions, when methoxy or C{sub {alpha}}-substituted alkyl groups occupy the N(1,3) positions, their elimination is observed. The elimination of methyl groups from N(1,3) was not observed. Product analyses of imidazolium liquids irradiated in the very-high-dose regime (6.7 MGy) reveal several detrimental processes, including volatilization, acidification, and oligomerization. The latter yields a polymer with m/z of 650 {+-} 300 whose radiolytic yield increases with dose (0.23 monomer units per 100 eV for 1-methyl-3-butylimidazolium

  5. Absolute differential and total cross sections for neutral fragments from dissociative collisions of triatomic hydrogen like ions on He

    NASA Astrophysics Data System (ADS)

    Yousif, F. B.; Fuentes, B. E.; Martínez, H.

    2010-12-01

    Neutral fragment products from dissociative collisions of triatomic hydrogen like ions incident on He atoms were studied. Absolute differential and total cross sections are reported here in the energy range of 1.00-5.00 keV and scattering angles between -5.0° and 5.0°. The differential cross sections show decreasing behaviour with a slight structure around 2.0°. The total cross sections for all triatomic molecular ions studied in this work are found to be comparable for the same velocity (E/M). The measured cross sections are between 0.7 × 10-17 cm2 and 0.9 × 10-16 cm2. The present results for the neutral total cross section correlate very well with previously measured total ions cross section for H+3, D+3 and HD+2 on He.

  6. Localization of Fatty Acyl and Double Bond Positions in Phosphatidylcholines Using a Dual Stage CID Fragmentation Coupled with Ion Mobility Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Castro-Perez, Jose; Roddy, Thomas P.; Nibbering, Nico M. M.; Shah, Vinit; McLaren, David G.; Previs, Stephen; Attygalle, Athula B.; Herath, Kithsiri; Chen, Zhu; Wang, Sheng-Ping; Mitnaul, Lyndon; Hubbard, Brian K.; Vreeken, Rob J.; Johns, Douglas G.; Hankemeier, Thomas

    2011-09-01

    A high content molecular fragmentation for the analysis of phosphatidylcholines (PC) was achieved utilizing a two-stage [trap (first generation fragmentation) and transfer (second generation fragmentation)] collision-induced dissociation (CID) in combination with travelling-wave ion mobility spectrometry (TWIMS). The novel aspects of this work reside in the fact that a TWIMS arrangement was used to obtain a high level structural information including location of fatty acyl substituents and double bonds for PCs in plasma, and the presence of alkali metal adduct ions such as [M + Li]+ was not required to obtain double bond positions. Elemental compositions for fragment ions were confirmed by accurate mass measurements. A very specific first generation fragment ion m/z 577 (M-phosphoryl choline) from the PC [16:0/18:1 (9Z)] was produced, which by further CID generated acylium ions containing either the fatty acyl 16:0 (C15H31CO+, m/z 239) or 18:1 (9Z) (C17H33CO+, m/z 265) substituent. Subsequent water loss from these acylium ions was key in producing hydrocarbon fragment ions mainly from the α-proximal position of the carbonyl group such as the hydrocarbon ion m/z 67 (+H2C-HC = CH-CH = CH2). Formation of these ions was of important significance for determining double bonds in the fatty acyl chains. In addition to this, and with the aid of 13C labeled lyso-phosphatidylcholine (LPC) 18:1 (9Z) in the ω-position (methyl) TAP fragmentation produced the ion at m/z 57. And was proven to be derived from the α-proximal (carboxylate) or distant ω-position (methyl) in the LPC.

  7. Some Dynamical Features of Molecular Fragmentation by Electrons and Swift Ions

    NASA Astrophysics Data System (ADS)

    Montenegro, E. C.; Sigaud, L.; Wolff, W.; Luna, H.; Natalia, Ferreira

    To date, the large majority of studies on molecular fragmentation by swift charged particles have been carried out using simple molecules, for which reliable Potential Energy Curves are available to interpret the measured fragmentation yields. For complex molecules the scenario is quite different and such guidance is not available, obscuring even a simple organization of the data which are currently obtained for a large variety of molecules of biological or technological interest. In this work we show that a general and relatively simple methodology can be used to obtain a broader picture of the fragmentation pattern of an arbitrary molecule. The electronic ionization or excitation cross section of a given molecular orbital, which is the first part of the fragmentation process, can be well scaled by a simple and general procedure at high projectile velocities. The fragmentation fractions arising from each molecular orbital can then be achieved by matching the calculated ionization with the measured fragmentation cross sections. Examples for Oxygen, Chlorodifluoromethane and Pyrimidine molecules are presented.

  8. Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS

    PubMed Central

    Bilbao, Aivett; Zhang, Ying; Varesio, Emmanuel; Luban, Jeremy; Strambio-De-Castillia, Caterina; Lisacek, Frédérique; Hopfgartner, Gérard

    2016-01-01

    Data-independent acquisition LC-MS/MS techniques complement supervised methods for peptide quantification. However, due to the wide precursor isolation windows, these techniques are prone to interference at the fragment ion level, which in turn is detrimental for accurate quantification. The “non-outlier fragment ion” (NOFI) ranking algorithm has been developed to assign low priority to fragment ions affected by interference. By using the optimal subset of high priority fragment ions these interfered fragment ions are effectively excluded from quantification. NOFI represents each fragment ion as a vector of four dimensions related to chromatographic and MS fragmentation attributes and applies multivariate outlier detection techniques. Benchmarking conducted on a well-defined quantitative dataset (i.e. the SWATH Gold Standard), indicates that NOFI on average is able to accurately quantify 11-25% more peptides than the commonly used Top-N library intensity ranking method. The sum of the area of the Top3-5 NOFIs produces similar coefficients of variation as compared to the library intensity method but with more accurate quantification results. On a biologically relevant human dendritic cell digest dataset, NOFI properly assigns low priority ranks to 85% of annotated interferences, resulting in sensitivity values between 0.92 and 0.80 against 0.76 for the Spectronaut interference detection algorithm. PMID:26412574

  9. Determination of the light ion abundances in the strong-helium star HR 3089

    NASA Technical Reports Server (NTRS)

    Lester, J. B.

    1975-01-01

    Using line blanketed model stellar atmospheres and a spectrum synthesis approach, a differential abundance study of the ultraviolet spectrum of HR 3089 relative to the normal star lambda Sco was performed. Both stars were found to have the same abundances of carbon and silicon, but the helium and nitrogen are significantly enhanced in HR 3089. The atmospheric parameters and the distribution of abundances found for HR 3089 agree well with the results of Osmer and Peterson on sharp-lined helium-rich stars. The rotational velocity of 160 km/sec found for HR 3089 places a constraint on the role of diffusion in producing the abundance anomalies. Examination of the resonance lines of C II, N II, Si III and Si IV shows no evidence for mass loss in either star.

  10. Conversion of 92 MeV/u38Ca/ 37K projectile fragments into thermalized ion beams

    NASA Astrophysics Data System (ADS)

    Weissman, L.; Morrissey, D. J.; Bollen, G.; Davies, D. A.; Kwan, E.; Lofy, P. A.; Schury, P.; Schwarz, S.; Sumithrarachchi, C.; Sun, T.; Ringle, R.

    2005-03-01

    The results of tests for stopping and extraction of energetic, 92 MeV/ u, short-lived 38Ca and 37K fragments of 0.5% and 0.1% full-width of momentum spread with the first version of the National Superconducting Cyclotron Laboratory (NSCL) gas cell are reported. The projectile fragments were thermalized in 51 cm of helium at 1 bar and were transported by electric fields and gas flow into an expansion chamber through a supersonic nozzle, guided by an radio frequency quadrupole (RFQ) guide and collected on a metallic wire. The extraction efficiency was measured for different implantation rates, different electrical field distributions inside the gas cell, and different values of beam degrader thicknesses. The extraction measurements were compared with the experimental stopping efficiency and measurement of ionization induced in the helium gas. Mechanisms responsible for ion losses were identified and possible improvements of the gas cell performance were discussed.

  11. Experimental determination of particle range and dose distribution in thick targets through fragmentation reactions of stable heavy ions

    NASA Astrophysics Data System (ADS)

    Inaniwa, Taku; Kohno, Toshiyuki; Tomitani, Takehiro; Urakabe, Eriko; Sato, Shinji; Kanazawa, Mitsutaka; Kanai, Tatsuaki

    2006-09-01

    In radiation therapy with highly energetic heavy ions, the conformal irradiation of a tumour can be achieved by using their advantageous features such as the good dose localization and the high relative biological effectiveness around their mean range. For effective utilization of such properties, it is necessary to evaluate the range of incident ions and the deposited dose distribution in a patient's body. Several methods have been proposed to derive such physical quantities; one of them uses positron emitters generated through projectile fragmentation reactions of incident ions with target nuclei. We have proposed the application of the maximum likelihood estimation (MLE) method to a detected annihilation gamma-ray distribution for determination of the range of incident ions in a target and we have demonstrated the effectiveness of the method with computer simulations. In this paper, a water, a polyethylene and a polymethyl methacrylate target were each irradiated with stable 12C, 14N, 16O and 20Ne beams. Except for a few combinations of incident beams and targets, the MLE method could determine the range of incident ions RMLE with a difference between RMLE and the experimental range of less than 2.0 mm under the circumstance that the measurement of annihilation gamma rays was started just after the irradiation of 61.4 s and lasted for 500 s. In the process of evaluating the range of incident ions with the MLE method, we must calculate many physical quantities such as the fluence and the energy of both primary ions and fragments as a function of depth in a target. Consequently, by using them we can obtain the dose distribution. Thus, when the mean range of incident ions is determined with the MLE method, the annihilation gamma-ray distribution and the deposited dose distribution can be derived simultaneously. The derived dose distributions in water for the mono-energetic heavy-ion beams of four species were compared with those measured with an ionization chamber

  12. Cluster ion emission from LiF induced by MeV Nq+ projectiles and 252Cf fission fragments

    NASA Astrophysics Data System (ADS)

    Hijazi, H.; Farenzena, L. S.; Rothard, H.; Boduch, Ph.; Grande, P. L.; da Silveira, E. F.

    2011-08-01

    Ion cluster desorption yields from LiF were measured at PUC-Rio with ≈0.1 MeV/u N q+ ( q = 2,4,5,6) ion beams by means of a time-of-fight (TOF) mass spectrometer. A 252Cf source mounted in the irradiation chamber allows immediate comparison of cluster emissions induced by ≈65 MeV fission fragments (FF). Emission of (LiF) n Li+ clusters are observed for both the N beams and the 252Cf fission fragments. The observed cluster size n varies from 1 to 6 for N q+ projectiles and from 1 to ≈40 for the 252Cf-FF. The size dependence of the Y( n) distributions suggests two cluster formation regimes: (i) recombination process in the outgoing gas phase after impact and (ii) emission of pre-formed clusters from the periphery of the impact site. The corresponding distribution of ejected negative cluster ions (LiF) n F- closely resembles that of the positive secondary (LiF) n Li+ ions. The desorption yields of positive ions scale as Y( n) ˜ q 5. A calculation with the CASP code shows that this corresponds to a cubic scaling ˜S{/e 3} with the electronic stopping power S e , as predicted by collective shock wave models for sputtering and models involving multiple excitons (Frenkel pair sputtering). We discuss possible interpretations of the functional dependence of the evolution of the cluster emission yield Y( n) with cluster size n, fitted by a number of statistical distributions.

  13. ORTHO-TO-PARA ABUNDANCE RATIO OF WATER ION IN COMET C/2001 Q4 (NEAT): IMPLICATION FOR ORTHO-TO-PARA ABUNDANCE RATIO OF WATER

    SciTech Connect

    Shinnaka, Yoshiharu; Kawakita, Hideyo; Kobayashi, Hitomi; Boice, Daniel C.; Martinez, Susan E.

    2012-04-20

    The ortho-to-para abundance ratio (OPR) of cometary molecules is considered to be one of the primordial characteristics of cometary ices, and contains information concerning their formation. Water is the most abundant species in cometary ices, and OPRs of water in comets have been determined from infrared spectroscopic observations of H{sub 2}O rovibrational transitions so far. In this paper, we present a new method to derive OPR of water in comets from the high-dispersion spectrum of the rovibronic emission of H{sub 2}O{sup +} in the optical wavelength region. The rovibronic emission lines of H{sub 2}O{sup +} are sometimes contaminated by other molecular emission lines but they are not affected seriously by telluric absorption compared with near-infrared observations. Since H{sub 2}O{sup +} ions are mainly produced from H{sub 2}O by photoionization in the coma, the OPR of H{sub 2}O{sup +} is considered to be equal to that of water based on the nuclear spin conservation through the reaction. We have developed a fluorescence excitation model of H{sub 2}O{sup +} and applied it to the spectrum of comet C/2001 Q4 (NEAT). The derived OPR of water is 2.54{sup +0.32}{sub -0.25}, which corresponds to a nuclear spin temperature (T{sub spin}) of 30{sup +10}{sub -4} K. This is consistent with the previous value determined in the near-infrared for the same comet (OPR = 2.6 {+-} 0.3, T{sub spin} = 31{sup +11}{sub -5} K).

  14. Formation of fragments in heavy-ion collisions using a modified clusterization method

    SciTech Connect

    Goyal, Supriya; Puri, Rajeev K.

    2011-04-15

    We study the formation and stability of the fragments by extending the minimum spanning tree method (MST) for clusterization. In this extension, each fragment is subjected to a binding-energy check calculated using the modified Bethe-Weizsaecker formula. Earlier, a constant binding-energy cut of 4 MeV/nucleon was imposed. Our results for {sup 197}Au+{sup 197}Au collisions are compared with ALADiN data and also with the calculations based on the simulated annealing technique. We shall show that the present modified version improves the agreement compared to the MST method.

  15. Fragmentation cross sections of 2.1-GeV/nucleon C-12 and O-16 ions

    NASA Technical Reports Server (NTRS)

    Cheshire, D. L.; Huggett, R. W.; Johnson, D. P.; Jones, W. V.; Rountree, S. P.; Verma, S. D.; Schmidt, W. K. H.; Kurz, R. J.; Bowen, T.; Krider, E. P.

    1974-01-01

    Measurement of the total fragmentation cross sections of C-12 and O-16 ions incident in CsI target and tungsten scintillator modules. The analysis described is based on a one-module criterion for determining the location of an interaction. The results are independent of the windows used, provided that corrections are made for interactions simulated by energy loss fluctuations in the individual modules and for Delta Z ? 1 interactions missed because of the use of wide windows. The cross sections obtained are in general agreement with the values obtained in other experiments for various target nuclei.

  16. Densities and abundances of hot cometary ions in the coma of P/Halley

    NASA Technical Reports Server (NTRS)

    Neugebauer, M.; Goldstein, R.; Goldstein, B. E.; Fuselier, S. A.; Balsiger, H.; Ip, W.-H.

    1991-01-01

    On its flight by P/Halley, the Giotto spacecraft carried a High Energy Range Spectrometer (HERS) for measuring the properties of cometary ions picked up by the solar wind in the nearly collisionless regions of the coma. Preliminary estimates of the ion densities observed by HERS were reevaluated and extended; density profiles along the Giotto trajectory are presented for 13 values of ion mass/charge. Comparison with the physical-chemical model of the interaction of sunlight and the solar wind with the comet by other researchers reveals that, with the exception of protons and H2(+), all ion densities were at least an order of magnitude higher than predicted. The high ion densities cannot be explained on the basis of compression of the plasma, but require additional or stronger ionization mechanisms. Ratios of the densities of different ion species reveal an overabundance of carbonaceous material and an underabundance of H2(+) compared to the predictions of the Schmidt. While the densities of solar wind ions (H(+) and He(++)) changed sharply across a magnetic discontinuity located 1.35(10)(exp 5) km from the comet, this feature, which has been called both the 'cometopause' and the 'magnetic pileup boundary' was barely distinguishable in the density profiles of hot cometary ions. This result is consistent with the interpretation that the magnetic pileup boundary detected by Giotto was caused by a discontinuity in the solar wind and is not an intrinsic feature of the interaction of the solar wind with an active comet.

  17. Ion Energy Distributions and their Relative Abundance in Inductively Coupled Plasmas

    NASA Technical Reports Server (NTRS)

    Kim, J. S.; Rao, M. V. V. S.; Cappelli, M. A.; Sharma, S. P.; Arnold, James O. (Technical Monitor)

    1998-01-01

    Study of kinetics of ions and neutrals produced in high density inductively coupled plasma (ICP) discharges is of great importance for achieving a high degree of plasma assisted deposition and etching. In this paper, we present the ion energy distributions (IEDs) of various ions arriving at the grounded lower electrode. The ions were energy as well as mass analyzed by a combination of electrostatic analyzer-quadrupole mass spectrometer for pure Ar and CF4/Ar mixtures. The measurements have been made at gas pressures ranging from 30 to 100 mTorr. In addition, the IEDs were measured when the wafer-supporting electrode was also rf-powered and the effect of the self-bias was observed in the energy distributions of ions. The shapes of the IEDs are discussed an related to the sheath properties and measured electrical waveforms, as a function of pressure and applied power. Relative ion intensities were obtained by integration of each ion kinetic energy distribution function over its energy range.

  18. Cluster ion distributions and correlation with fragment valence in laser-induced mass spectra of oxides

    SciTech Connect

    Michiels, E.; Bijbels, R.

    1984-06-01

    Laser microprobe mass analysis (LAMMA) spectra are described for binary oxides belonging to different groups in the periodic table. The positive and negative cluster ion distributions show a strong correlation with the valence electron configuration of the metal in the oxide. The bond dissociation energy of the MO/sup +/ ion also affects the intensity distributions. 20 references, 10 figures.

  19. An Isoratio Method to Study Free Energy and Temperature Effects in Intermediate Mass Fragments Produced in Heavy-Ion Collisions

    NASA Astrophysics Data System (ADS)

    Ma, Chun-Wang; Qiao, Chun-Yuan; Ding, Tian-Tian; Niu, Fei; Song, Yi-Dan; Niu, Yi-Fei

    2016-07-01

    An isoratio method, i.e., the isotopic (isotonic) ratio among three isotopes (isotones), is proposed to study the free energy and temperature effects in the intermediate mass fragments produced in heavy-ion collisions. The parameterizations for the free energy of nucleus at low temperature, which have been proposed in the framework of the density functional theory using the SKM skymre interaction, are adopted to calculate the temperature-dependent free energy of fragment. By analyzing the measured yields of fragments in the 140A MeV 58,64Ni + 9Be reactions, it is verified that the free energy in the isoratio is almost the same for different reactions. A temperature-dependent pairing-energy is introduced into the parameterizations for free energy, which reveals that the weakened pairing energy at the low temperature accounts for the weakened or disappearing odd-even staggering in isoratio. Supported by the Program for Science and Technology Innovation Talents in Universities of Henan Province under Grant No. 13HASTIT046, the Creative Experimental Project of National Undergraduate Students (CEPNU201510476017)

  20. Characterization of fragmented heavy-ion beams using a three-stage telescope detector: detector configuration and instrumentation.

    PubMed

    Llacer, J; Schmidt, J B; Tobias, C A

    1990-01-01

    Accelerated heavy-ion beams used in biological and medical research are often utilized in conjunction with absorbers which lead to the fragmentation of the beam. The BERKLET, initially a two-stage solid-state telescope detector, was designed to make rapid, on-line energy and linear energy transfer (LET) measurements of individual particles in a heavy-ion beam, thus allowing characterization of fragmented beams. From data collected with the BERKLET, one is able to determine a number of important parameters. These include: residual energy and LET histograms for the full beam and for the individual Z components, relative number of particles with a given Z, and dose and track average LET's for the full beam and for the individual Z's. Improvements to the BERKLET design and changes in data analysis are discussed and contrasted with the results of an earlier BERKLET configuration. The most notable improvements are the addition of a thin scintillation detector for improved LET measurement, a tenfold improvement in the dynamic range of the event discriminator, reported here as 1:2000, and dual high-and low-gain amplification of the LET signals, permitting the identification of particles with Z's ranging from 12 down to 1. PMID:2333041

  1. Correlation dynamics between electrons and ions in the fragmentation of D{sub 2} molecules by short laser pulses

    SciTech Connect

    Tong, X.M.; Zhao, Z.X.; Lin, C.D.

    2003-10-01

    We studied the recollision dynamics between the electrons and D{sub 2}{sup +} ions following the tunneling ionization of D{sub 2} molecules in an intense short pulse laser field. The returning electron collisionally excites the D{sub 2}{sup +} ion to excited electronic states; from there D{sub 2}{sup +} can dissociate or be further ionized by the laser field, resulting in D{sup +}+D or D{sup +}+D{sup +}, respectively. We modeled the fragmentation dynamics and calculated the resulting kinetic-energy spectrum of D{sup +} to compare with recent experiments. Since the recollision time is locked to the tunneling ionization time which occurs only within a fraction of an optical cycle, the peaks in the D{sup +} kinetic-energy spectra provide a measure of the time when the recollision occurs. This collision dynamics forms the basis of the molecular clock where the clock can be read with attosecond precision, as first proposed by Corkum and co-workers. By analyzing each of the elementary processes leading to the fragmentation quantitatively, we identified how the molecular clock is to be read from the measured kinetic-energy spectra of D{sup +} and what laser parameters are to be used to measure the clock more accurately.

  2. Particle and light fragment emission in peripheral heavy ion collisions at Fermi energies

    SciTech Connect

    Piantelli, S.; Maurenzig, P. R.; Olmi, A.; Bardelli, L.; Bartoli, A.; Bini, M.; Casini, G.; Coppi, C.; Mangiarotti, A.; Pasquali, G.; Poggi, G.; Stefanini, A. A.; Taccetti, N.; Vanzi, E.

    2006-09-15

    A systematic investigation of the average multiplicities of light charged particles and intermediate mass fragments emitted in peripheral and semiperipheral collisions is presented as a function of the beam energy, violence of the collision, and mass of the system. The data have been collected with the FIASCO setup in the reactions {sup 93}Nb+{sup 93}Nb at (17,23,30,38)A MeV and {sup 116}Sn+{sup 116}Sn at (30,38)A MeV. The midvelocity emission has been separated from the emission of the projectile-like fragment. This last component appears to be compatible with an evaporation from an equilibrated source at normal density, as described by the statistical code GEMINI at the appropriate excitation energy. On the contrary, the midvelocity emission presents remarkable differences in both the dependence of the multiplicities on the energy deposited in the midvelocity region and the isotopic composition of the emitted light charged particles.

  3. Secondary ion mass spectrometry combined with alpha track detection for isotope abundance ratio analysis of individual uranium-bearing particles.

    PubMed

    Esaka, Fumitaka; Magara, Masaaki

    2014-03-01

    Secondary ion mass spectrometry (SIMS) was used in combination with alpha track detection for the efficient analysis of uranium-bearing particles with higher (235)U abundances in environmental samples. A polycarbonate film containing particles was prepared and placed in contact with a CR-39 plastic detector. After exposure for 28 days, the detector was etched in a NaOH solution and each uranium-bearing particle was identified through observation of the alpha tracks recorded in the detector. A portion of the film containing each uranium-bearing particle was cut out and put onto a glassy carbon planchet. The films on the planchet were decomposed through plasma ashing for subsequent uranium abundance ratio analysis with SIMS. The alpha track-SIMS analysis of 10 uranium-bearing particles in a sample taken from a nuclear facility enabled n((235)U)/n((238)U) abundance ratios in the range 0.0072-0.25 to be detected, which were significantly higher than those obtained by SIMS without alpha track detection. The duration of the whole analytical process for analysis of 10 particles was about 32 days. The detection efficiency was calculated to be 27.1±6.5%, based on the analysis of the particles in uranium reference materials. The detection limits, defined as the diameter of the particle which produces alpha tracks more than one for a 28-days exposure, were estimated to be 0.8, 0.9, 1.1, 2.1 and 3.0 μm for the particles having the same uranium abundance ratios with NBL CRM U850, U500, U350, U050 and U010 reference materials, respectively. The use of alpha track detection for subsequent SIMS analysis is an inexpensive and an efficient way to measure uranium-bearing particles with higher (235)U abundances. PMID:24468381

  4. Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community

    PubMed Central

    de la Fuente, Gabriel; Belanche, Alejandro; Girwood, Susan E.; Pinloche, Eric; Wilkinson, Toby; Newbold, C. Jamie

    2014-01-01

    The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population. PMID:25051490

  5. A 4 π charged-particle detector array for light-ion-induced nuclear fragmentation studies

    NASA Astrophysics Data System (ADS)

    Kwiatkowski, K.; Alexander, A.; Bracken, D. S.; Brzychczyk, J.; Dorsett, J.; Ensman, R.; Renshaw Foxford, E.; Hamilton, T.; Komisarcik, K.; McDonald, K. N.; Morley, K. B.; Poehlman, J.; Powell, C.; Viola, V. E.; Yoder, N. R.; Ottarson, J.; Madden, N.

    1994-12-01

    Operating characteristics of the Indiana Silicon Sphere 4 π detector array are outlined. The detector geometry is spherical, with 90 telescopes in the forward hemisphere and 72 at backward angles, covering a total solid angle of 74% of 4π. Each telescope consists of a simple gas-ion chamber, operated with C3F8 gas, followed by a 0.5 mm thick ion-implanted silicon detector and a 28 mm CsI(Tl) crystal, readout by a photodiode. Custom-built bias supplies and NIM preamp/shaper modules were used in conjunction with commercial CFD, TDC and ADC CAMAC units.

  6. Holmium target fragmentation induced by intermediate energy /sup 12/C and /sup 16/O ions

    SciTech Connect

    Kraus, R.H. Jr.

    1986-01-01

    Target fragment (40 < A < 180) production cross sections were measured using off-line gamma-ray spectroscopy for the interaction of 208 MeV /sup 12/C, 272 MeV /sup 16/O, 442 MeV/sup 12/C, 1020 MeV /sup 12/C, and 1635 MeV /sup 16/O with /sup 165/Ho. Target fragment isobaric yields were deduced from these measurements. Trans-target nuclides were identified for all reaction systems. Nuclides up to 4 Z-units above the target were identified for 208 MeV /sup 12/C and 272 MeV /sup 16/O induced reactions, to 3 Z-units above the target for 442 MeV /sup 12/C and 1020 MeC /sup 12/C induced reactions, and to 2 Z-units above the target for 1635 MeV /sup 16/O induced reactions. Fission was observed to decrease between 17 MeV/A and 37 MeV/A from 13% of the reaction cross section to 4% for /sup 12/C induced reactions. No fission contribution was observed for 1020 MeV /sup 12/C and 1635 MeV /sup 16/O induced interactions.

  7. DNA double-strand breaks in mammalian cells exposed to gamma-rays and very heavy ions. Fragment-size distributions determined by pulsed-field gel electrophoresis.

    PubMed

    Kraxenberger, F; Weber, K J; Friedl, A A; Eckardt-Schupp, F; Flentje, M; Quicken, P; Kellerer, A M

    1998-07-01

    The spatial distribution of DNA double-strand breaks (DSB) was assessed after treatment of mammalian cells (V79) with densely ionizing radiation. Cells were exposed to beams of heavy charged particles (calcium ions: 6.9 MeV/u, 2.1.10(3) keV/microm; uranium ions: 9.0 MeV/u, 1.4.10(4) keV/microm) at the linear accelerator UNILAC of GSI, Darmstadt. DNA was isolated in agarose plugs and subjected to pulsed-field gel electrophoresis under conditions that separated DNA fragments of size 50 kbp to 5 Mbp. The measured fragment distributions were compared to those obtained after gamma-irradiation and were analyzed by means of a convolution and a deconvolution technique. In contrast to the finding for gamma-radiation, the distributions produced by heavy ions do not correspond to the random breakage model. Their marked overdispersion and the observed excess of short fragments reflect spatial clustering of DSB that extends over large regions of the DNA, up to several mega base pairs (Mbp). At fluences of 0.75 and 1.5/microm2, calcium ions produce nearly the same shape of fragment spectrum, merely with a difference in the amount of DNA entering the gel; this suggests that the DNA is fragmented by individual calcium ions. At a fluence of 0.8/microm2 uranium ions produce a profile that is shifted to smaller fragment sizes in comparison to the profile obtained at a fluence of 0.4/microm2; this suggests cumulative action of two separate ions in the formation of fragments. These observations are not consistent with the expectation that the uranium ions, with their much larger LET, should be more likely to produce single particle action than the calcium ions. However, a consideration of the greater lateral extension of the tracks of the faster uranium ions explains the observed differences; it suggests that the DNA is closely coiled so that even DNA locations several Mbp apart are usually not separated by less than 0. 1 or 0.2 microm. PMID:9728743

  8. Study of near-stability nuclei populated as fission fragments in heavy-ion fusion reactions

    SciTech Connect

    Fotiadis, Nikolaos; Nelson, Ronald O; Devlin, Matthew; Cizewski, Jolie A; Krucken, Reiner; Clark, R M; Fallon, Paul; Lee, I Yang; Macchiavelli, Agusto O; Becker, John A; Younes, Walid

    2010-01-01

    Examples are presented to illustrate the power of prompt {gamma}-ray spectroscopy of fission fragments from compound nuclei with A {approx} 200 formed in fusion-evaporation reactions in experiments using the Gammasphere Ge-detector array. Complementary methods, such as Coulomb excitation and deep-inelastic processes, are also discussed. In other cases (n, xn{gamma}) reactions on stable isotopes have been used to establish neutron excitation functions for {gamma}-rays using a pulsed 'white'-neutron source, coupled to a high-energy-resolution germanium-detector array. The excitation functions can unambiguously assign {gamma}-rays to a specific reaction product. Results from all these methods bridge the gaps in the systematics of high-spin states between the neutron-deficient and neutron-rich nuclei. Results near shell closures should motivate new shell model calculations.

  9. Significance of the Fragmentation Region in Ultrarelativistic Heavy-Ion Collisions

    NASA Astrophysics Data System (ADS)

    Back, B. B.; Baker, M. D.; Barton, D. S.; Betts, R. R.; Ballintijn, M.; Bickley, A. A.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Decowski, M. P.; García, E.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Heintzelman, G. A.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; McLeod, D.; Michałowski, J.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Roland, C.; Roland, G.; Rosenberg, L.; Sagerer, J.; Sarin, P.; Sawicki, P.; Skulski, W.; Steadman, S. G.; Steinberg, P.; Stephans, G. S.; Stodulski, M.; Sukhanov, A.; Tang, J.-L.; Teng, R.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Verdier, R.; Wadsworth, B.; Wolfs, F. L.; Wosiek, B.; Woźniak, K.; Wuosmaa, A. H.; Wysłouch, B.

    2003-08-01

    We present measurements of the pseudorapidity distribution of primary charged particles produced in Au+Au collisions at three energies, (sNN)=19.6, 130, and 200GeV, for a range of collision centrali­ties. The distribution narrows for more central collisions and excess particles are produced at high pseudorapidity in peripheral collisions. For a given centrality, however, the distributions are found to scale with energy according to the “limiting fragmentation” hypothesis. The universal fragmentation region described by this scaling grows in pseudorapidity with increasing collision energy, extending well away from the beam rapidity and covering more than half of the pseudorapidity range over which particles are produced. This approach to a universal limiting curve appears to be a dominant feature of the pseudorapidity distribution and therefore of the total particle production in these collisions.

  10. A novel “correlated ion and neutral time of flight” method: Event-by-event detection of neutral and charged fragments in collision induced dissociation of mass selected ions

    SciTech Connect

    Teyssier, C.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.

    2014-01-15

    A new tandem mass spectrometry (MS/MS) method based on time of flight measurements performed on an event-by-event detection technique is presented. This “correlated ion and neutral time of flight” method allows to explore Collision Induced Dissociation (CID) fragmentation processes by directly identifying not only all ions and neutral fragments produced but also their arrival time correlations within each single fragmentation event from a dissociating molecular ion. This constitutes a new step in the characterization of molecular ions. The method will be illustrated here for a prototypical case involving CID of protonated water clusters H{sup +}(H{sub 2}O){sub n=1–5} upon collisions with argon atoms.

  11. Energy-dependent Charge States and Their Connection with Ion Abundances in Impulsive Solar Energetic Particle Events

    NASA Astrophysics Data System (ADS)

    DiFabio, R.; Guo, Z.; Möbius, E.; Klecker, B.; Kucharek, H.; Mason, G. M.; Popecki, M.

    2008-11-01

    Impulsive solar energetic particle (SEP) events show substantial enhancements of heavy ions and 3He over the composition in the Sun's atmosphere. Mass per charge dependent acceleration mechanisms have been proposed to account for this preferential acceleration. However, a problem emerged for all the preferential acceleration models with the measurement of ionization states near 1 MeV nucleon-1, which showed that ions from C to Mg are fully stripped, a challenge that had been recognized early on. Since all models relied on differences in the charge-to-mass ratio to enable preferential acceleration, the proposed mechanisms were incompatible with this observation. Recent observations of the ionic charge states at lower energies have revealed a dependence on energy, with the charge states decreasing for lower energy ions. This raises the possibility that the low-energy charge states reflect the plasma conditions at the acceleration site, while the high-energy charge states are due to stripping low in the solar corona. In a survey of impulsive events we show that the increase of the Fe charge states with energy is highly significant for the sample of events and thus most likely a general feature of impulsive events. To see whether there is a connection between the enhancements and charge states, we extended the ACE SEPICA charge-state observations to lower energies and combined them with the ion fluxes from ACE ULEIS for impulsive events observed between 1997 and 2000. We find a positive correlation between the abundance ratios and the charge states at low energy, while the charge states at the highest energy do not demonstrate such dependence. This supports the idea that the higher mass particles are preferentially accelerated before being stripped.

  12. Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet*

    PubMed Central

    Keller, Andrew; Bader, Samuel L.; Shteynberg, David; Hood, Leroy; Moritz, Robert L.

    2015-01-01

    Proteomics by mass spectrometry technology is widely used for identifying and quantifying peptides and proteins. The breadth and sensitivity of peptide detection have been advanced by the advent of data-independent acquisition mass spectrometry. Analysis of such data, however, is challenging due to the complexity of fragment ion spectra that have contributions from multiple co-eluting precursor ions. We present SWATHProphet software that identifies and quantifies peptide fragment ion traces in data-independent acquisition data, provides accurate probabilities to ensure results are correct, and automatically detects and removes contributions to quantitation originating from interfering precursor ions. Integration in the widely used open source Trans-Proteomic Pipeline facilitates subsequent analyses such as combining results of multiple data sets together for improved discrimination using iProphet and inferring sample proteins using ProteinProphet. This novel development should greatly help make data-independent acquisition mass spectrometry accessible to large numbers of users. PMID:25713123

  13. Cross Sections for Electron Impact Excitation of Astrophysically Abundant Atoms and Ions

    NASA Technical Reports Server (NTRS)

    Tayal, S. S.

    2006-01-01

    Electron collisional excitation rates and transition probabilities are important for computing electron temperatures and densities, ionization equilibria, and for deriving elemental abundances from emission lines formed in the collisional and photoionized astrophysical plasmas. Accurate representation of target wave functions that properly account for the important correlation and relaxation effects and inclusion of coupling effects including coupling to the continuum are essential components of a reliable collision calculation. Non-orthogonal orbitals technique in multiconfiguration Hartree-Fock approach is used to calculate oscillator strengths and transition probabilities. The effect of coupling to the continuum spectrum is included through the use of pseudostates which are chosen to account for most of the dipole polarizabilities of target states. The B-spline basis is used in the R-matrix approach to calculate electron excitation collision strengths and rates. Results for oscillator strengths and electron excitation collision strengths for transitions in N I, O I, O II, O IV, S X and Fe XIV have been produced

  14. Abundances, charge states, and energy spectra of helium and heavy ions during solar particle events

    NASA Technical Reports Server (NTRS)

    Gloeckler, G.; Sciambi, R.; Fan, C. Y.; Hovestadt, D.

    1975-01-01

    Carbon and oxygen energy spectra observed during several solar events indicate a systematic deviation of these spectra from a simple power law: the spectra bend down below about 100 keV/nuc and the amount of this bending is highly correlated with the size of the flare, as measured by the 'event averaged' flux of 130-220 keV protons. The energy spectra of helium computed for the same time periods do not show a similar feature. A large variability of the alpha/CNO ratio is found from event to event (from 2 to about 20 at 40 keV/nuc), and in all cases examined the carbon and oxygen nuclei are nearly fully stripped. These results are interpreted as evidence for storage of energetic ions in hot coronal regions, followed by strong adiabatic deceleration.

  15. Coordination Environment of Cu(II) Ions Bound to N-Terminal Peptide Fragments of Angiogenin Protein

    PubMed Central

    Magrì, Antonio; Munzone, Alessia; Peana, Massimiliano; Medici, Serenella; Zoroddu, Maria Antonietta; Hansson, Orjan; Satriano, Cristina; Rizzarelli, Enrico; La Mendola, Diego

    2016-01-01

    Angiogenin (Ang) is a potent angiogenic factor, strongly overexpressed in patients affected by different types of cancers. The specific Ang cellular receptors have not been identified, but it is known that Ang–actin interaction induces changes both in the cell cytoskeleton and in the extracellular matrix. Most in vitro studies use the recombinant form (r-Ang) instead of the form that is normally present in vivo (“wild-type”, wt-Ang). The first residue of r-Ang is a methionine, with a free amino group, whereas wt-Ang has a glutamic acid, whose amino group spontaneously cyclizes in the pyro-glutamate form. The Ang biological activity is influenced by copper ions. To elucidate the role of such a free amino group on the protein–copper binding, we scrutinized the copper(II) complexes with the peptide fragments Ang(1–17) and AcAng(1–17), which encompass the sequence 1–17 of angiogenin (QDNSRYTHFLTQHYDAK-NH2), with free amino and acetylated N-terminus, respectively. Potentiometric, ultraviolet-visible (UV-vis), nuclear magnetic resonance (NMR) and circular dichroism (CD) studies demonstrate that the two peptides show a different metal coordination environment. Confocal microscopy imaging of neuroblastoma cells with the actin staining supports the spectroscopic results, with the finding of different responses in the cytoskeleton organization upon the interaction, in the presence or not of copper ions, with the free amino and the acetylated N-terminus peptides. PMID:27490533

  16. AUTOMATED DETERMINATION OF PRECURSOR ION, PRODUCT ION, AND NEUTRAL LOSS COMPOSITIONS AND DECONVOLUTION OF COMPOSITE MASS SPECTRA USING ION CORRELATION BASED ON EXACT MASSES AND RELATIVE ISOTOPIC ABUNDANCES

    EPA Science Inventory

    After a dispersive event, rapid determination of elemental compositions of ions in mass spectra is essential for tentatively identifying compounds. A Direct Analysis in Real Time (DART)® ion source interfaced to a JEOL AccuTOF® mass spectrometer provided exact masses accurate to ...

  17. Evolution of the Relationships between Helium Abundance, Minor Ion Charge State, and Solar Wind Speed over the Solar Cycle

    NASA Astrophysics Data System (ADS)

    Kasper, J. C.; Stevens, M. L.; Korreck, K. E.; Maruca, B. A.; Kiefer, K. K.; Schwadron, N. A.; Lepri, S. T.

    2012-02-01

    The changing relationships between solar wind speed, helium abundance, and minor ion charge state are examined over solar cycle 23. Observations of the abundance of helium relative to hydrogen (A He ≡ 100 × n He/n H) by the Wind spacecraft are used to examine the dependence of A He on solar wind speed and solar activity between 1994 and 2010. This work updates an earlier study of A He from 1994 to 2004 to include the recent extreme solar minimum and broadly confirms our previous result that A He in slow wind is strongly correlated with sunspot number, reaching its lowest values in each solar minima. During the last minimum, as sunspot numbers reached their lowest levels in recent history, A He continued to decrease, falling to half the levels observed in slow wind during the previous minimum and, for the first time observed, decreasing even in the fastest solar wind. We have also extended our previous analysis by adding measurements of the mean carbon and oxygen charge states observed with the Advanced Composition Explorer spacecraft since 1998. We find that as solar activity decreased, the mean charge states of oxygen and carbon for solar wind of a given speed also fell, implying that the wind was formed in cooler regions in the corona during the recent solar minimum. The physical processes in the coronal responsible for establishing the mean charge state and speed of the solar wind have evolved with solar activity and time.

  18. Anionic derivatives of uracil: fragmentation and reactivity.

    PubMed

    Cole, Callie A; Wang, Zhe-Chen; Snow, Theodore P; Bierbaum, Veronica M

    2014-09-01

    Uracil is an essential biomolecule for terrestrial life, yet its prebiotic formation mechanisms have proven elusive for decades. Meteorites have been shown to contain uracil and the interstellar abundance of aromatic species and nitrogen-containing molecules is well established, providing support for uracil's presence in the interstellar medium (ISM). The ion chemistry of uracil may provide clues to its prebiotic synthesis and role in the origin of life. The fragmentation of biomolecules provides valuable insights into their formation. Previous research focused primarily on the fragmentation and reactivity of cations derived from uracil. In this study, we explore deprotonated uracil-5-carboxylic acid and its anionic fragments to elucidate novel reagents of uracil formation and to characterize the reactivity of uracil's anionic derivatives. The structures of these fragments are identified through theoretical calculations, further fragmentation, experimental acidity bracketing, and reactivity with several detected and potential interstellar species (SO2, OCS, CS2, NO, N2O, CO, NH3, O2, and C2H4). Fragmentation is achieved through collision induced dissociation (CID) in a commercial ion trap mass spectrometer, and all reaction rate constants are measured using a modification of this instrument. Experimental data are supported by theoretical calculations at the B3LYP/6-311++G(d,p) level of theory. Lastly, the astrochemical implications of the observed fragmentation and reaction processes are discussed. PMID:25036757

  19. Determination of the sulfur isotope ratio in carbonyl sulfide using gas chromatography/isotope ratio mass spectrometry on fragment ions 32S+, 33S+, and 34S+.

    PubMed

    Hattori, Shohei; Toyoda, Akari; Toyoda, Sakae; Ishino, Sakiko; Ueno, Yuichiro; Yoshida, Naohiro

    2015-01-01

    Little is known about the sulfur isotopic composition of carbonyl sulfide (OCS), the most abundant atmospheric sulfur species. We present a promising new analytical method for measuring the stable sulfur isotopic compositions (δ(33)S, δ(34)S, and Δ(33)S) of OCS using nanomole level samples. The direct isotopic analytical technique consists of two parts: a concentration line and online gas chromatography-isotope ratio mass spectrometry (GC-IRMS) using fragmentation ions (32)S(+), (33)S(+), and (34)S(+). The current levels of measurement precision for OCS samples greater than 8 nmol are 0.42‰, 0.62‰, and 0.23‰ for δ(33)S, δ(34)S, and Δ(33)S, respectively. These δ and Δ values show a slight dependence on the amount of injected OCS for volumes smaller than 8 nmol. The isotope values obtained from the GC-IRMS method were calibrated against those measured by a conventional SF6 method. We report the first measurement of the sulfur isotopic composition of OCS in air collected at Kawasaki, Kanagawa, Japan. The δ(34)S value obtained for OCS (4.9 ± 0.3‰) was lower than the previous estimate of 11‰. When the δ(34)S value for OCS from the atmospheric sample is postulated as the global signal, this finding, coupled with isotopic fractionation for OCS sink reactions in the stratosphere, explains the reported δ(34)S for background stratospheric sulfate. This suggests that OCS is a potentially important source for background (nonepisodic or nonvolcanic) stratospheric sulfate aerosols. PMID:25439590

  20. Binning of shallowly sampled metagenomic sequence fragments reveals that low abundance bacteria play important roles in sulfur cycling and degradation of complex organic polymers in an acid mine drainage community

    NASA Astrophysics Data System (ADS)

    Dick, G. J.; Andersson, A.; Banfield, J. F.

    2007-12-01

    Our understanding of environmental microbiology has been greatly enhanced by community genome sequencing of DNA recovered directly the environment. Community genomics provides insights into the diversity, community structure, metabolic function, and evolution of natural populations of uncultivated microbes, thereby revealing dynamics of how microorganisms interact with each other and their environment. Recent studies have demonstrated the potential for reconstructing near-complete genomes from natural environments while highlighting the challenges of analyzing community genomic sequence, especially from diverse environments. A major challenge of shotgun community genome sequencing is identification of DNA fragments from minor community members for which only low coverage of genomic sequence is present. We analyzed community genome sequence retrieved from biofilms in an acid mine drainage (AMD) system in the Richmond Mine at Iron Mountain, CA, with an emphasis on identification and assembly of DNA fragments from low-abundance community members. The Richmond mine hosts an extensive, relatively low diversity subterranean chemolithoautotrophic community that is sustained entirely by oxidative dissolution of pyrite. The activity of these microorganisms greatly accelerates the generation of AMD. Previous and ongoing work in our laboratory has focused on reconstrucing genomes of dominant community members, including several bacteria and archaea. We binned contigs from several samples (including one new sample and two that had been previously analyzed) by tetranucleotide frequency with clustering by Self-Organizing Maps (SOM). The binning, evaluated by comparison with information from the manually curated assembly of the dominant organisms, was found to be very effective: fragments were correctly assigned with 95% accuracy. Improperly assigned fragments often contained sequences that are either evolutionarily constrained (e.g. 16S rRNA genes) or mobile elements that are

  1. Fragmentation, auto-modification and post ionisation proton bound dimer ion formation: the differential mobility spectrometry of low molecular weight alcohols.

    PubMed

    Ruszkiewicz, D M; Thomas, C L P; Eiceman, G A

    2016-08-01

    Differential mobility spectrometry (DMS) is currently being used for environmental monitoring of space craft atmospheres and has been proposed for the rapid assessment of patients at accident and emergency receptions. Three studies investigated hitherto undescribed complexity in the DMS spectra of methanol, ethanol, propan-1-ol and butan-1-ol product ions formed from a (63)Ni ionisation source. 54 000 DMS spectra obtained over a concentration range of 0.01 mg m(-3)(g) to 1.80 g m(-3)(g) revealed the phenomenon of auto-modification of the product ions. This occurred when the neutral vapour concentration exceeded the level required to induce a neutral-ion collision during the low field portion of the dispersion field waveform. Further, post-ionisation cluster-ion formation or protonated monomer/proton bound dimer inter-conversion within the ion-filter was indicated by apparent shifts in the values of the protonated monomer compensation field maximum; indicative of post-ionisation conversion of the protonated monomer to a proton-bound dimer. APCI-DMS-quadrupole mass spectrometry studies enabled the ion dissociation products from dispersion-field heating to be monitored and product ion fragmentation relationships to be proposed. Methanol was not observed to dissociate, while propan-1-ol and butan-1-ol underwent dissociation reactions consistent with dehydration processes that led ultimately to the generation of what is tentatively assigned as a cyclo-C3H3(+) ion (m/z 39) and hydrated protons. Studies of the interaction of ion filter temperature with dispersion-field heating of product ions isolated dissociation/fragmentation product ions that have not been previously described in DMS. The implications of these combined findings with regard to data sharing and data interpretation were highlighted. PMID:27227997

  2. An (e, 2e + ion) study of low-energy electron-impact ionization and fragmentation of tetrahydrofuran with high mass and energy resolutions

    SciTech Connect

    Ren, Xueguang Pflüger, Thomas; Weyland, Marvin; Baek, Woon Yoon; Rabus, Hans; Ullrich, Joachim; Dorn, Alexander

    2014-10-07

    We study the low-energy (E{sub 0} = 26 eV) electron-impact induced ionization and fragmentation of tetrahydrofuran using a reaction microscope. All three final-state charged particles, i.e., two outgoing electrons and one fragment ion, are detected in triple coincidence such that the momentum vectors and, consequently, the kinetic energies for charged reaction products are determined. The ionic fragments are clearly identified in the experiment with a mass resolution of 1 amu. The fragmentation pathways of tetrahydrofuran are investigated by measuring the ion kinetic energy spectra and the binding energy spectra where an energy resolution of 1.5 eV has been achieved using the recently developed photoemission electron source. Here, we will discuss the fragmentation reactions for the cations C{sub 4}H{sub 8}O{sup +}, C{sub 4}H{sub 7}O{sup +}, C{sub 2}H{sub 3}O{sup +}, C{sub 3}H{sub 6}{sup +}, C{sub 3}H{sub 5}{sup +}, C{sub 3}H{sub 3}{sup +}, CH{sub 3}O{sup +}, CHO{sup +}, and C{sub 2}H{sub 3}{sup +}.

  3. An (e, 2e + ion) study of low-energy electron-impact ionization and fragmentation of tetrahydrofuran with high mass and energy resolutions.

    PubMed

    Ren, Xueguang; Pflüger, Thomas; Weyland, Marvin; Baek, Woon Yoon; Rabus, Hans; Ullrich, Joachim; Dorn, Alexander

    2014-10-01

    We study the low-energy (E0 = 26 eV) electron-impact induced ionization and fragmentation of tetrahydrofuran using a reaction microscope. All three final-state charged particles, i.e., two outgoing electrons and one fragment ion, are detected in triple coincidence such that the momentum vectors and, consequently, the kinetic energies for charged reaction products are determined. The ionic fragments are clearly identified in the experiment with a mass resolution of 1 amu. The fragmentation pathways of tetrahydrofuran are investigated by measuring the ion kinetic energy spectra and the binding energy spectra where an energy resolution of 1.5 eV has been achieved using the recently developed photoemission electron source. Here, we will discuss the fragmentation reactions for the cations C4H8O(+), C4H7O(+), C2H3O(+), C3H6(+), C3H5(+), C3H3(+), CH3O(+), CHO(+), and C2H3(+). PMID:25296813

  4. EVOLUTION OF THE RELATIONSHIPS BETWEEN HELIUM ABUNDANCE, MINOR ION CHARGE STATE, AND SOLAR WIND SPEED OVER THE SOLAR CYCLE

    SciTech Connect

    Kasper, J. C.; Stevens, M. L.; Korreck, K. E.; Maruca, B. A.; Kiefer, K. K.; Schwadron, N. A.; Lepri, S. T.

    2012-02-01

    The changing relationships between solar wind speed, helium abundance, and minor ion charge state are examined over solar cycle 23. Observations of the abundance of helium relative to hydrogen (A{sub He} {identical_to} 100 Multiplication-Sign n{sub He}/n{sub H}) by the Wind spacecraft are used to examine the dependence of A{sub He} on solar wind speed and solar activity between 1994 and 2010. This work updates an earlier study of A{sub He} from 1994 to 2004 to include the recent extreme solar minimum and broadly confirms our previous result that A{sub He} in slow wind is strongly correlated with sunspot number, reaching its lowest values in each solar minima. During the last minimum, as sunspot numbers reached their lowest levels in recent history, A{sub He} continued to decrease, falling to half the levels observed in slow wind during the previous minimum and, for the first time observed, decreasing even in the fastest solar wind. We have also extended our previous analysis by adding measurements of the mean carbon and oxygen charge states observed with the Advanced Composition Explorer spacecraft since 1998. We find that as solar activity decreased, the mean charge states of oxygen and carbon for solar wind of a given speed also fell, implying that the wind was formed in cooler regions in the corona during the recent solar minimum. The physical processes in the coronal responsible for establishing the mean charge state and speed of the solar wind have evolved with solar activity and time.

  5. Automated LC-HRMS(/MS) Approach for the Annotation of Fragment Ions Derived from Stable Isotope Labeling-Assisted Untargeted Metabolomics

    PubMed Central

    2014-01-01

    Structure elucidation of biological compounds is still a major bottleneck of untargeted LC-HRMS approaches in metabolomics research. The aim of the present study was to combine stable isotope labeling and tandem mass spectrometry for the automated interpretation of the elemental composition of fragment ions and thereby facilitate the structural characterization of metabolites. The software tool FragExtract was developed and evaluated with LC-HRMS/MS spectra of both native 12C- and uniformly 13C (U-13C)-labeled analytical standards of 10 fungal substances in pure solvent and spiked into fungal culture filtrate of Fusarium graminearum respectively. Furthermore, the developed approach is exemplified with nine unknown biochemical compounds contained in F. graminearum samples derived from an untargeted metabolomics experiment. The mass difference between the corresponding fragment ions present in the MS/MS spectra of the native and U-13C-labeled compound enabled the assignment of the number of carbon atoms to each fragment signal and allowed the generation of meaningful putative molecular formulas for each fragment ion, which in turn also helped determine the elemental composition of the precursor ion. Compared to laborious manual analysis of the MS/MS spectra, the presented algorithm marks an important step toward efficient fragment signal elucidation and structure annotation of metabolites in future untargeted metabolomics studies. Moreover, as demonstrated for a fungal culture sample, FragExtract also assists the characterization of unknown metabolites, which are not contained in databases, and thus exhibits a significant contribution to untargeted metabolomics research. PMID:24965664

  6. Fragmentation energy index for universalization of fragmentation energy in ion trap mass spectrometers for the analysis of chemical weapon convention related chemicals by atmospheric pressure ionization-tandem mass spectrometry analysis.

    PubMed

    Palit, Meehir; Mallard, Gary

    2009-04-01

    The use of mass spectra generated at 70 eV in electron ionization (EI) as a universal standard for EI has helped in the generation of searchable library databases and had a profound influence on the analytical applications of gas chromatography/mass spectrometry (GC/MS), similarly for liquid chromatography tandem mass spectrometry (LC-MS/MS), suggesting a novel method to normalize the collisional energy for the universalization of fragmentation energy for the analysis of Chemical Weapon Convention (CWC)-related chemicals by atmospheric pressure ionization-tandem mass spectrometry (API-MS(n)) using three-dimensional (3D) ion trap instruments. For normalizing fragmentation energy a "fragmentation energy index" (FEI) is proposed which is an arbitrary scale based on the fact of specific MS/MS fragmentation obtained at different collisional energies for the reference chemicals which are not CWC scheduled compounds. FEI 6 for the generation of an MS(n) library-searchable mass spectral database is recommended. PMID:19331429

  7. A reference substance free diagnostic fragment ion-based approach for rapid identification of non-target components in Pudilan Xiaoyan oral liquid by high resolution mass spectrometry.

    PubMed

    Dai, Chen; Wang, Chong; Zhang, Chunhua; Wang, Guoxiang; Wang, Jin; Chen, Jun; Guo, Bin; Yang, Tianshu; Cai, Bo

    2016-05-30

    Rapid and reliable identification of non-target components in herbal preparations remains a primary challenge, especially when corresponding reference substances are inaccessible. In this work, an efficient post-experiment data processing methodology, named reference substance free diagnostic fragment ion (RSFDFI), was developed based on ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap tandem mass spectrometry (UHPLC/LTQ-Orbitrap). The first step of this approach was to cluster the components that share common fragment ions into several groups. After querying the database using a predicted chemical formula, the component with the fewest primary hits was preferentially deduced based on its MS/MS spectrum. Once the structure was characterized, its common fragment ions could be used as the prior structural information to select the possible candidates that would facilitate the subsequent identification for each group. Taking Pudilan Xiaoyan oral liquid (PDL) as a model herbal preparation, which has been extensively used for the treatment of epidemic parotitis and children with hand-foot-mouth diseases, this strategy enables a nearly eight-fold narrowing of the database hits, with fifty-two components, including lignans, flavonoids, alkaloids and steroids, being rapidly identified. In conclusion, our work clearly demonstrates that integrating RSFDFI with high-resolution mass spectrometry is a powerful methodology for rapid identification of non-target components from herbal prescriptions and may open new avenues for chemical analysis in other complex mixtures. PMID:26938159

  8. Correction of precursor and product ion relative abundances in order to standardize CID spectra and improve Ecom50 accuracy for non-targeted metabolomics

    PubMed Central

    Dubey, Ritvik; Hill, Dennis W.; Lai, Steven; Ming-Hui, Chen; Grant, David F.

    2014-01-01

    Quantitative biases in the abundance of precursor and product ions due to mass discrimination in RF-only ion guides results in inaccurate collision induced dissociation (CID) spectra. We evaluated the effects of collision cell RF voltage and collision energy on CID spectra using ten singly protonated compounds (46–854 Da) in an orthogonal acceleration time-of-flight mass spectrometer. The relative ion transfer efficiency, i.e. the relative amount of ions transferred through the ion guide at any particular RF voltage was shown to be dependent on the ion’s m/z. We developed an algorithm to correct for the mass discriminating effects of RF voltage on CID spectra. The algorithm was tested for both precursor and product ions at multiple RF voltages and collision energies in order to ensure reliability. Our results suggest that compounds that generate major product ions with m/z values <150 have peak intensities that deviate substantially from their actual abundance. This has implications for small molecule metabolomics research, particularly for studies that rely on CID spectra matching methods for structure identification. PMID:25960696

  9. African Viper Poly-His Tag Peptide Fragment Efficiently Binds Metal Ions and Is Folded into an α-Helical Structure.

    PubMed

    Watly, Joanna; Simonovsky, Eyal; Barbosa, Nuno; Spodzieja, Marta; Wieczorek, Robert; Rodziewicz-Motowidlo, Sylwia; Miller, Yifat; Kozlowski, Henryk

    2015-08-17

    Snake venoms are complex mixtures of toxic and often spectacularly biologically active components. Some African vipers contain polyhistidine and polyglycine peptides, which play a crucial role in the interaction with metal ions during the inhibition of snake metalloproteases. Polyhistidine peptide fragments, known as poly-His tags, play many important functions, e.g., in metal ion transport in bacterial chaperon proteins. In this paper, we report a detailed characterization of Cu(2+), Ni(2+), and Zn(2+) complexes with the EDDHHHHHHHHHG peptide fragment (pHG) derived from the venom of the rough scale bush viper (Atheris squamigera). In order to determine the thermodynamic properties, stoichiometry, binding sites, and structures of the metal-pHG complexes, we used a combination of experimental techniques (potentiometric titrations, electrospray ionization mass spectrometry, UV-vis spectroscopy, circular dichroism spectroscopy, and electron paramagnetic resonance spectroscopy) and extensive computational tools (molecular dynamics simulations and density functional theory calculations). The results showed that pHG has a high affinity toward metal ions. The numerous histidine residues located along this sequence are efficient metal ion chelators with high affinities toward Cu(2+), Ni(2+), and Zn(2+) ions. The formation of an α-helical structure induced by metal ion coordination and the occurrence of polymorphic binding states were observed. It is proposed that metal ions can "move along" the poly-His tag, which serves as a metal ion transport pathway. The coordination of Cu(2+), Ni(2+), and Zn(2+) ions to the histidine tag is very effective in comparison with other histidine-rich peptides. The stabilities of the metal-pHG complexes increase in the order Zn(2+) < Ni(2+)≪ Cu(2+). PMID:26214303

  10. Effects of landscape composition and wetland fragmentation on frog and toad abundance and species richness in Iowa and Wisconsin, U.S.A

    USGS Publications Warehouse

    Knutson, Melinda G.; Sauer, John R.; Olsen, Douglas A.; Mossman, Michael J.; Hemesath, Lisa M.; Lannoo, Michael J.

    1999-01-01

    Management of amphibian populations to reverse recent declines will require defining high-quality habitat for individual species or groups of species, followed by efforts to retain or restore these habitats on the landscape. We examined landscape-level habitat relationships for frogs and toads by measuring associations between relative abundance and species richness based on survey data derived from anuran calls and features of land-cover maps for Iowa and Wisconsin. The most consistent result across all anuran guilds was a negative association with the presence of urban land. Upland and wetland forests and emergent wetlands tended to be positively associated with anurans. Landscape metrics that represent edges and patch diversity also had generally positive associations, indicating that anurans benefit from a complex of habitats that include wetlands. In Iowa the most significant associations with relative abundance were the length of the edge between wetland and forest ( positive) and the presence of urban land (negative). In Wisconsin the two most significant associations with relative abundance were forest area and agricultural area ( both positive). Anurans had positive associations with agriculture in Wisconsin but not in Iowa. Remnant forest patches in agricultural landscapes may be providing refuges for some anuran species. Differences in anuran associations with deep water and permanent wetlands between the two states suggest opportunities for management action. Large-scale maps can contribute to predictive models of amphibian habitat use, but water quality and vegetation information collected from individual wetlands will likely be needed to strengthen those predictions. Landscape habitat analyses provide a framework for future experimental and intensive research on specific factors affecting the health of anurans.

  11. Studies of complex fragment emission in heavy ion reactions. Progress report, January 1, 1990--August 5, 1992

    SciTech Connect

    Charity, R.J.; Sobotka, L.G.

    1992-09-01

    Our work involves the study of intermediate energy heavy-ion nuclear reactions. This work has two foci. On the one hand, we desire to learn about the properties of nuclear matter under abnormal conditions, in this energy domain, predominately low densities. This purpose runs abreast of the second, which is the study of the relevant reaction mechanisms. The two objectives are inexorably linked because our experimental laboratory for studying nuclear matter properties is a dynamic one. We are forced to ask how nuclear matter properties, such as phase transitions, are reflected in the dynamics of the reactions. It may be that irrefutable information about nuclear matter will not be extracted from the reaction work. Nevertheless, we are compelled to undertake this effort not only because it is the only game in town and as yet we do not know that information cannot be extracted, but also because of our second objective. The process leads to an understanding of the reaction mechanism themselves and therefore to the response characteristics of finite, perhaps non-equilibrium, strongly interacting systems. Our program has been: To study energy, mass, and angular momentum deposition by studying incomplete fusion reactions. To gain confidence that we understand how highly excited systems decompose by studying all emissions from the highly excited systems. To push these kinds of studies into the intermediate energy domain, with excitation function studies. And attempt to learn about the dynamics of the decays using particle-particle correlations. In the last effort, we have decided to focus on simple systems, where we believe, definitive statements are possible. These avenues of research share a common theme, large complex fragment production.

  12. Precision Measurement of the Hyperfine Structure of Laser-Cooled Radioactive {sup 7}Be{sup +} Ions Produced by Projectile Fragmentation

    SciTech Connect

    Okada, K.; Wada, M.; Nakamura, T.; Takamine, A.; Schury, P.; Ishida, Y.; Sonoda, T.; Kanai, Y.; Kojima, T. M.; Lioubimov, V.; Ogawa, M.; Yamazaki, Y.; Yoshida, A.; Kubo, T.; Katayama, I.; Ohtani, S.; Wollnik, H.; Schuessler, H. A.

    2008-11-21

    The ground state hyperfine splitting of {sup 7}Be{sup +} has been measured by laser-microwave double-resonance spectroscopy in the online rf trap of RIKEN's slow RI-beam facility. Be ions produced by projectile fragmentation of {sup 13}C at {approx_equal}1 GeV were thermalized in a rf ion guide gas cell and subsequently laser cooled in the ion trap to {approx_equal}1 {mu}eV. This 10{sup 15}-fold reduction of the kinetic energy allows precision spectroscopy of these ions. A magnetic hfs constant of A=-742.772 28(43) MHz was measured for {sup 7}Be{sup +}, from which a nuclear magnetic moment of {mu}{sub I}=-1.399 28(2){mu}{sub N} was deduced.

  13. Kinetic-energy release in N{sub 2} fragmentation by charge-changing collisions of 2-MeV C{sup +} ions

    SciTech Connect

    Mizuno, T.; Yamada, T.; Tsuchida, H.; Itoh, A.; Nakai, Y.

    2010-11-15

    Collision-induced fragmentation of N{sub 2} was investigated for 2-MeV C{sup +} ions under charge-changing conditions of C{sup +{yields}}C{sup q+} (q=0,2,3). Coincidence measurement of fragment ions was performed by means of a momentum three-dimensional imaging technique at scattering angles of {theta}=0 and 1.0 mrad. Kinetic-energy release (KER) obtained for a fragmentation channel of N{sub 2}{sup 2+{yields}}N{sup +}+N{sup +} was found to differ significantly in electron loss and capture collisions. In two-electron-loss collisions (C{sup +{yields}}C{sup 3+}), KER spectra were essentially identical for {theta}=0 and 1.0 mrad. It is concluded that the energy level of dissociating excited states of N{sub 2}{sup 2+} may be saturated when the interaction strength, defined as (q/vb), exceeds 0.65, where q and v are the charge and the velocity, respectively, of an incident ion, and b is the impact parameter.

  14. Fragmentation of H2O by 1 -- 5 keV He^2+ ions: Experiment and Theory

    NASA Astrophysics Data System (ADS)

    Stolterfoht, N.; Hellhammer, R.; Sobocinski, P.; Cabrera-Trujillo, R.; Ohrn, Y.; Deumens, E.; Sabin, J.

    2006-05-01

    Fragmentation of H2O molecules induced by ^3He^2+ impact was investigated experimentally as a function of the energy in the range from 1-5 keV. Collisions at large impact parameters are found to produce fragment protons with energies centered around peaks at 6 eV and 15 eV. The H^+ fragments were detected in the angular range from 25 to 135 with respect to the incident beam direction. Absolute fragmentation cross sections dσ/dφ, differential in the emission angle are found to be anisotropic, with protons preferentially emitted at angles near 90 . In addition to the experiments, we performed quantum-mechanical calculations to understand the fragmentation mechanisms producing protons at preferred energies and angles. The theoretical results are obtained using the Electron-Nuclear Dynamics formalism (END), which solves the time-dependent Schr"odinger equation.

  15. Phase space analysis and contribution of participant-spectator matter towards fragments formed in heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Kaur, Sukhjit

    2016-05-01

    We study the contribution of participant and spectator matter towards different kinds of fragments. We find higher contribution of spectator matter towards heavier fragments compared to lighter fragments. We also notice that heavier IMFs preserve the time correlations. The nucleons emerging as lighter IMFs however, are well separated in the phase space at the start of the reaction and form the cluster at later times. The neutron-richness of the reacting partners is found to have negligible effect on the participant-spectator matter.

  16. Determination of site selectivity of different carcinogens for preferential mutational hot spots in oligonucleotide fragments by ion-pair reversed-phase nano liquid chromatography tandem mass spectrometry.

    PubMed

    Sharma, Vaneet K; Xiong, Wennan; Glick, James; Vouros, Paul

    2014-01-01

    Ion-pair reversed-phase nano liquid chromatography coupled with nanospray ion trap mass spectrometry was used to investigate site selectivity of the known carcinogens N-acetoxy-2-acetylaminofluorene, N-hydroxy-4-aminobiphenyl and (+/-)-anti-benzo[a]pyrene diol epoxide with the synthetic double-strand 14-mer long oligonucleotide fragment of the p53 gene containing two mutational hot-spot codons (5'-P-ACC155 CGC156 GTC157 CGC158 GC/5'-GCG CGG ACG CGG GT). The investigation was performed using a monolithic polystyrene divinylbenzene capillary column and triethylammonium bicarbonate as an ion-pair reagent. The exact location of the carcinogen on the modified oligonucleotide backbone was determined using characteristic collision-induced dissociation fragmentation patterns obtained under negative-ion mode ionization. In all these cases, the adducted, isomeric oligonucleotides formed were chromatographically resolved and structural identification was performed without any prior deoxyribonucleic acid cleavage or hydrolysis. The knowledge of the site specificity of a carcinogen, especially at purported mutational hot spots, is of paramount importance (1) in establishing the identity of biomarkers for an early risk assessment of the formed DNA adducts, (2) developing repair mechanisms for the formed carcinogen adducted DNA, and (3) understanding the nature of the covalent bond formed and mapping the frequency of the adduction process. PMID:24881456

  17. Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment.

    PubMed

    Maus, Irena; Cibis, Katharina Gabriela; Bremges, Andreas; Stolze, Yvonne; Wibberg, Daniel; Tomazetto, Geizecler; Blom, Jochen; Sczyrba, Alexander; König, Helmut; Pühler, Alfred; Schlüter, Andreas

    2016-08-20

    The genome sequence of Defluviitoga tunisiensis L3 originating from a thermophilic biogas-production plant was established and recently published as Genome Announcement by our group. The circular chromosome of D. tunisiensis L3 has a size of 2,053,097bp and a mean GC content of 31.38%. To analyze the D. tunisiensis L3 genome sequence in more detail, a phylogenetic analysis of completely sequenced Thermotogae strains based on shared core genes was performed. It appeared that Petrotoga mobilis DSM 10674(T), originally isolated from a North Sea oil-production well, is the closest relative of D. tunisiensis L3. Comparative genome analyses of P. mobilis DSM 10674(T) and D. tunisiensis L3 showed moderate similarities regarding occurrence of orthologous genes. Both genomes share a common set of 1351 core genes. Reconstruction of metabolic pathways important for the biogas production process revealed that the D. tunisiensis L3 genome encodes a large set of genes predicted to facilitate utilization of a variety of complex polysaccharides including cellulose, chitin and xylan. Ethanol, acetate, hydrogen (H2) and carbon dioxide (CO2) were found as possible end-products of the fermentation process. The latter three metabolites are considered to represent substrates for methanogenic Archaea, the key organisms in the final step of the anaerobic digestion process. To determine the degree of relatedness between D. tunisiensis L3 and dominant biogas community members within the thermophilic biogas-production plant, metagenome sequences obtained from the corresponding microbial community were mapped onto the L3 genome sequence. This fragment recruitment revealed that the D. tunisiensis L3 genome is almost completely covered with metagenome sequences featuring high matching accuracy. This result indicates that strains highly related or even identical to the reference strain D. tunisiensis L3 play a dominant role within the community of the thermophilic biogas-production plant. PMID

  18. Statistical Examination of the a and a + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions.

    PubMed

    Morrison, Lindsay J; Rosenberg, Jake A; Singleton, Jonathan P; Brodbelt, Jennifer S

    2016-09-01

    Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue. Graphical Abstract ᅟ. PMID:27206509

  19. DNA double-strand breaks induced by high-energy neon and iron ions in human fibroblasts. II. Probing individual notI fragments by hybridization.

    PubMed

    Löbrich, M; Rydberg, B; Cooper, P K

    1994-08-01

    The initial yields of DNA double-strand breaks induced by energetic heavy ions (425 MeV/u neon and 250, 400 and 600 MeV/u iron) in comparison to X rays were measured in normal human diploid fibroblast cells within three small areas of the genome, defined by NotI fragments of 3.2, 2.0 and 1.2 Mbp. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated cells, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with probes recognizing single-copy sequences within the three NotI fragments. The gradual disappearance of the full-size NotI fragment with dose and the appearance of a smear of broken DNA molecules are quantified. Assuming Poisson statistics for the number of double-strand breaks induced per NotI fragment of known size, absolute yields of DNA double-strand breaks were calculated and determined to be linear with dose in all cases, with the neon ion (LET 32 keV/microns) producing 4.4 x 10(-3) breaks/Mbp/Gy and all three iron-ion beams (LETs from 190 to 350 keV/microns) producing 2.8 x 10(-3) breaks/Mbp/Gy, giving RBE values for production of double-strand breaks of 0.76 for neon and 0.48 for iron in comparison to our previously determined X-ray induction rate of 5.8 x 10(-3) breaks/Mbp/Gy. These RBE values are in good agreement with results of measurements over the whole genome as reported in the accompanying paper (B. Rydberg, M. Löbrich and P. Cooper, Radiat. Res. 139, 133-141, 1994). The distribution of broken DNA molecules was similar for the various radiations, supporting a random distribution of double-strand breaks induced by the heavy ions over Mbp distances; however, correlated breaks (clusters) over much smaller distances are not ruled out. Reconstitution of the 3.2 Mbp NotI fragment was studied during postirradiation incubation of the cells as a measure of rejoining of correct DNA ends. The proportion of breaks repaired decreased with increasing LET. PMID:8052689

  20. R vs. S fluoroproline ring substitution: trans/cis effects on the formation of b2 ions in gas-phase peptide fragmentation.

    PubMed

    Bernier, Matthew C; Chamot-Rooke, Julia; Wysocki, Vicki H

    2016-01-21

    The b2 structures of model systems Xxx-Flp-Ala (Flp = 4R-fluoroproline) and Xxx-flp-Ala (flp = 4S-fluoroproline) (where Xxx is Val or Tyr) were studied by action IRMPD spectroscopy. Proline ring substitutions influence the trans/cis isomerization of the precursor ion, resulting in different b2 fragment ion structures by collision induced dissociation. Vibrational spectra of the b2 ions of Val-Flp and Val-flp exhibit highly intense bands at ~1970 cm(-1), revealing that the dominant ion in each case is an oxazolone. The major difference between the spectra of b2 ions for R vs. S fluoroproline is a collection of peaks at 1690 and 1750 cm(-1), characteristic of a diketopiperazine structure, which were only present in the 4S-fluoroproline (flp) cases. This suggests only one b2 ion structure (oxazolone) is being formed for Flp-containing peptides, whereas flp-containing peptides produce a mixture of a dominant oxazolone with a lower population of diketopiperazine. In solution, Flp is known to possess a higher trans percentage in the N-terminally adjacent peptide bond, with flp inducing a greater proportion of the cis conformation. The diketopiperazine formation observed here correlates directly with the Ktrans/cis trend previously shown in solution, highlighting that the trans/cis isomerization likelihood for proline residues modified in the 4(th) position is retained in the gas-phase. PMID:26690386

  1. Jahn-Teller coupling and fragmentation after core-shell excitation in CF{sub 4} investigated by partial-ion-yield spectroscopy

    SciTech Connect

    Guillemin, Renaud; Stolte, Wayne C.; Lindle, Dennis W.; Piancastelli, Maria Novella

    2010-10-15

    We investigate fragmentation processes induced by core-level photoexcitation in CF{sub 4} at both the carbon and fluorine K edges by means of partial-ion-yield spectroscopy. The molecule CF{sub 4} is a textbook example of systems in which Jahn-Teller coupling strongly manifests itself in the photoabsorption spectrum. Spectral features related to Jahn-Teller and quasi-Jahn-Teller splitting are observed, and important differences in the fragmentation pathways are revealed depending on the symmetries of the core-excited states. We interpret these experimental observations on the grounds of symmetry lowering from the T{sub d} to the C{sub 3v} point group as well as preferential orientation with respect to the polarization vector of the incident radiation.

  2. Enhanced Detection of Low-Abundance Host Cell Protein Impurities in High-Purity Monoclonal Antibodies Down to 1 ppm Using Ion Mobility Mass Spectrometry Coupled with Multidimensional Liquid Chromatography.

    PubMed

    Doneanu, Catalin E; Anderson, Malcolm; Williams, Brad J; Lauber, Matthew A; Chakraborty, Asish; Chen, Weibin

    2015-10-20

    The enormous dynamic range of proteinaceous species present in protein biotherapeutics poses a significant challenge for current mass spectrometry (MS)-based methods to detect low-abundance HCP impurities. Previously, an HCP assay based on two-dimensional chromatographic separation (high pH/low pH) coupled to high-resolution quadrupole time-of-flight (QTOF) mass spectrometry and developed in the author's laboratory has been shown to achieve a detection limit of about 50 ppm (parts per milion) for the identification and quantification of HCPs present in monoclonal antibodies following Protein A purification.1 To improve the HCP detection limit we have explored the utility of several new analytical techniques for HCP analysis and thereby developed an improved liquid chromatography-mass spectrometry (LC-MS) methodology for enhanced detection of HCPs. The new method includes (1) the use of a new charge-surface-modified (CSH) C18 stationary phase to mitigate the challenges of column saturation, peak tailing, and distortion that are commonly observed in the HCP analysis; (2) the incorporation of traveling-wave ion mobility (TWIM) separation of coeluting peptide precursors, and (3) the improvement of fragmentation efficiency of low-abundance HCP peptides by correlating the collision energy used for precursor fragmentation with their mobility drift time. As a result of these improvements, the detection limit of the new methodology was greatly improved, and HCPs present at a concentration as low as 1 ppm (1 ng HCP/mg mAb) were successfully identified and quantified. The newly developed method was applied to analyze two high-purity mAbs (NIST mAb and Infliximab) expressed in a murine cell line. For both samples, low-abundance HCPs (down to 1 ppm) were confidently identified, and the identities of the HCPs were further confirmed by targeted MS/MS experiments. In addition, the performance of the assay was evaluated by an interlaboratory study in which three independent

  3. A scaling phenomenon in the difference of Shannon information uncertainty of fragments in heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Ma, Chun-Wang; Song, Yi-Dan; Qiao, Chun-Yuan; Wang, Shan-Shan; Wei, Hui-Ling; Ma, Yu-Gang; Cao, Xi-Guang

    2016-08-01

    Shannon information-entropy uncertainty is used to analyze fragments in the measured 140A MeV {}{40,48}Ca + 9Be and {}{58,64}Ni + 9Be reactions. A scaling phenomenon is found in the information-uncertainty difference of fragments between the reactions. The scaling phenomenon is explained in the manner of canonical ensemble theory, and is reproduced in simulated reactions using the antisymmetric molecular dynamics (AMD) and AMD + GEMINI models. The probes based on information uncertainty, requiring no equilibrium state of reaction, can be used in the non-equilibrium system, and bridge the results of the static thermodynamics models and the evolving dynamical transport models.

  4. Using the Doubly Charged Selected Ion Coupled with MS/MS Fragments Monitoring (DCSI-MS/MS) Mode for the Identification of Gelatin Species.

    PubMed

    Cheng, Xian-Long; Wei, Feng; Chen, Jia; Li, Ming-Hua; Zhang, Lei; Zhao, Ying-Yong; Xiao, Xin-Yue; Ma, Shuang-Cheng; Lin, Rui-Chao

    2014-01-01

    In electrospray ionization (ESI) mode, peptides and proteins can be multiply charged ions; in this situation a doubly charged selected ion (DCSI) coupled with mass spectrometry (MS/MS) fragments monitoring (DCSI-MS/MS) method is the most suitable scanning mode to detect known peptides in complex samples when an ion-trap mass spectrometer is the instrument used for the analysis. In this mode, the MS detector is programmed to only select a doubly charged ion as a precursor and to perform continuous MS/MS on one or more of the selected precursors, either during a specific time interval or along the whole chromatographic run. Gelatin is a mixture of high molecular weight polypeptides from the hydrolysis of collagen. In this study, the DCSI-MS/MS monitoring mode was applied to the detection of previously characterized species-specific peptides from different gelatins. The proposed methodology makes use of tryptic digestion for sample preparation and peptide separation and identification by rapid resolution liquid chromatography coupled to an ion trap working in the DCSI-MS/MS mode for the analysis. This methodology was applied to the differential classification of five commercial, homological species of gelatins and proved to be an excellent tool for gelatin product authentication. PMID:24744960

  5. Applying 'Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra' (SWATH) for systematic toxicological analysis with liquid chromatography-high-resolution tandem mass spectrometry.

    PubMed

    Arnhard, Kathrin; Gottschall, Anna; Pitterl, Florian; Oberacher, Herbert

    2015-01-01

    Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become an indispensable analytical technique in clinical and forensic toxicology for detection and identification of potentially toxic or harmful compounds. Particularly, non-target LC-MS/MS assays enable extensive and universal screening requested in systematic toxicological analysis. An integral part of the identification process is the generation of information-rich product ion spectra which can be searched against libraries of reference mass spectra. Usually, 'data-dependent acquisition' (DDA) strategies are applied for automated data acquisition. In this study, the 'data-independent acquisition' (DIA) method 'Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra' (SWATH) was combined with LC-MS/MS on a quadrupole-quadrupole-time-of-flight (QqTOF) instrument for acquiring informative high-resolution tandem mass spectra. SWATH performs data-independent fragmentation of all precursor ions entering the mass spectrometer in 21m/z isolation windows. The whole m/z range of interest is covered by continuous stepping of the isolation window. This allows numerous repeat analyses of each window during the elution of a single chromatographic peak and results in a complete fragment ion map of the sample. Compounds and samples typically encountered in forensic casework were used to assess performance characteristics of LC-MS/MS with SWATH. Our experiments clearly revealed that SWATH is a sensitive and specific identification technique. SWATH is capable of identifying more compounds at lower concentration levels than DDA does. The dynamic range of SWATH was estimated to be three orders of magnitude. Furthermore, the >600,000 SWATH spectra matched led to only 408 incorrect calls (false positive rate = 0.06 %). Deconvolution of generated ion maps was found to be essential for unravelling the full identification power of LC-MS/MS with SWATH. With the available software, however, only semi

  6. Probing the binding of Cu(2+) ions to a fragment of the Aβ(1-42) polypeptide using fluorescence spectroscopy, isothermal titration calorimetry and molecular dynamics simulations.

    PubMed

    Makowska, Joanna; Żamojć, Krzysztof; Wyrzykowski, Dariusz; Żmudzińska, Wioletta; Uber, Dorota; Wierzbicka, Małgorzata; Wiczk, Wiesław; Chmurzyński, Lech

    2016-09-01

    Steady-state and time-resolved fluorescence quenching measurements supported by isothermal titration calorimetry (ITC) and molecular dynamics simulations (MD), with the NMR-derived restraints, were used to investigate the interactions of Cu(2+) ions with a fragment of the Aβ(1-42) polypeptide, Aβ(5-16) with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, denoted as HZ1. The studies presented in this paper, when compared with our previous results (Makowska et al., Spectrochim. Acta A 153: 451-456), show that the affinity of the peptide to metal ions is conformation-dependent. All the measurements were carried out in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution, pH6.0. The Stern-Volmer equations, along with spectroscopic observations, were used to determine the quenching and binding parameters. The obtained results unequivocally suggest that Cu(2+) ions quench the fluorescence of HZ1 only through a static quenching mechanism, in contrast to the fragment from the N-terminal part of the FPB28 protein, with sequence Ac-Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr- NH2 (D9) and its derivative with a single point mutation: Ac-Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr- NH2 (D9_M), where dynamic quenching occurred. The thermodynamic parameters (ΔITCH, ΔITCS) for the interactions between Cu(2+) ions and the HZ1 peptide were determined from the calorimetric data. The conditional thermodynamic parameters suggest that, under the experimental conditions, the formation of the Cu(2+)-HZ1 complex is both an enthalpy and entropy driven process. PMID:27398680

  7. Epithelial remodeling and claudin mRNA abundance in the gill and kidney of puffer fish (Tetraodon biocellatus) acclimated to altered environmental ion levels.

    PubMed

    Duffy, Nicole M; Bui, Phuong; Bagherie-Lachidan, Mazdak; Kelly, Scott P

    2011-02-01

    In water of varying ion content, the gills and kidney of fishes contribute significantly to the maintenance of salt and water balance. However, little is known about the molecular architecture of the tight junction (TJ) complex and the regulation of paracellular permeability characteristics in these tissues. In the current studies, puffer fish (Tetraodon biocellatus) were acclimated to freshwater (FW), seawater (SW) or ion-poor freshwater (IPW) conditions. Following acclimation, alterations in systemic endpoints of hydromineral status were examined in conjunction with changes in gill and kidney epithelia morphology/morphometrics, as well as claudin TJ protein mRNA abundance. T. biocellatus were able to maintain endpoints of hydromineral status within relatively tight limits across the broad range of water ion content examined. Both gill and kidney tissue exhibited substantial alterations in morphology as well as claudin TJ protein mRNA abundance. These responses were particularly pronounced when comparing fish acclimated to SW versus those acclimated to IPW. TEM observations of IPW-acclimated fish gills revealed the presence of cells that exhibited the typical characteristics of gill mitochondria-rich cells (e.g. voluminous, Na(+)-K(+)-ATPase-immunoreactive, exposed to the external environment at the apical surface), but were not mitochondria-rich. To our knowledge, this type of cell has not previously been described in hyperosmoregulating fish gills. Furthermore, modifications in the morphometrics and claudin mRNA abundance of kidney tissue support the notion that spatial alterations in claudin TJ proteins along the nephron of fishes will likely play an important role in the regulation of salt and water balance in these organisms. PMID:20976602

  8. [An ultra-high-pressure liquid chromatography/linear ion trap-Orbitrap mass spectrometry method coupled with a diagnostic fragment ions-searching-based strategy for rapid identification and characterization of chemical components in Polygonum cuspidatum].

    PubMed

    Pan, Zhiran; Liang, Hailong; Liang, Chabhufi; Xu, Wen

    2015-01-01

    A method for qualitative analysis of constituents in Polygonum cuspidatum by ultra-high-pressure liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry (UHPLC-LTQ-Orbitrap MS) has been established. The methanol extract of Polygonum cuspidatumrn was separated on a Waters UPLC C18 column using acetonitrile-water (containing formic acid) eluting system and detected by LTQ-Orbitrap hybrid mass spectrometer in negative mode. The targeted components were further fragmented in LTQ and high accuracy data were acquired by Orbitrap MS. The summarized fragmentation pathways of typical reference components and a diagnostic fragment ions-searching-based strategy were used for detection and identification of the main phenolic components in Polygonum cuspidatum. Other clues such as nitrogen rule, even electron rule, degree of unsaturation rule and isotopic peak data were included for the structural elucidation as well. The whole analytical procedure was within 10 min and more than 30 components were identified or tentatively identified. This method is helpful for further phytochemical research and quality control on Polygonum cuspidatum and related preparations. PMID:25958663

  9. Primary isotope yields and characteristic properties of the fragmenting source in heavy-ion reactions near the Fermi energy

    NASA Astrophysics Data System (ADS)

    Liu, X.; Lin, W.; Wada, R.; Huang, M.; Chen, Z.; Xiao, G. Q.; Zhang, S.; Jin, X.; Han, R.; Liu, J.; Shi, F.; Zheng, H.; Natowitz, J. B.; Bonasera, A.

    2014-07-01

    For central collisions of Ca40+Ca40 at 35 MeV/nucleon, the density and temperature of a fragmenting source have been evaluated in a self-consistent manner using the ratio of the symmetry energy coefficient relative to the temperature, asym/T, extracted from the yields of primary isotopes produced in antisymmetrized molecular dynamics (AMD) simulations. The asym/T values are extracted from all isotope yields using an improved method based on the modified Fisher model (MFM). The values of asym/T obtained, using different interactions with different density dependencies of the symmetry energy term, are correlated with the values of the symmetry energies at the density of fragment formation. Using this correlation, the fragment formation density is found to be ρ /ρ0=0.67±0.02. Using the input symmetry energy value for each interaction temperature values are extracted as a function of isotope mass A. The extracted temperature values are compared with those evaluated from the fluctuation thermometer with a radial flow correction.

  10. ANOMALOUS REACTION MEAN FREE PATHS OF NUCLEAR PROJECTILE FRAGMENTS FROM HEAVY ION COLLISIONS AT 2 AGeV

    SciTech Connect

    Friedlander, E.M.; Gimpel, R.W.; Heckman, H.H.; Karant, Y.J.; Judek, B.; Ganssauge, E.

    1982-08-01

    We present in detail the description and the analysis of two independent experiments using Bevalac beams of {sup 16}O and {sup 56}Fe. From their results it is concluded that the reaction mean free paths of relativistic projectile fragments, 3 {<=} Z {<=} 26, are shorter for a few centimeters after emission than at large distances where they are compatible with values predicted from experiments on beam nuclei. The probability that this effect is due to a statistical fluctuation is <10{sup -3}. The effect is enhanced in later generations of fragments, the correlation between successive generations suggesting a kind of "memory" for the anomaly. Various systematic and spurious effects as well as conventional explanations are discussed mainly on the basis of direct experimental observations internal to our data, and found not to explain our results. The data can be interpreted by the relatively rare occurrence of anomalous fragments that interact with an unexpectedly large cross section. The statistical methods used in the analysis of the observations are fully described.

  11. Humidity Effects on Fragmentation in Plasma-Based Ambient Ionization Sources.

    PubMed

    Newsome, G Asher; Ackerman, Luke K; Johnson, Kevin J

    2016-01-01

    Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility. PMID:26384684

  12. Humidity Effects on Fragmentation in Plasma-Based Ambient Ionization Sources

    NASA Astrophysics Data System (ADS)

    Newsome, G. Asher; Ackerman, Luke K.; Johnson, Kevin J.

    2016-01-01

    Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility.

  13. Determination of N-linked glycosylation in viral glycoproteins by negative ion mass spectrometry and ion mobility

    PubMed Central

    Bitto, David; Harvey, David J.; Halldorsson, Steinar; Doores, Katie J.; Pritchard, Laura K.; Huiskonen, Juha T.; Bowden, Thomas A.; Crispin, Max

    2016-01-01

    Summary Glycan analysis of virion-derived glycoproteins is challenging due to the difficulties in glycoprotein isolation and low sample abundance. Here, we describe how ion mobility mass spectrometry can be used to obtain spectra from virion samples. We also describe how negative ion fragmentation of glycans can be used to probe structural features of virion glycans. PMID:26169737

  14. Strategy integrating stepped fragmentation and glycan diagnostic ion-based spectrum refinement for the identification of core fucosylated glycoproteome using mass spectrometry.

    PubMed

    Cao, Qichen; Zhao, Xinyuan; Zhao, Qing; Lv, Xiaodong; Ma, Cheng; Li, Xianyu; Zhao, Yan; Peng, Bo; Ying, Wantao; Qian, Xiaohong

    2014-07-15

    Core fucosylation (CF) is a special glycosylation pattern of proteins that has a strong relationship with cancer. The Food and Drug Administration (FDA) has approved the core fucosylated α-fetoprotein as a biomarker for the early diagnosis of hepatocellular carcinoma (HCC). The technology for identifying core fucosylated proteins has significant practical value. The major method for core fucosylated glycoprotein/glycopeptide analysis is neutral loss-based MS(3) scanning under collision-induced dissociation (CID) by ion trap mass spectrometry. However, due to the limited speed and low resolution of the MS(3) scan mode, it is difficult to achieve high-throughput, with only dozens of core fucosylated proteins identified in a single run. In this work, we developed a novel strategy for the identification of CF glycopeptides at a large scale, integrating the stepped fragmentation function, one novel feature of quadrupole-orbitrap mass spectrometry, with "glycan diagnostic ion"-based spectrum optimization. By using stepped fragmentation, we were able to obtain both highly accurate glycan and peptide information of a simplified CF glycopeptide in one spectrum. Moreover, the spectrum could be recorded with the same high speed as the conventional MS(2) scan. By using the "glycan diagnostic ion"-based spectrum refinement method, the efficiency of the CF glycopeptide discovery was significantly improved. We demonstrated the feasibility and reproducibility of our method by analyzing CF glycoproteomes of mouse liver tissue and HeLa cell samples spiked with standard CF glycoprotein. In total, 1364 and 856 CF glycopeptides belonging to 702 and 449 CF glycoproteins were identified, respectively, within a 78-min gradient analysis, which was approximately a 7-fold increase in the identification efficiency of CF glycopeptides compared to the currently used method. In this work, we took core fucosylated glycopeptides as a practical example to demonstrate the great potential of our

  15. Abundance of zinc ions in synaptic terminals of mocha mutant mice: zinc transporter 3 immunohistochemistry and zinc sulphide autometallography.

    PubMed

    Stoltenberg, Meredin; Nejsum, Lene N; Larsen, Agnete; Danscher, Gorm

    2004-02-01

    The mocha mouse is an autosomal recessive pigment mutant on mouse chromosome 10 caused by a deletion in the gene for the delta subunit of the adaptor-like complex AP-3. Based on zinc transporter 3 (ZnT3) immunohistochemistry, zinc TSQ fluorescence and a modified Timm method, previous studies found a lack of histochemically-detectable zinc and a substantial reduction in the ZnT3 immunoreactivity. It has, therefore, been suggested that the mocha mouse could serve as a model for studies of the significance of zinc ions in zinc-enriched (ZEN) neurons. We have chosen the mocha-zinc-model in a study of the significance of ZEN neurons in hypoxia-caused damage in mouse brain. In order to establish that the model was either void of zinc ions or had a significantly decreased level of zinc ions in their ZEN terminals, we repeated the studies that had lead to the above assumption, the only methodology difference being that we used the zinc specific Neo-Timm method instead of the Timm method applied in the original study. We found that, although the ZnS autometallography (AMG) technique revealed a reduction in staining intensity as compared to the littermate controls, there were still plenty of zinc ions in the ZEN terminals, in particular visible in telencephalic structures like neocortex and hippocampus. At ultrastructural levels the zinc ions were found in a pool of vesicles of the ZEN terminals as in the control animals, but additionally zinc ions could be traced in ZEN neuronal somata in the neocortex and hippocampus. The mossy fibres in the hippocampus of mocha mice also bind with TSQ, though less than in the controls. We found ZnS AMG grains in ZEN neuronal somata, which were also immunoreactive for ZnT3. Our study confirmed the decreased ZnT3 immunoreactivity in ZEN terminals of the mocha mouse found in the original study. Based on these findings, we suggest that the mocha mouse may not be an ideal model for studies of the histochemically-detectable zinc ion pool of the

  16. Fluctuations in nuclear fragmentation

    SciTech Connect

    Aranda, A.; Dorso, C.O.; Furci, V.; Lopez, J.A.

    1995-12-01

    Heavy ion collisions can be used to study the thermodynamics of hot and dense nuclear matter only if the initial mass and energy fluctuations that lead to fragmentation are of thermal origin and survive the disassembly process. If this is the case, the observed fragment multiplicity should be directly related to those initial fluctuations and to the conditions of temperature and density causing them. The feasibility of this scenario is demonstrated with a molecular dynamics study of the evolution of mass and energy fluctuations, and fluctuations of the phase-space density. First, it is verified that the fluctuations leading to fragmentation are indeed early ones. Second, it is determined that different initial conditions of density and temperature can indeed produce varying final fragment multiplicities. The {rho}-{ital T} plane is mapped to the fragment multiplicity with good precision. This mapping should be easily reproducible with existing experimental data.

  17. Students' Understanding of External Representations of the Potassium Ion Channel Protein Part II: Structure-Function Relationships and Fragmented Knowledge

    ERIC Educational Resources Information Center

    Harle, Marissa; Towns, Marcy H.

    2012-01-01

    Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations. This study focuses on students' understanding of three external representations (ribbon diagram, wireframe, and hydrophobic/hydrophilic) of the potassium ion channel protein. Analysis…

  18. Economical way to synthesize SSZ-13 with abundant ion-exchanged Cu+ for an extraordinary performance in selective catalytic reduction (SCR) of NOx by ammonia.

    PubMed

    Chen, Biaohua; Xu, Ruinian; Zhang, Runduo; Liu, Ning

    2014-12-01

    In this study, an economical way for SSZ-13 preparation with the essentially cheap choline chloride as template has been attempted. The as-synthesized SSZ-13 zeolite after ion exchange by copper nitrate solution exhibited a superior SCR performance (over 95% NOx conversion across a broad range from 150 to 400 °C) to the traditional zeolite-based catalysts of Cu-Beta and Cu-ZSM-5. Furthermore, the opportune size of pore opening (∼3.8 Å) made Cu-SSZ-13 exhibiting the best selectivity to N2 as well as satisfactory tolerance toward SO2 and C3H6 poisonings. The characterization (XRD, XPS, XRF, and H2-TPR) of samples confirmed that Cu-SSZ-13 possessed the most abundant Cu cations among three investigated Cu-zeolites; furthermore, either on the surface or in the bulk the ratio of Cu(+)/Cu(2+) ions for Cu-SSZ-13 is also the highest. New finding was announced that CHA-type topology is in favor of the formation of copper cations, especially generating much more Cu(+) ions than the others, rather than CuO. The activity test of Cu(CuCl)-ZSM-5 (prepared by a solid-state ion-exchange method) clearly indicated that Cu(+) ions could make a major contribution to the low-temperature deNOx activity. The activity of protonic zeolites (H-SSZ-13, H-Beta, H-ZSM-5) revealed the topology effect on SCR performances. PMID:25365767

  19. Etude du mecanisme de predissociation de l'ion moleculaire de protoxyde d'azote par la mesure de l'energie cinetique des fragments de l'oxyde nitrique et de l'oxygene

    NASA Astrophysics Data System (ADS)

    Delisle, Claude

    La reaction N2 + O+ ↔ NO + + N, laquelle joue un role important dans la physique de la haute atmosphere, a ete le sujet de plusieurs etudes. Bien que cette reaction ait ete l'objet d'une quantite importante de travaux, ces derniers ne permettent toutefois pas de comprendre entierement le mecanisme d'un point de vue quantique, particulierement les niveaux d'energie excites des fragments qui permettent cette reaction. Puisque cette reaction n'est pas tres facile a reproduire en laboratoire, nous avons utilise la spectroscopie laser sur faisceaux d'ions rapides afin d'explorer les limites de dissociation de l'ion moleculaire intermediaire de cette reaction, a savoir l'ion N2O+. Le faisceau d'ions N2O+ rapides, apres excitation de l'ion moleculaire vers un niveau predissocie de l'etat A2Sigma+, se dissocie pour produire les fragments ioniques O+ et NO+. Par la mesure de la variation du nombre de fragments ioniques en fonction de l'energie cinetique des ions N2O+, nous avons enregistre les spectres de predissociation de l'ion N2O+. Lorsque c'etait possible, nous avons procede a l'analyse de ces spectres de dissociation afin d'en tirer les constantes moleculaires. Pour certaines des transitions rotationnelles intenses, nous avons mesure l'energie cinetique acquise par les fragments lors de la predissociation de l'ion N 2O+. Afin d'analyser les distributions en energie cinetique, nous avons developpe une simulation de l'experience en considerant, entre autres choses, la position des niveaux de vibration et de rotation des fragments diatomiques de chacune des limites de dissociation de N2O+. Les resultats de l'analyse sont exprimes en termes de population des niveaux de vibration des fragments diatomiques pour une distribution donnee de la population des niveaux de rotation des fragments. Les resultats ainsi obtenus, montrent que les fragments diatomiques sont produits dans des niveaux de vibration fortement excites. De tels niveaux d'excitation ne correspondent pas aux

  20. Probing the direct step of relativistic heavy ion fragmentation: (/sup 12/C, /sup 11/B+p) at 2. 1 GeV/nucleon with C and CH/sub 2/ targets

    SciTech Connect

    Webb, M.L.

    1987-06-01

    Relativistic heavy ion collisions may be classified as central (and near central), peripheral, and grazing with each collision type producing different proton and other charged projectile fragment scattering mechanisms and characteristics. This report focuses on peripheral and grazing collisions in the fragmentation of Carbon-12 into Boron-11 and a proton, testing models of the kinetics involved in this reaction. The data were measured at the Heavy Ion Superconducting Spectrometer (HISS) at Lawrence Berkeley Laboratory and include excitation energy for the p/Boron-11 pair, and rapidity versus transverse momentum for protons and Boron-11. 58 refs., 35 figs., 8 tabs. (DWL)

  1. First Identification of 5,11-Dideoxytetrodotoxin in Marine Animals, and Characterization of Major Fragment Ions of Tetrodotoxin and Its Analogs by High Resolution ESI-MS/MS

    PubMed Central

    Yotsu-Yamashita, Mari; Abe, Yuka; Kudo, Yuta; Ritson-Williams, Raphael; Paul, Valerie J.; Konoki, Keiichi; Cho, Yuko; Adachi, Masaatsu; Imazu, Takuya; Nishikawa, Toshio; Isobe, Minoru

    2013-01-01

    Even though tetrodotoxin (TTX) is a widespread toxin in marine and terrestrial organisms, very little is known about the biosynthetic pathway used to produce it. By describing chemical structures of natural analogs of TTX, we can start to identify some of the precursors that might be important for TTX biosynthesis. In the present study, an analog of TTX, 5,11-dideoxyTTX, was identified for the first time in natural sources, the ovary of the pufferfish and the pharynx of a flatworm (planocerid sp. 1), by comparison with totally synthesized (−)-5,11-dideoxyTTX, using high resolution ESI-LC-MS. Based on the presence of 5,11-dideoxyTTX together with a series of known deoxy analogs, 5,6,11-trideoxyTTX, 6,11-dideoxyTTX, 11-deoxyTTX, and 5-deoxyTTX, in these animals, we predicted two routes of stepwise oxidation pathways in the late stages of biosynthesis of TTX. Furthermore, high resolution masses of the major fragment ions of TTX, 6,11-dideoxyTTX, and 5,6,11-trideoxyTTX were also measured, and their molecular formulas and structures were predicted to compare them with each other. Although both TTX and 5,6,11-trideoxyTTX give major fragment ions that are very close, m/z 162.0660 and 162.1020, respectively, they are distinguishable and predicted to be different molecular formulas. These data will be useful for identification of TTXs using high resolution LC-MS/MS. PMID:23924959

  2. Opaque rock fragments

    SciTech Connect

    Abhijit, B.; Molinaroli, E.; Olsen, J.

    1987-05-01

    The authors describe a new, rare, but petrogenetically significant variety of rock fragments from Holocene detrital sediments. Approximately 50% of the opaque heavy mineral concentrates from Holocene siliciclastic sands are polymineralic-Fe-Ti oxide particles, i.e., they are opaque rock fragments. About 40% to 70% of these rock fragments show intergrowth of hm + il, mt + il, and mt + hm +/- il. Modal analysis of 23,282 opaque particles in 117 polished thin sections of granitic and metamorphic parent rocks and their daughter sands from semi-arid and humid climates show the following relative abundances. The data show that opaque rock fragments are more common in sands from igneous source rocks and that hm + il fragments are more durable. They assume that equilibrium conditions existed in parent rocks during the growth of these paired minerals, and that the Ti/Fe ratio did not change during oxidation of mt to hm. Geothermometric determinations using electron probe microanalysis of opaque rock fragments in sand samples from Lake Erie and the Adriatic Sea suggest that these rock fragments may have equilibrated at approximately 900/sup 0/ and 525/sup 0/C, respectively.

  3. Competitive proton and hydride transfer reactions via ion-neutral complexes: fragmentation of deprotonated benzyl N-phenylcarbamates in mass spectrometry.

    PubMed

    Yao, Liqing; Chai, Yunfeng; Sun, Cuirong; Pan, Yuanjiang

    2015-02-01

    The gas-phase chemistry of deprotonated benzyl N-phenylcarbamates was investigated by electrospray ionization tandem mass spectrometry. Characteristic losses of a substituted phenylcarbinol and a benzaldehyde from the precursor ion were proposed to be derived from an ion-neutral complex (INC)-mediated competitive proton and hydride transfer reactions. The intermediacy of the INC consisting of a substituted benzyloxy anion and a phenyl isocyanate was supported by both ortho-site-blocking experiments and density functional theory calculations. Within the INC, the benzyloxy anion played the role of either a proton abstractor or a hydride donor toward its neutral counterpart. Relative abundances of the product ions were influenced by the nature of the substituents. Electron-withdrawing groups at the N-phenyl ring favored the hydrogen transfer process (including proton and hydride transfer), whereas electron-donating groups favored direct decomposition to generate the benzyloxy anion (or substituted benzyloxy anion). By contrast, electron-withdrawing and electron-donating substitutions at the O-benzyl ring exhibited opposite effects. PMID:25800018

  4. Shielding and fragmentation studies.

    PubMed

    Zeitlin, C; Guetersloh, S; Heilbronn, L; Miller, J

    2005-01-01

    Radiation dosimetry for manned spaced missions depends on the ability to adequately describe the process of high-energy ion transport through many materials. Since the types of possible nuclear interactions are many and complex, transport models are used which depend upon a reliable source of experimental data. To expand the heavy ion database used in the models we have been measuring charge-changing cross sections and fragment production cross sections from heavy-ion interactions in various elementa targets. These include materials flown on space missions such as carbon and aluminium, as well as those important in radiation dosimetry such as hydrogen, nitrogen and water. Measuring heavy-ion fragmentation through these targets also gives us the ability to determine the effectiveness of new materials proposed for shielding such as graphite composites and polyethylene hybrids. Measurement without a target present gives an indication of the level of contamination of the primary beam, which is also important in radiobiology experiments. PMID:16604611

  5. A DFT study of addition reaction between fragment ion (CH₂) units and fullerene (C₆₀) molecule.

    PubMed

    Zaragoza, Irineo Pedro; Vergara, Jaime; Pérez-Manríquez, Liliana; Salcedo, Roberto

    2011-05-01

    The theoretical study of the interaction between CH(2) and fullerene (C(60)) suggests the existence of an addition reaction mechanism; this feature is studied by applying an analysis of electronic properties. Several different effects are evident in this interaction as a consequence of the particular electronic transfer which occurs during the procedure. The addition or insertion of the methylene group results in a process, where the inclusion of CH(2) into a fullerene bond produces the formation of several geometric deformations. A simulation of these procedures was carried out, taking advantage of the dynamic semi-classical Born-Oppenheimer approximation. Dynamic aspects were analyzed at different speeds, for the interaction between the CH(2) group and the two bonds: CC (6, 6) and CC (6, 5) respectively on the fullerene (C(60)) rings. All calculations which involved electrons employed DFT as well as exchange and functional correlation. The results indicate a tendency for the CH(2) fragment to attack the CC (6, 5) bond. PMID:20658255

  6. Rb, Sr and strontium isotopic composition, K/Ar age and large ion lithophile trace element abundances in rocks and glasses from the Wanapitei Lake impact structure

    NASA Technical Reports Server (NTRS)

    Winzer, S. R.; Lum, R. K. L.; Schuhmann, S.

    1976-01-01

    Shock metamorphosed rocks and shock-produced melt glasses from the Wanapitei Lake impact structure have been examined petrographically and by electron microprobe. Eleven clasts exhibiting varying degrees of shock metamorphism and eight impact-produced glasses have been analyzed for Rb, Sr and Sr isotopic composition. Five clasts and one glass have also been analyzed for large ion lithophile (LIL) trace element abundances including Li, Rb, Sr, and Ba and the REE's. The impact event forming the Wanapitei Lake structure occurred 37 m.y. ago based on K/Ar dating of glass and glassy whole-rock samples. Rb/Sr isotopic dating failed to provide a meaningful whole-rock or internal isochron. The isotopic composition of the glasses can be explained by impact-produced mixing and melting of metasediments.

  7. U, Th, Pb and REE abundances and Pb 207/Pb 206 ages of individual minerals in returned lunar material by ion microprobe mass analysis.

    NASA Technical Reports Server (NTRS)

    Andersen, C. A.; Hinthorne, J. R.

    1972-01-01

    Results of ion microprobe analyses of Apollo 11, 12 and 14 material, showing that U, Th, Pb and REE are concentrated in accessory minerals such as apatite, whitlockite, zircon, baddeleyite, zirkelite, and tranquillityite. Th/U ratios are found to vary by over a factor of 40 in these minerals. K, Ba, Rb and Sr have been localized in a K rich, U and Th poor glass phase that is commonly associated with the U and Th bearing accessory minerals. Li is observed to be fairly evenly distributed between the various accessory phases. The phosphates have been found to have REE abundance patterns (normalized to the chondrite abundances) that are fairly flat, while the Zr bearing minerals have patterns that rise steeply, by factors of ten or more, from La to Gd. All the accessory minerals have large negative Eu anomalies. Radiometric age dates (Pb 207/Pb 206) of the individual U and Th bearing minerals compare favorably with the Pb 207/Pb 206 age of the bulk rocks.

  8. Development of a fast cyclotron gas stopper for intense rare isotope beams from projectile fragmentation: Study of ion extraction with a radiofrequency carpet

    SciTech Connect

    Bollen, Georg; Morrissey, David

    2011-01-16

    Research and development has been performed in support of the design of a future rare isotope beam facility in the US. An important aspect of plans for earlier RIA (Rare Isotope Accelerator) and a requirement of FRIB (Facility of Rare Isotope Beams) to be built at Michigan State University are the availability of so-called “stopped beams” for research that contributes to answering questions like how elements in the universe are created and to provide better insight into the nature of Fundamental Interactions. In order to create “stopped beams” techniques are required that transform fast rare isotopes beams as they are available directly after addresses questions like the origin of that will allow and High priority is given to the evaluation of intensity limitations and the efficiency of stopping of fast fragment beams in gas cells and to the exploration of options to increase the efficiency and the reduction of space charge effects. Systematic studies performed at MSU as part of the RIA R&D with a linear gas cell under conditions close to those expected at RIA and related simulations confirm that the efficiency of stopping and extracting ions decreases with increasing beam intensity. Similar results have also been observed at RIKEN in Japan. These results indicate the concepts presently under study will not be able to cover the full range of intensities of fast beams expected at RIA without major losses. The development of a more robust concept is therefore critical to the RIA concept. Recent new beam simulation studies performed at the NSCL show that the stopping of heavy ions in a weakly focusing gas-filled magnetic field can overcome the intensity limitation of present systems while simultaneously providing a much faster ion extraction. We propose to design and build such a cyclotron gas stopper and to test it at the NSCL under conditions as close as possible to those found at RIA.

  9. Selective and Nonselective Cleavages in Positive and Negative CID of the Fragments Generated from In-Source Decay of Intact Proteins in MALDI-MS

    NASA Astrophysics Data System (ADS)

    Takayama, Mitsuo; Sekiya, Sadanori; Iimuro, Ryunosuke; Iwamoto, Shinichi; Tanaka, Koichi

    2014-01-01

    Selective and nonselective cleavages in ion trap low-energy collision-induced dissociation (CID) experiments of the fragments generated from in-source decay (ISD) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) of intact proteins are described in both positive and negative ion modes. The MALDI-ISD spectra of the proteins demonstrate common, discontinuous, abundant c- and z'-ions originating from cleavage at the N-Cα bond of Xxx-Asp/Asn and Gly-Xxx residues in both positive- and negative-ion modes. The positive ion CID of the c- and z'-ions resulted in product ions originating from selective cleavage at Asp-Xxx, Glu-Xxx and Cys-Xxx residues. Nonselective cleavage product ions rationalized by the mechanism of a "mobile proton" are also observed in positive ion CID spectra. Negative ion CID of the ISD fragments results in complex product ions accompanied by the loss of neutrals from b-, c-, and y-ions. The most characteristic feature of negative ion CID is selective cleavage of the peptide bonds of acidic residues, Xxx-Asp/Glu/Cys. A definite influence of α-helix on the CID product ions was not obtained. However, the results from positive ion and negative ion CID of the MALDI-ISD fragments that may have long α-helical domains suggest that acidic residues in helix-free regions tend to degrade more than those in helical regions.

  10. Enhanced identification of zero-length chemical crosslinks using label-free quantitation and high-resolution fragment ion spectra

    PubMed Central

    Sriswasdi, Sira; Harper, Sandra L.; Tang, Hsin-Yao; Speicher, David W.

    2014-01-01

    Chemical crosslinking coupled with mass spectrometry provides structural information that is useful for probing protein conformations and providing experimental support for molecular models. “Zero-length” crosslinks have greater value for these applications than longer crosslinks because they provide more stringent distance constraints. However, this method is less commonly utilized because it cannot take advantage of isotopic labels, MS-labile bonds, or enrichment tags to facilitate identification. In this study, we combined label-free precursor ion quantitation and targeted tandem mass spectrometry with a new software tool, Zero-length Crosslink Miner (ZXMiner), to form a multi-tiered analysis strategy. A major, critical objective was to simultaneously achieve very high accuracy with essentially no false positive crosslink identifications, while maintaining a good depth of analysis. Our strategy was optimized on several proteins with known crystal structures. Comparison of ZXMiner to several existing crosslink analysis software showed that other algorithms detected less true positive crosslinks and were far less accurate. Although prior use of zero-length crosslinking was typically restricted to small proteins, ZXMiner and the associated strategy enables facile analysis of very large protein complexes. This was demonstrated by identification of zero-length crosslinks using purified 526 kDa spectrin heterodimers and intact red cell membranes and membrane skeletons. PMID:24369724

  11. Electron Capture Dissociation Studies of the Fragmentation Patterns of Doubly Protonated and Mixed Protonated-Sodiated Peptoids

    NASA Astrophysics Data System (ADS)

    Bogdanov, Bogdan; Zhao, Xiaoning; Robinson, David B.; Ren, Jianhua

    2014-07-01

    The fragmentation patterns of a group of doubly protonated ([P + 2H]2+) and mixed protonated-sodiated ([P + H + Na]2+) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C'-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z•-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z•'-series of ions in addition to the C'-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H]•+) and the sodiated peptoids ([P + H + Na]•+). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.

  12. Fragmentation of condensed-phase DNA components by hyperthermal He{sup +} impact

    SciTech Connect

    Deng Zongwu; Imhoff, Marjorie; Bald, Ilko; Illenberger, Eugen; Huels, Michael A.

    2006-07-15

    We have observed severe damage to films of DNA components (thymine, D-ribose, 2-deoxy-D-ribose, and thymidine) induced by 10 to 100 eV He{sup +} ions (2.5-25 eV/amu). The damage is attributed to the kinetic and potential energies, as well as the chemical reactivity of the He{sup +} projectiles. Hyperthermal He{sup +} ion impact on these films results in the complete destruction of the molecules via fragmentation, and direct and indirect (secondary fragment) reactive scattering, all of which leads to the desorption of abundant cation and anion fragments. The chemical composition of the fragments is identified, and the fragmentation patterns are compared to those produced by Ar{sup +} irradiation. While the lower mass of He{sup +} ions causes less efficient desorption of very heavy fragments, several reactive collisions are also observed, including hydrogen abstraction by incident He{sup +} from any of the molecules studied to yield desorbing HeH{sup +}. This process likely occurs via the formation of an intermediate molecular ion (He-H-R)*{sup +}, which decays to HeH{sup +}+R . Compared to Ar{sup +}, here a significant (x23) enhancement in H{sup +} desorption is observed during He{sup +} ion irradiation, which likely involves (a) the decay of the intermediate (He-H-R)*{sup +}, or desorbing HeH{sup +}, and (b) Auger or quasiresonant excitations of C, N, or O atom centers (or C-H, N-H, or O-H bonds) by the incident He{sup +} ion. The formation of several molecular cations, e.g., H{sub 3}O{sup +}, also requires hydrogen abstraction from its parent or adjacent molecules by initial cation fragments prior to desorption.

  13. Factors Affecting the Production of Aromatic Immonium Ions in MALDI 157 nm Photodissociation Studies

    NASA Astrophysics Data System (ADS)

    DeGraan-Weber, Nick; Ashley, Daniel C.; Keijzer, Karlijn; Baik, Mu-Hyun; Reilly, James P.

    2016-05-01

    Immonium ions are commonly observed in the high energy fragmentation of peptide ions. In a MALDI-TOF/TOF mass spectrometer, singly charged peptides photofragmented with 157 nm VUV light yield a copious abundance of immonium ions, especially those from aromatic residues. However, their intensities may vary from one peptide to another. In this work, the effect of varying amino acid position, peptide length, and peptide composition on immonium ion yield is investigated. Internal immonium ions are found to have the strongest intensity, whereas immonium ions arising from C-terminal residues are the weakest. Peptide length and competition among residues also strongly influence the immonium ion production. Quantum calculations provide insights about immonium ion structures and the fragment ion conformations that promote or inhibit immonium ion formation.

  14. Magma Fragmentation

    NASA Astrophysics Data System (ADS)

    Gonnermann, Helge M.

    2015-05-01

    Magma fragmentation is the breakup of a continuous volume of molten rock into discrete pieces, called pyroclasts. Because magma contains bubbles of compressible magmatic volatiles, decompression of low-viscosity magma leads to rapid expansion. The magma is torn into fragments, as it is stretched into hydrodynamically unstable sheets and filaments. If the magma is highly viscous, resistance to bubble growth will instead lead to excess gas pressure and the magma will deform viscoelastically by fracturing like a glassy solid, resulting in the formation of a violently expanding gas-pyroclast mixture. In either case, fragmentation represents the conversion of potential energy into the surface energy of the newly created fragments and the kinetic energy of the expanding gas-pyroclast mixture. If magma comes into contact with external water, the conversion of thermal energy will vaporize water and quench magma at the melt-water interface, thus creating dynamic stresses that cause fragmentation and the release of kinetic energy. Lastly, shear deformation of highly viscous magma may cause brittle fractures and release seismic energy.

  15. 213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns

    NASA Astrophysics Data System (ADS)

    Halim, Mohammad A.; Girod, Marion; MacAleese, Luke; Lemoine, Jérôme; Antoine, Rodolphe; Dugourd, Philippe

    2016-03-01

    Characterization of acidic peptides and proteins is greatly hindered due to lack of suitable analytical techniques. Here we present the implementation of 213 nm ultraviolet photodissociation (UVPD) in high-resolution quadrupole-Orbitrap mass spectrometer in negative polarity for peptide anions. Radical-driven backbone fragmentation provides 22 distinctive fragment ion types, achieving the complete sequence coverage for all reported peptides. Hydrogen-deficient radical anion not only promotes the cleavage of Cα-C bond but also stimulates the breaking of N-Cα and C-N bonds. Radical-directed loss of small molecules and specific side chain of amino acids are detected in these experiments. Radical containing side chain of amino acids (Tyr, Ser, Thr, and Asp) may possibly support the N-Cα backbone fragmentation. Proline comprising peptides exhibit the unusual fragment ions similar to reported earlier. Interestingly, basic amino acids such as Arg and Lys also stimulated the formation of abundant b and y ions of the related peptide anions. Loss of hydrogen atom from the charge-reduced radical anion and fragment ions are rationalized by time-dependent density functional theory (TDDFT) calculation, locating the potential energy surface (PES) of ππ* and repulsive πσ* excited states of a model amide system.

  16. 213 nm Ultraviolet Photodissociation on Peptide Anions: Radical-Directed Fragmentation Patterns.

    PubMed

    Halim, Mohammad A; Girod, Marion; MacAleese, Luke; Lemoine, Jérôme; Antoine, Rodolphe; Dugourd, Philippe

    2016-03-01

    Characterization of acidic peptides and proteins is greatly hindered due to lack of suitable analytical techniques. Here we present the implementation of 213 nm ultraviolet photodissociation (UVPD) in high-resolution quadrupole-Orbitrap mass spectrometer in negative polarity for peptide anions. Radical-driven backbone fragmentation provides 22 distinctive fragment ion types, achieving the complete sequence coverage for all reported peptides. Hydrogen-deficient radical anion not only promotes the cleavage of Cα-C bond but also stimulates the breaking of N-Cα and C-N bonds. Radical-directed loss of small molecules and specific side chain of amino acids are detected in these experiments. Radical containing side chain of amino acids (Tyr, Ser, Thr, and Asp) may possibly support the N-Cα backbone fragmentation. Proline comprising peptides exhibit the unusual fragment ions similar to reported earlier. Interestingly, basic amino acids such as Arg and Lys also stimulated the formation of abundant b and y ions of the related peptide anions. Loss of hydrogen atom from the charge-reduced radical anion and fragment ions are rationalized by time-dependent density functional theory (TDDFT) calculation, locating the potential energy surface (PES) of ππ* and repulsive πσ* excited states of a model amide system. PMID:26545767

  17. Auger Stimulated Ion Desorption of Negative Ions via K -Capture Radioactive Decay

    SciTech Connect

    Verkhoturov, S. V.; Schweikert, E. A.; Chechik, Victor; Sabapathy, Rajaram C.; Crooks, Richard M.; Parilis, E. S.

    2001-07-16

    We report on Auger stimulated ion desorption via Coulomb explosion from surface self-assembled alkylthiol and fluorocarbon molecular layers, triggered by K -capture decay of an imbedded radioactive {sup 55}Fe atom. The charge state of the ejecta is determined by charge exchange in binary atomic collisions in bulk and electron tunneling outside the solid, as well as by fragmentation of electronically excited molecules or molecular fragments. We describe the first nonbeam experiments documenting positive and abundant negative ion desorption due solely to core electron excitation after radioactive decay.

  18. Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Shukla, Anil; Bogdanov, Bogdan

    2015-02-01

    Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry (collision-induced dissociation with N2). Singly as well as multiply charged clusters were formed in both positive and negative ion modes with the general formulae, (HCOOLi)nLi+, (HCOOLi)nLimm+, (HCOOLi)nHCOO-, and (HCOOLi)n(HCOO)mm-. Several magic number cluster (MNC) ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi)3Li+ being the most abundant and stable cluster ion. Fragmentations of singly charged positive clusters proceed first by the loss of a dimer unit ((HCOOLi)2) followed by the loss of monomer units (HCOOLi) although the former remains the dominant dissociation process. In the case of positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi)3Li+ as the most abundant fragment ion at higher collision energies which then fragments further to dimer and monomer ions at lower abundances. In the negative ion mode, however, singly charged clusters dissociated via sequential loss of monomer units. Multiply charged clusters in both positive and negative ion modes dissociated mainly via Coulomb repulsion. Quantum chemical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the central lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.

  19. Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

    SciTech Connect

    Shukla, Anil; Bogdanov, Bogdan

    2015-02-14

    Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry (collision-induced dissociation with N{sub 2}). Singly as well as multiply charged clusters were formed in both positive and negative ion modes with the general formulae, (HCOOLi){sub n}Li{sup +}, (HCOOLi){sub n}Li{sub m}{sup m+}, (HCOOLi){sub n}HCOO{sup −}, and (HCOOLi){sub n}(HCOO){sub m}{sup m−}. Several magic number cluster (MNC) ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi){sub 3}Li{sup +} being the most abundant and stable cluster ion. Fragmentations of singly charged positive clusters proceed first by the loss of a dimer unit ((HCOOLi){sub 2}) followed by the loss of monomer units (HCOOLi) although the former remains the dominant dissociation process. In the case of positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi){sub 3}Li{sup +} as the most abundant fragment ion at higher collision energies which then fragments further to dimer and monomer ions at lower abundances. In the negative ion mode, however, singly charged clusters dissociated via sequential loss of monomer units. Multiply charged clusters in both positive and negative ion modes dissociated mainly via Coulomb repulsion. Quantum chemical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the central lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.

  20. Peptide and metal ion-dependent association of isolated helix-loop-helix calcium binding domains: studies of thrombic fragments of calmodulin.

    PubMed Central

    Brokx, R. D.; Vogel, H. J.

    2000-01-01

    Calmodulin (CaM), the ubiquitous, eukaryotic, bilobal calcium-binding regulatory protein, has been cleaved by thrombin to create two fragments. TM1 (1-106) and TM2 (107-148). NMR and CD results indicate that TMI and TM2 can associate in the presence of Ca2+ to form a complex similar to native CaM, even though the cleavage site is not in the linker region between two helix-loop-helix domains, but rather within an alpha-helix. Cadmium-113 NMR results show that this complex has enhanced metal-ion binding properties when compared to either TM1 or TM2 alone. This complex can bind several CaM-binding target peptides, as shown by gel bandshift assays, circular dichroism spectra, and 13C NMR spectra of biosynthetically methyl-13C-Met-labeled TM1 and TM2; moreover, gel bandshift assays show that the addition of a target peptide strengthens the interactions between TM1 and TM2 and increases the stability of the complex. Cadmium-113 NMR spectra indicate that the TM1:TM2 complex can also bind the antipsychotic drug trifluoperazine. However, in contrast to CaM:peptide complexes, the TM1:TM2:peptide complexes are disrupted by 4 M urea; moreover, TM1 and TM2 in combination are unable to activate CaM-dependent enzymes. This suggests that TM1:TM2 mixtures cannot bind target molecules as tightly as intact CaM, or perhaps that binding occurs but additional interactions with the target enzymes that are necessary for proper activation are perturbed by the proteolytic cleavage. The results presented here reflect the importance of the existence of helix-loop-helix Ca2+-binding domains in pairs in proteins such as CaM, and extend the understanding of the association of such domains in this class of proteins in general. PMID:10850806

  1. Are liquid chromatography/electrospray tandem quadrupole fragmentation ratios unequivocal confirmation criteria?

    PubMed

    Kaufmann, Anton; Butcher, Patrick; Maden, Kathryn; Widmer, Mirjam; Giles, Kevin; Uría, Diana

    2009-04-01

    Multiple reaction monitoring (MRM) ratios as provided by tandem mass spectrometers are used to confirm positive residue findings (e.g. veterinary drugs or pesticides). The Commission Decision 2002/657/EEC defines tolerance levels for MRM ratios, which are intended to prevent the reporting of false positives. This paper reports findings where blank sample extracts have been spiked by a drug (difloxacin) and the corresponding measured MRM ratios significantly deviated from MRM ratios observed in matrix-free solution. The observation was explained by the formation of two different [M+H](+) analyte ions within the electrospray ionization (ESI) interface. These two ions vary only by the site of analyte protonation. Since they are isobaric, they are equally transmitted through the first quadrupole, but are differently fragmented in the collision chamber. The existence of two isobaric ions was deduced by statistical data and the observation of a doubly charged analyte ion. It was hypothesized that the combined presence of [M+H](+) and [M+2H](2+) implies the existence of two different singly charged ion species differing only by the site of protonation. Low- and high-energy interface-induced fragmentation was performed on the samples. The surviving precursor ion population was mass selected and again fragmented in the collision chamber. Equal product ion spectra would be expected. However, very different product ion spectra were observed for the two interface regimes. This is consistent with the assumption that the two postulated isobaric precursor ions show different stability in the interface. Hence the abundance ratio among the two types of surviving precursor ions will shift and change the resulting product ion spectra. The existence of the postulated singly charged ions with multiple chargeable sites was finally confirmed by successful ion mobility separation. PMID:19241450

  2. On the gas phase fragmentation of protonated uracil: a statistical perspective.

    PubMed

    Rossich Molina, Estefanía; Salpin, Jean-Yves; Spezia, Riccardo; Martínez-Núñez, Emilio

    2016-06-01

    The potential energy surface of protonated uracil has been explored by an automated transition state search procedure, resulting in the finding of 1398 stationary points and 751 reactive channels, which can be categorized into isomerizations between pairs of isomers, unimolecular fragmentations and bimolecular reactions. The use of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory and Kinetic Monte Carlo (KMC) simulations allowed us to determine the relative abundances of each fragmentation channel as a function of the ion's internal energy. The KMC/RRKM product abundances are compared with novel mass spectrometry (MS) experiments in the collision energy range 1-6 eV. To facilitate the comparison between theory and experiments, further dynamics simulations are carried out to determine the fraction of collision energy converted into the ion's internal energy. The KMC simulations show that the major fragmentation channels are isocyanic acid and ammonia losses, in good agreement with experiments. The third predominant channel is water loss according to both theory and experiments, although the abundance obtained in the KMC simulations is very low, suggesting that non-statistical dynamics might play an important role in this channel. Isocyanic acid (HNCOH(+)) is also an important product in the KMC simulations, although its abundance is only significant at internal energies not accessible in the MS experiments. PMID:27194127

  3. Forest Fragmentation

    EPA Science Inventory

    This indicator describes forest fragmentation in the contiguous United States circa 2001. This information provides a broad, recent picture of the spatial pattern of the nation’s forests and the extent to which they are being broken into smaller patches and pierced or interspe...

  4. Lithium Formate Ion Clusters Formation during Electrospray Ionization: Evidence of Magic Number Clusters by Mass Spectrometry and ab initio Calculations

    SciTech Connect

    Shukla, Anil K.; Bogdanov, Bogdan

    2015-02-10

    Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry. Singly as well as multiply charged clusters were formed with the general formulae, (HCOOLi)nLi+, (HCOOLi)nLimm+, (HCOOLi)nHCOO- and (HCOOLi)n(HCOO)mm-. Several magic number cluster ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi)3Li+ being the most abundant and stable cluster ions. Fragmentations of singly charged clusters proceed first by the loss of a dimer unit ((HCOOLi)2) followed by sequential loss of monomer units (HCOOLi). In the case of positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi)3Li+ at higher collision energies which later fragments to dimer and monomer ions in lower abundance. Quantum mechanical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.

  5. Diagnostic fragment-ion-based and extension strategy coupled to DFIs intensity analysis for identification of chlorogenic acids isomers in Flos Lonicerae Japonicae by HPLC-ESI-MS(n).

    PubMed

    Zhang, Jia-Yu; Zhang, Qian; Li, Ning; Wang, Zi-Jian; Lu, Jian-Qiu; Qiao, Yan-Jiang

    2013-01-30

    A method of modified diagnostic fragment-ion-based extension strategy (DFIBES) coupled to DFIs (diagnostic fragmentation ions) intensity analysis was successfully established to simultaneously screen and identify the chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ) by HPLC-ESI-MS(n). DFIs, such as m/z 191 [quinic acid-H](-), m/z 179 [caffeic acid-H](-) and m/z 173 [quinic acid-H-H2O](-) were determined or proposed from the fragmentation patterns analysis of corresponding reference substances for every chemical family of CGAs. A "structure extension" method was then proposed based on the well-demonstrated fragmentation patterns and was successively applied into the rapid screening of CGAs in FLJ. Considering that substitution isomerism is a common phenomenon, a full ESI-MS(n) fragmentation analysis according to the intensity of DFIs has been performed to identify the CGA isomers. Based on the DFIs and intensity analysis, 41 peaks attributed to CGAs including 4 caffeoylquinic acids (CQA), 7 CQA glycosides, 6 dicaffeoylquinic acids (DiCQA), 10 DiCQA glycosides, 1 tricaffeoylquinic acids (TriCQA), 4p-coumaroylquinic acids (pCoQA), 3 feruloylquinic acids (FQA) and 6 caffeoylferuloylquinic acids (CFQA) were identified preliminarily in a 65-min chromatographic run. It was the first time to systematically report the presence of CGAs in FLJ, especially for CQA glycosides, DiCQA glycosides, TriCQA, pCoQA and CFQA. All the results indicated that the method of developed DFIBES coupled to DFIs analysis was feasible, reliable and universal for screening and identifying the constituents with the same carbon skeletons especially the isomeric compounds from the complex extract of TCMs. PMID:23597880

  6. Observation of anomalous reaction mean free paths of nuclear-projectile fragments in research emulsion from 2 A GeV heavy-ion collisions

    SciTech Connect

    Karant, Y.J.

    1981-07-01

    From an analysis of 1460 projectile fragment collisions in nuclear research emulsion exposed to 2.1 A GeV /sup 16/O and 1.9 A GeV /sup 56/Fe at the Bevalac, evidence is presented for the existence of an anomalously short interaction mean free path of projectile fragments for the first several cm after emission. The result is significant to beyond the 3 standard deviation confidence level.

  7. Target fragmentation in radiobiology

    NASA Technical Reports Server (NTRS)

    Wilson, John W.; Cucinotta, Francis A.; Shinn, Judy L.; Townsend, Lawrence W.

    1993-01-01

    Nuclear reactions in biological systems produce low-energy fragments of the target nuclei seen as local high events of linear energy transfer (LET). A nuclear-reaction formalism is used to evaluate the nuclear-induced fields within biosystems and their effects within several biological models. On the basis of direct ionization interaction, one anticipates high-energy protons to have a quality factor and relative biological effectiveness (RBE) of unity. Target fragmentation contributions raise the effective quality factor of 10 GeV protons to 3.3 in reasonable agreement with RBE values for induced micronuclei in bean sprouts. Application of the Katz model indicates that the relative increase in RBE with decreasing exposure observed in cell survival experiments with 160 MeV protons is related solely to target fragmentation events. Target fragment contributions to lens opacity given an RBE of 1.4 for 2 GeV protons in agreement with the work of Lett and Cox. Predictions are made for the effective RBE for Harderian gland tumors induced by high-energy protons. An exposure model for lifetime cancer risk is derived from NCRP 98 risk tables, and protraction effects are examined for proton and helium ion exposures. The implications of dose rate enhancement effects on space radiation protection are considered.

  8. Fragmentation pathways analysis for the gas phase dissociation of protonated carnosine-oxaliplatin complexes.

    PubMed

    Ritacco, Ida; Moustafa, Eslam M; Sicilia, Emilia; Russo, Nino; Shoeib, Tamer

    2015-03-14

    Collision-induced dissociation (CID) experiments on the protonated carnosine-oxaliplatin complex, [Carnosine + OxPt + H](+) using several collision energies were shown to yield nine different fragment ions. Energy-resolved CID experiments on [Carnosine + OxPt + H](+) showed that the generation of the product ion [Carnosine - H + Pt(dach)](+) (where dach is 1,2-diaminocyclohexane) is the lowest energy process. At slightly higher collision energies, the loss of neutral carnosine from [Carnosine + OxPt + H](+) to produce [OxPt + H](+) was observed, followed by the loss of oxaliplatin from the same precursor ion to produce [Carnosine + H](+). At significantly higher energies, the ion [OxPt - CO2 + H](+) was shown to be formed, while the last two investigated ions [Carnosine + OxPt - CO2 + H](+) and [Carnosine - NH3 - H + Pt(dach)](+) did not attain any significant relative abundance. Density functional calculations at the B3LYP/LANL2DZ level were employed to probe the fragmentation mechanisms that account for all experimental data. The lowest free energy barriers for the generation of each of the ions [Carnosine - H + Pt(dach)](+), [OxPt + H](+), [Carnosine + H](+), [Carnosine + OxPt - CO2 + H](+) and [Carnosine - NH3 - H + Pt(dach)](+) from [Carnosine + OxPt + H](+) according to the fragmentation mechanisms offered here were calculated to be 31.9, 38.8, 49.3, 75.2, and 85.6 kcal mol(-1), respectively. PMID:25325236

  9. Investigation of bn-44 Peptide Fragments Using High Resolution Mass Spectrometry and Isotope Labeling

    NASA Astrophysics Data System (ADS)

    Wang, Bing; Yu, Jiayi; Wang, Huixin; Wei, Zhonglin; Guo, Xinhua; Xiao, Zhaohui; Zeng, Zhoufang; Kong, Wei

    2014-12-01

    An N-terminal deuterohemin-containing hexapeptide (DhHP-6) was designed as a short peptide cytochrome c (Cyt c) mimetic to study the effect of N-terminal charge on peptide fragmentation pathways. This peptide gave different dissociation patterns than normal tryptic peptides. Upon collision-induced dissociation (CID) with an ion trap mass spectrometer, the singly charged peptide ion containing no added proton generated abundant and characteristic bn-44 ions instead of bn-28 (an) ions. Studies by high resolution mass spectrometry (HRMS) and isotope labeling indicate that elimination of 44 Da fragments from b ions occurs via two different pathways: (1) loss of CH3CHO (44.0262) from a Thr side chain; (2) loss of CO2 (43.9898) from the oxazolone structure in the C-terminus. A series of analogues were designed and analyzed. The experimental results combined with Density Functional Theory (DFT) calculations on the proton affinity of the deuteroporphyrin demonstrate that the production of these novel bn-44 ions is related to the N-terminal charge via a charge-remote rather than radical-directed fragmentation pathway.

  10. Electron Capture by a Hydrated Gaseous Peptide: Effects of Water on Fragmentation and Molecular Survival

    PubMed Central

    Prell, James S.; O'Brien, Jeremy T.; Holm, Anne I. S.; Leib, Ryan D.; Donald, William A.; Williams, Evan R.

    2008-01-01

    The effects of water on electron capture dissociation products, molecular survival, and recombination energy are investigated for diprotonated Lys-Tyr-Lys solvated by between zero and 25 water molecules. For peptide ions with between 12 and 25 water molecules attached, electron capture results in a narrow distribution of product ions corresponding to primarily the loss of 10-12 water molecules from the reduced precursor. From these data, the recombination energy (RE) is determined to be equal to the energy that is lost by evaporating on average 10.7 water molecules, or 4.3 eV. Because water stabilizes ions, this value is a lower limit to the RE of the unsolvated ion, but it indicates that the majority of the available RE is deposited into internal modes of the peptide ion. Plotting the fragment ion abundances for ions formed from precursors with fewer than 11 water molecules as a function of hydration extent results in an energy resolved breakdown curve from which the appearance energies of the b2+, y2+, z2+•, c2+, and (KYK + H)+ fragment ions formed from this peptide ion can be obtained; these values are 78, 88, 42, 11, and 9 kcal/mol, respectively. The propensity for H atom loss and ammonia loss from the precursor changes dramatically with the extent of hydration, and this change in reactivity can be directly attributed to a “caging” effect by the water molecules. These are the first experimental measurements of the RE and appearance energies of fragment ions due to electron capture dissociation of a multiply charged peptide. This novel ion nanocalorimetry technique can be applied more generally to other exothermic reactions that are not readily accessible to investigation by more conventional thermochemical methods. PMID:18761457

  11. Neutral fragment filtering for rapid identification of new diester-diterpenoid alkaloids in roots of Aconitum carmichaeli by ultra-high-pressure liquid chromatography coupled with linear ion trap-orbitrap mass spectrometry.

    PubMed

    Zhang, Jing; Huang, Zhi Hai; Qiu, Xiao Hui; Yang, Yi Ming; Zhu, Da Yuan; Xu, Wen

    2012-01-01

    A rapid and effective method was developed for separation and identification of diester-diterpenoid alkaloids (DDA) in the roots of Aconitum carmichaeli by ultra-high-pressure liquid chromatography coupled with high resolution LTQ-Orbitrap tandem mass spectrometry (UHPLC-LTQ-Orbitrap-MS(n)). According to accurate mass measurement and the characteristic neutral loss filtering strategy, a total of 42 diester-diterpenoid alkaloids (DDA) were rapidly detected and characterized or tentatively identified. Meanwhile, the proposed fragmentation pathways and the major diagnostic fragment ions of aconitine, mesaconitine and hypaconitine were investigated to trace DDA derivatives in crude plant extracts. 23 potential new compounds were successfully screened and characterized in Aconitum carmichaeli, including 16 short chain fatty acyls DDA, 4 N-dealkyl DDA and several isomers of aconitine, mesaconitine and hypaconitine. PMID:23285005

  12. Perturbative fragmentation

    SciTech Connect

    Kopeliovich, B. Z.; Pirner, H.-J.; Potashnikova, I. K.; Schmidt, Ivan; Tarasov, A. V.

    2008-03-01

    The Berger model of perturbative fragmentation of quarks to pions is improved by providing an absolute normalization and keeping all terms in a (1-z) expansion, which makes the calculation valid at all values of fractional pion momentum z. We also replace the nonrelativistic wave function of a loosely bound pion by the more realistic procedure of projecting to the light-cone pion wave function, which in turn is taken from well known models. The full calculation does not confirm the (1-z){sup 2} behavior of the fragmentation function (FF) predicted in [E. L. Berger, Z. Phys. C 4, 289 (1980); Phys. Lett. 89B, 241 (1980] for z>0.5, and only works at very large z>0.95, where it is in reasonable agreement with phenomenological FFs. Otherwise, we observe quite a different z-dependence which grossly underestimates data at smaller z. The disagreement is reduced after the addition of pions from decays of light vector mesons, but still remains considerable. The process dependent higher twist terms are also calculated exactly and found to be important at large z and/or p{sub T}.

  13. State-selective enhanced production of positive ions and excited neutral fragments of gaseous CH2Cl2 following Cl 2p core-level photoexcitation

    NASA Astrophysics Data System (ADS)

    Lu, K. T.; Chen, J. M.; Lee, J. M.; Haw, S. C.; Chen, S. A.; Liang, Y. C.; Chen, S. W.

    2010-09-01

    Following photoexcitation of Cl2p electrons to various resonances, the dissociation dynamics of ionic and excited neutral fragments of gaseous CH2Cl2 was investigated by combined measurements of photon-induced ionic dissociation, x-ray absorption, and uv-visible dispersed fluorescence. The Cl2p core-to-Rydberg excitations near the ionization threshold produce a notable enhancement of excited neutral fragments (C* and CH*), which is attributed to the contribution from a shake-modified resonant Auger decay and postcollision interaction. The excitation Cl2p→10a1* induces an enhanced yield of CH2+, possibly originating from fast dissociation via a strongly repulsive surface. The experimental results provide insight into the dissociation dynamics of ionic and excited neutral fragment production following core-level excitation.

  14. Fragmentation pathways of 2,3-dimethyl-2,3-dinitrobutane cations in the gas phase.

    PubMed

    Paine, Martin R L; Kirk, Benjamin B; Ellis-Steinborner, Simon; Blanksby, Stephen J

    2009-09-01

    2,3-Dimethyl-2,3-dinitrobutane (DMNB) is an explosive taggant added to plastic explosives during manufacture making them more susceptible to vapour-phase detection systems. In this study, the formation and detection of gas-phase [M+H](+), [M+Li](+), [M+NH(4)](+) and [M+Na](+) adducts of DMNB was achieved using electrospray ionisation on a triple quadrupole mass spectrometer. The [M+H](+) ion abundance was found to have a strong dependence on ion source temperature, decreasing markedly at source temperatures above 50 degrees C. In contrast, the [M+Na](+) ion demonstrated increasing ion abundance at source temperatures up to 105 degrees C. The relative susceptibility of DMNB adduct ions toward dissociation was investigated by collision-induced dissociation. Probable structures of product ions and mechanisms for unimolecular dissociation have been inferred based on fragmentation patterns from tandem mass (MS/MS) spectra of source-formed ions of normal and isotopically labelled DMNB, and quantum chemical calculations. Both thermal and collisional activation studies suggest that the [M+Na](+) adduct ions are significantly more stable toward dissociation than their protonated analogues and, as a consequence, the former provide attractive targets for detection by contemporary rapid screening methods such as desorption electrospray ionisation mass spectrometry. PMID:19670345

  15. Fragmentation of Allylmethylsulfide by Chemical Ionization: Dependence on Humidity and Inhibiting Role of Water

    PubMed Central

    2013-01-01

    We report on a previously unknown reaction mechanism involving water in the fragmentation reaction following chemical ionization. This result stems from a study presented here on the humidity-dependent and energy-dependent endoergic fragmentation of allyl methyl sulfide (AMS) upon protonation in a proton transfer reaction-mass spectrometer (PTR-MS). The fragmentation pathways were studied with experimental (PTR-MS) and quantum chemical methods (polarizable continuum model (PCM), microhydration, studied at the MP2/6-311+G(3df,2p)//MP2/6-31G(d,p) level of theory). We report in detail on the energy profiles, reaction mechanisms, and proton affinities (G4MP2 calculations). In the discovered reaction mechanism, water reduces the fragmentation of protonated species in chemical ionization. It does so by direct interaction with the protonated species via covalent binding (C3H5+) or via association (AMS·H+). This stabilizes intermediate complexes and thus overall increases the activation energy for fragmentation. Water thereby acts as a reusable inhibitor (anticatalyst) in chemical ionization. Moreover, according to the quantum chemical (QC) results, when water is present in abundance it has the opposite effect and enhances fragmentation. The underlying reason is a concentration-dependent change in the reaction principle from active inhibition of fragmentation to solvation, which then enhances fragmentation. This amphoteric behavior of water is found for the fragmentation of C3H5+ to C3H3+, and similarly for the fragmentation of AMS·H+ to C3H5+. The results support humidity-dependent quantification efforts for PTR-MS and chemical ionization mass spectrometry (CIMS). Moreover, the results should allow for a better understanding of ion-chemistry in the presence of water. PMID:23682687

  16. Differentiation of regioisomeric aromatic ketocarboxylic acids by atmospheric pressure chemical ionization CAD tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer

    SciTech Connect

    Amundson, Lucas M.; Owen, Ben C.; Gallardo, Vanessa A.; Habicht, S. C.; Fu, M.; Shea, R. C.; Mossman, A. B.; Kenttämaa, Hilkka I.

    2011-01-01

    Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS n ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at different collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.

  17. Differentiation of Regioisomeric Aromatic Ketocarboxylic Acids by Positive Mode Atmospheric Pressure Chemical Ionization Collision-Activated Dissociation Tandem Mass Spectrometry in a Linear Quadrupole Ion Trap Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Amundson, Lucas M.; Owen, Benjamin C.; Gallardo, Vanessa A.; Habicht, Steven C.; Fu, Mingkun; Shea, Ryan C.; Mossman, Allen B.; Kenttämaa, Hilkka I.

    2011-04-01

    Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS n ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at different collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.

  18. Unusual Fragmentation Pathways in Collagen Glycopeptides

    NASA Astrophysics Data System (ADS)

    Perdivara, Irina; Perera, Lalith; Sricholpech, Marnisa; Terajima, Masahiko; Pleshko, Nancy; Yamauchi, Mitsuo; Tomer, Kenneth B.

    2013-07-01

    Collagens are the most abundant glycoproteins in the body. One characteristic of this protein family is that the amino acid sequence consists of repeats of three amino acids -(X—Y—Gly)n. Within this motif, the Y residue is often 4-hydroxyproline (HyP) or 5-hydroxylysine (HyK). Glycosylation in collagen occurs at the 5-OH group in HyK in the form of two glycosides, galactosylhydroxylysine (Gal-HyK) and glucosyl galactosylhydroxylysine (GlcGal-HyK). In collision induced dissociation (CID), collagen tryptic glycopeptides exhibit unexpected gas-phase dissociation behavior compared to typical N- and O-linked glycopeptides (i.e., in addition to glycosidic bond cleavages, extensive cleavages of the amide bonds are observed). The Gal- or GlcGal- glycan modifications are largely retained on the fragment ions. These features enable unambiguous determination of the amino acid sequence of collagen glycopeptides and the location of the glycosylation site. This dissociation pattern was consistent for all analyzed collagen glycopeptides, regardless of their length or amino acid composition, collagen type or tissue. The two fragmentation pathways—amide bond and glycosidic bond cleavage—are highly competitive in collagen tryptic glycopeptides. The number of ionizing protons relative to the number of basic sites (i.e., Arg, Lys, HyK, and N-terminus) is a major driving force of the fragmentation. We present here our experimental results and employ quantum mechanics calculations to understand the factors enhancing the labile character of the amide bonds and the stability of hydroxylysine glycosides in gas phase dissociation of collagen glycopeptides.

  19. Population kinetics of laser levels of neodymium ions in POCl{sub 3}-SnCl{sub 4}-{sup 235}UO{sub 2}{sup 2+}-Nd{sup 3+} excited by fission fragments

    SciTech Connect

    Seregina, E A; Dobrovol'skii, A F; Kabakov, D V; Seregin, A A; Tikhonov, G V

    2009-08-31

    The population kinetics of laser levels of neodymium ions in the uranium-containing POCl{sub 3}-SnCl{sub 4}-{sup 235}UO{sub 2}{sup 2+}-Nd{sup 3+} laser liquid irradiated in a BARS-6 pulsed reactor is studied experimentally and theoretically. The relations between the populations of the upper and lower laser levels are studied at different time moments with respect to the pump pulse. An inverse population of laser levels is observed and found to be directly proportional to the pump power. The efficiency of pumping of the upper laser level of neodymium ions in the laser medium by uranium fission fragments is determined, and quantitative information is obtained on the inverse population, gain, and their dependences on the pump power. (active media)

  20. Quantification and micron-scale imaging of spatial distribution of trace beryllium in shrapnel fragments and metallurgic samples with correlative fluorescence detection method and secondary ion mass spectrometry (SIMS).

    PubMed

    Abraham, J L; Chandra, S; Agrawal, A

    2014-11-01

    Recently, a report raised the possibility of shrapnel-induced chronic beryllium disease from long-term exposure to the surface of retained aluminum shrapnel fragments in the body. Since the shrapnel fragments contained trace beryllium, methodological developments were needed for beryllium quantification and to study its spatial distribution in relation to other matrix elements, such as aluminum and iron, in metallurgic samples. In this work, we developed methodology for quantification of trace beryllium in samples of shrapnel fragments and other metallurgic sample-types with main matrix of aluminum (aluminum cans from soda, beer, carbonated water and aluminum foil). Sample preparation procedures were developed for dissolving beryllium for its quantification with the fluorescence detection method for homogenized measurements. The spatial distribution of trace beryllium on the sample surface and in 3D was imaged with a dynamic secondary ion mass spectrometry instrument, CAMECA IMS 3f secondary ion mass spectrometry ion microscope. The beryllium content of shrapnel (∼100 ppb) was the same as the trace quantities of beryllium found in aluminum cans. The beryllium content of aluminum foil (∼25 ppb) was significantly lower than cans. SIMS imaging analysis revealed beryllium to be distributed in the form of low micron-sized particles and clusters distributed randomly in X-Y- and Z dimensions, and often in association with iron, in the main aluminum matrix of cans. These observations indicate a plausible formation of Be-Fe or Al-Be alloy in the matrix of cans. Further observations were made on fluids (carbonated water) for understanding if trace beryllium in cans leached out and contaminated the food product. A direct comparison of carbonated water in aluminum cans and plastic bottles revealed that beryllium was below the detection limits of the fluorescence detection method (∼0.01 ppb). These observations indicate that beryllium present in aluminum matrix was either

  1. In Situ Plasma Measurements of Fragmented Comet 73P Schwassmann-Wachmann 3

    NASA Astrophysics Data System (ADS)

    Gilbert, J. A.; Lepri, S. T.; Rubin, M.; Combi, M.; Zurbuchen, T. H.

    2015-12-01

    The interiors of comets contain some of the most pristine material in the solar system. Comet 73P/Schwassmann-Wachmann 3, discovered in 1930, is a Jupiter-family comet with a 5.34-year period. This comet split into 5 fragments in 1995 and disintegrated into nearly 70 major pieces in 2006. In 2006 May and June, recently ionized cometary particles originating from fragments including and surrounding some of these major objects were collected with the ACE/SWICS and Wind/STICS sensors. Due to a combination of the instrument characteristics and the close proximity of the fragments passing between those spacecraft and the Sun, unique measurements regarding the charge state composition and the elemental abundances of both cometary and heliospheric plasma were made during that time. The cometary material released from some of these fragments can be identified by the concentrations of water-group pickup ions having a mass-per-charge ratio of 16-18 amu e-1, indicating that while these fragments are small, they are still actively sublimating. We present an analysis of cometary composition, spatial distribution, and heliospheric interactions, with a focus on helium, C+/O+, and water-group ions.

  2. Imidate-Based Cross-Linkers for Structural Proteomics: Increased Charge of Protein and Peptide Ions and CID and ECD Fragmentation Studies

    NASA Astrophysics Data System (ADS)

    Koolen, Hector H. F.; Gomes, Alexandre F.; Schwab, Nicolas V.; Eberlin, Marcos N.; Gozzo, Fabio C.

    2014-07-01

    Chemical cross-linking is an attractive low-resolution technique for structural studies of protein complexes. Distance constraints obtained from cross-linked peptides identified by mass spectrometry (MS) are used to construct and validate protein models. Amidinating cross-linkers such as diethyl suberthioimidate (DEST) have been used successfully in chemical cross-linking experiments. In this work, the application of a commercial diimidate cross-linking reagent, dimethyl suberimidate (DMS), was evaluated with model peptides and proteins. The peptides were designed with acetylated N-termini followed by random sequences containing two Lys residues separated by an Arg residue. After cross-linking reactions, intra- and intermolecular cross-linked species were submitted to CID and ECD dissociations to study their fragmentation features in the gas phase. Fragmentation of intramolecular peptides by collision induced dissociation (CID) demonstrates a unique two-step fragmentation pathway involving formation of a ketimine as intermediate. Electron capture and electron transfer dissociation (ECD and ETD) experiments demonstrated that the cyclic moiety is not dissociated. Intermolecular species demonstrated previously described fragmentation behavior in both CID and ECD experiments. The charge state distributions (CSD) obtained after reaction with DMS were compared with those obtained with disuccinimidyl suberate (DSS). CSDs for peptides and proteins were increased after their reaction with DMS, owing to the higher basicity of DMS modified species. These features were also observed in LC-MS experiments with bovine carbonic anhydrase II (BCA) after cross-linking with DMS and tryptic proteolysis. Cross-linked peptides derived from this protein were identified at high confidence and those species were in agreement with the crystal structure of BCA.

  3. Electron impact fragmentation of adenine: partial ionization cross sections for positive fragments

    NASA Astrophysics Data System (ADS)

    van der Burgt, Peter J. M.; Finnegan, Sinead; Eden, Samuel

    2015-07-01

    Using computer-controlled data acquisition we have measured mass spectra of positive ions for electron impact on adenine, with electron energies up to 100 eV. Ion yield curves for 50 ions have been obtained and normalized by comparing their sum to the average of calculated total ionization cross sections. Appearance energies have been determined for 37 ions; for 20 ions for the first time. All appearance energies are consistent with the fragmentation pathways identified in the literature. Second onset energies have been determined for 12 fragment ions (for 11 ions for the first time), indicating the occurrence of more than one fragmentation process e.g. for 39 u (C2HN+) and 70 u (C2H4N3+). Matching ion yield shapes (118-120 u, 107-108 u, 91-92 u, and 54-56 u) provide new evidence supporting closely related fragmentation pathways and are attributed to hydrogen rearrangement immediately preceding the fragmentation. We present the first measurement of the ion yield curve of the doubly charged parent ion (67.5 u), with an appearance energy of 23.5 ± 1.0 eV. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

  4. Ion-induced triple fragmentation of CO{sub 2}{sup 3+} into C{sup +}+O{sup +}+O{sup +}

    SciTech Connect

    Jana, M. R.; Ghosh, P. N.; Bapat, B.; Kushawaha, R. K.; Saha, K.; Prajapati, I. A.; Safvan, C. P.

    2011-12-15

    Dissociation of CO{sub 2}{sup 3+} formed in fast, heavy-ion-induced ionization of CO{sub 2}, using 5 MeV u{sup -1} Si{sup 12+} ions as projectiles, has been studied by the technique of multi-ion coincidence momentum imaging. From the momentum correlation between the ejected ions, we conclude that dissociation of CO{sub 2}{sup 3+} into C{sup +}+O{sup +}+O{sup +} is a concerted process involving linear and bent conformations of CO{sub 2}{sup 3+}. The kinetic-energy-release spectrum of the dissociation channel CO{sub 2}{sup 3+}{yields}C{sup +}+O{sup +}+O{sup +} is measured and the possible excited states of CO{sub 2}{sup 3+} are computed ab initio.

  5. N-terminal sequence tagging using reliably determined b2 ions: a useful approach to deconvolute tandem mass spectra of co-fragmented peptides in proteomics.

    PubMed

    Kryuchkov, Fedor; Verano-Braga, Thiago; Kjeldsen, Frank

    2014-05-30

    With the recent introduction of higher-energy collisional dissociation (HCD) in Orbitrap mass spectrometry, the popularity of that technique has grown tremendously in the proteomics society. HCD spectra, however, are characterized by a limited distribution of bn-type ions, which permit the generation of reliable sequence tags based on complementary b,y pairs both for de novo sequencing and sequence tagging strategies. Instead, most peptide HCD spectra (~95%) are dominated with b2 ions. In this work, we analyzed positive predictive values of b2 ions in HCD, and found that b2 ions can be determined with >97% certainty in the presence of a2 and its complementary yn-2 ions. Analytically, b2 ions provide information on the composition of the first two N-terminal amino acids in peptides. Their utilization in N-terminal sequence tagging leads to a significant decrease in false discovery rate by filtering out false positives while retaining true positive identifications. As a consequence, the number of peptide spectrum matches (PSMs) increased by 4.8% at fixed FDR (1%). This approach allows for deconvolution of mixture spectra and increased the number of PSM to 9.2% in a complex human sample and to 24% in a complex sample of synthetic peptides at 1% FDR. PMID:24726481

  6. Secondary ion emission induced by fission fragment impact in CO-NH(3) and CO-NH(3)-H(2)O ices: modification in the CO-NH(3) ice structure.

    PubMed

    Martinez, R; Farenzena, L S; Iza, P; Ponciano, C R; Homem, M G P; de Brito, A Naves; Wien, K; da Silveira, E F

    2007-10-01

    CO-NH(3) and CO-NH(3)-H(2)O ices at 25-130 K were bombarded by (252)Cf fission fragments ( approximately 65 MeV at the target surface) and the emitted secondary ions were analyzed by time-of-flight mass spectrometry (TOF-SIMS). It is observed that the mass spectra obtained from both ices have similar patterns. The production of hybrid ions (formed from CO and NH(3) molecules) emitted from CO-NH(3) ice has already been reported by R. Martinez et al., Int. J. Mass. Spectrom. 262 (2006) 195; here, the secondary ion emission and the modifications of the CO--NH(3) ice structure during the temperature increase of the ice are addressed. These studies are expected to throw light on the sputtering from planetary and interstellar ices and the possible formation of new organic molecules in CO-NH(3)-H(2)O ice by megaelectronvolt ion bombardment. The presence of water in the CO-NH(3) ice mixture generates molecular ion series such as (NH(3))(p-q)(H(2)O)(q)CO(+) and replaces the cluster series (NH(3))(n)NH(4) (+) emission by the hybrid series (NH(3))(I-i)(H(2)O)(i=1, 2...I)H(+). The distribution of NH(3) and H(2)O molecules within the cluster groups indicates that ammonia and water mix homogeneously in the icy condensate at T = 25 K. The desorption yield distribution of the cluster series (NH(3))(n)NH(4) (+) is described by the sum of two exponential functions: one, slow-decreasing, attributed to the fragmentation of the solid target into clusters; and another, fast-decreasing, due to a local sublimation followed by recombination of ammonia molecules. The analysis of the time-temperature dependence of these two yield components gives information on the formation process of molecular ions, the transient composition of the ice target and structural changes of the ice. Data suggest that the amorphous and porous structure of the NH(3) ice, formed by the condensation of the CO--NH(3) gas at T = 25 K, survives CO sublimation until the occurrence of a phase transition around 80 K

  7. Stellar Oxygen Abundances

    NASA Astrophysics Data System (ADS)

    King, Jeremy

    1994-04-01

    younger clusters. The O abundances in the younger clusters are significantly larger than those seen in H II regions, planetary nebulae, and supergiants. It is suggested, and supported with observational evidence, that this may be due to incomplete stellar models and the possibility that a significant fraction of O in gaseous nebulae is locked up in dust grains. Examining our results in a broader sense, we suggest that: a) the formation of the Galactic halo was a slow process but b) did not involve the merger of independent "fragments" c) Type Ia supernovae are dominated by CO-He white dwarf systems having Fe production timescales of a few Gyr d) The hiatus between the end of halo formation and the beginning of star formation in the disk, possibly required if CO-He white dwarfs are the dominant source of Type Ia supernovae, may be confirmed as the observed gap in the [O/H] distribution e) The long timescale (10^9 - 10^10 yr) of Fe production by CO-He white dwarf systems is also seen to be consistent with the lack of any correlation between age and [Fe/H] in our open cluster sample and the large scatter present in the [Fe/H] vs. age relations for field stars. (SECTION: Dissertation Summaries)

  8. Quantification and micron-scale imaging of spatial distribution of trace beryllium in shrapnel fragments and metallurgic samples with correlative fluorescence detection method and secondary ion mass spectrometry (SIMS)

    PubMed Central

    Abraham, Jerrold L.; Chandra, Subhash; Agrawal, Anoop

    2014-01-01

    Recently, a report raised the possibility of shrapnel-induced chronic beryllium disease (CBD) from long-term exposure to the surface of retained aluminum shrapnel fragments in the body. Since the shrapnel fragments contained trace beryllium, methodological developments were needed for beryllium quantification and to study its spatial distribution in relation to other matrix elements, such as aluminum and iron, in metallurgic samples. In this work, we developed methodology for quantification of trace beryllium in samples of shrapnel fragments and other metallurgic sample-types with main matrix of aluminum (aluminum cans from soda, beer, carbonated water, and aluminum foil). Sample preparation procedures were developed for dissolving beryllium for its quantification with the fluorescence detection method for homogenized measurements. The spatial distribution of trace beryllium on the sample surface and in 3D was imaged with a dynamic secondary ion mass spectrometry (SIMS) instrument, CAMECA IMS 3f SIMS ion microscope. The beryllium content of shrapnel (~100 ppb) was the same as the trace quantities of beryllium found in aluminum cans. The beryllium content of aluminum foil (~25 ppb) was significantly lower than cans. SIMS imaging analysis revealed beryllium to be distributed in the form of low micron-sized particles and clusters distributed randomly in X-Y-and Z dimensions, and often in association with iron, in the main aluminum matrix of cans. These observations indicate a plausible formation of Be-Fe or Al-Be alloy in the matrix of cans. Further observations were made on fluids (carbonated water) for understanding if trace beryllium in cans leached out and contaminated the food product. A direct comparison of carbonated water in aluminum cans and plastic bottles revealed that beryllium was below the detection limits of the fluorescence detection method (~0.01 ppb). These observations indicate that beryllium present in aluminum matrix was either present in an

  9. HRMS studies on the fragmentation pathways of metallapentalyne

    NASA Astrophysics Data System (ADS)

    Lin, Zhiwei; Zhu, Congqing; Xia, Haiping

    2015-02-01

    The electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) using collision-induced dissociation (CID) method was applied to investigate the characteristic fragment ions of metalla-aromatic complexes for the first time. The fragmentation process of osmapentalyne, which contained metal-carbon triple bond in a five-membered ring, was discussed in detail. The ESI FT-ICR MS CID experimental results at high resolution mass spectra (HRMS) demonstrated the elemental composition of fragment ions unambiguously, thus a reasonable fragmentation pathway of osmapentalyne was proposed. In addition, the characteristic fragment ions have been investigated, which were specific and useful for the identification of some osmapentalynes complexes. These characteristic fragmentation pathways were helpful to analyze and interpret the stability and property of the parent ion. Also, this method could be used for the characterization of other organometallic complexes, especially containing characteristic isotopic peaks.

  10. Fragmentation in the First Galaxies

    NASA Astrophysics Data System (ADS)

    Safranek-Shrader, Chalence; Bromm, Volker; Milosavljević, Miloš

    2010-11-01

    Motivated by recent simulations of galaxy formation in which protogalaxies acquire their baryonic content through cold accretion, we study the gravitational fragmentation of cold streams flowing into a typical first galaxy. We use a one-zone hydrodynamical model to examine the thermal evolution of the gas flowing into a 108 M sun dark matter halo at redshift z = 10. The goal is to gain an understanding of the expected fragmentation mass scale and thus the characteristic mass of the first population of stars to form by shock fragmentation. Our model accurately describes the chemical and thermal evolution of the gas as we are specifically concerned with how the chemical abundances and initial conditions of the low-density, metal-enriched, cold accretion streams that pass an accretion shock alter the cooling properties and tendency to fragment in the post-shock gas. Cold accretion flows are not shock heated at the virial radius but instead flow along high-baryonic-density filaments of the cosmic web and penetrate deep into the host halo of the protogalaxy. In this physical regime, if molecular cooling is absent because of a strong Lyman-Werner background, we find there to be a sharp drop in the fragmentation mass at a metallicity of Z ~ 10-4 Z sun. If, however, H2 and HD molecules are present, they dominate the cooling at T < 104 K, and metallicity then has no effect on the fragmentation properties of the cold stream. For a solar abundance pattern of metallicity, O is the most effective metal coolant throughout the evolution, while for a pair instability supernova (PISN) metallicity yield, Si+ is the most effective coolant. PISN abundance patterns also exhibit a slightly smaller critical metallicity. Dust grains are not included in our chemical model, but we argue that their inclusion would not significantly alter the results. We also find that this physical scenario allows for the formation of stellar clusters and large, 104 M sun bound fragments, possibly the

  11. FRAGMENTATION IN THE FIRST GALAXIES

    SciTech Connect

    Safranek-Shrader, Chalence; Bromm, Volker; Milosavljevic, Milos

    2010-11-10

    Motivated by recent simulations of galaxy formation in which protogalaxies acquire their baryonic content through cold accretion, we study the gravitational fragmentation of cold streams flowing into a typical first galaxy. We use a one-zone hydrodynamical model to examine the thermal evolution of the gas flowing into a 10{sup 8} M{sub sun} dark matter halo at redshift z = 10. The goal is to gain an understanding of the expected fragmentation mass scale and thus the characteristic mass of the first population of stars to form by shock fragmentation. Our model accurately describes the chemical and thermal evolution of the gas as we are specifically concerned with how the chemical abundances and initial conditions of the low-density, metal-enriched, cold accretion streams that pass an accretion shock alter the cooling properties and tendency to fragment in the post-shock gas. Cold accretion flows are not shock heated at the virial radius but instead flow along high-baryonic-density filaments of the cosmic web and penetrate deep into the host halo of the protogalaxy. In this physical regime, if molecular cooling is absent because of a strong Lyman-Werner background, we find there to be a sharp drop in the fragmentation mass at a metallicity of Z {approx} 10{sup -4} Z{sub sun}. If, however, H{sub 2} and HD molecules are present, they dominate the cooling at T < 10{sup 4} K, and metallicity then has no effect on the fragmentation properties of the cold stream. For a solar abundance pattern of metallicity, O is the most effective metal coolant throughout the evolution, while for a pair instability supernova (PISN) metallicity yield, Si{sup +} is the most effective coolant. PISN abundance patterns also exhibit a slightly smaller critical metallicity. Dust grains are not included in our chemical model, but we argue that their inclusion would not significantly alter the results. We also find that this physical scenario allows for the formation of stellar clusters and large

  12. Structural characterization of fragment ions by electrospray ionization and Q-TOF mass spectrometry to support regulatory analysis of veterinary drug residues in foods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    RATIONALE: Monitoring of veterinary drug residues in foods is often conducted using liquid chromatography – tandem mass spectrometry (LC-MS/MS). Results have high economic stakes for producers, but the ions monitored are usually selected due to signal intensities without structural interpretation. ...

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

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

  14. Hyperthermal (1-100 eV) nitrogen ion scattering damage to D-ribose and 2-deoxy-D-ribose films.

    PubMed

    Deng, Zongwu; Bald, Ilko; Illenberger, Eugen; Huels, Michael A

    2007-10-14

    Highly charged heavy ion traversal of a biological medium can produce energetic secondary fragment ions. These fragment ions can in turn cause collisional and reactive scattering damage to DNA. Here we report hyperthermal (1-100 eV) scattering of one such fragment ion (N(+)) from biologically relevant sugar molecules D-ribose and 2-deoxy-D-ribose condensed on polycrystalline Pt substrate. The results indicate that N(+) ion scattering at kinetic energies down to 10 eV induces effective decomposition of both sugar molecules and leads to the desorption of abundant cation and anion fragments. Use of isotope-labeled molecules (5-(13)C D-ribose and 1-D D-ribose) partly reveals some site specificity of the fragment origin. Several scattering reactions are also observed. Both ionic and neutral nitrogen atoms abstract carbon from the molecules to form CN(-) anion at energies down to approximately 5 eV. N(+) ions also abstract hydrogen from hydroxyl groups of the molecules to form NH(-) and NH(2) (-) anions. A fraction of OO(-) fragments abstract hydrogen to form OH(-). The formation of H(3)O(+) ions also involves hydrogen abstraction as well as intramolecular proton transfer. These findings suggest a variety of severe damaging pathways to DNA molecules which occur on the picosecond time scale following heavy ion irradiation of a cell, and prior to the late diffusion-limited homogeneous chemical processes. PMID:17935431

  15. Application of Fragment Ion Information as Further Evidence in Probabilistic Compound Screening Using Bayesian Statistics and Machine Learning: A Leap Toward Automation.

    PubMed

    Woldegebriel, Michael; Zomer, Paul; Mol, Hans G J; Vivó-Truyols, Gabriel

    2016-08-01

    In this work, we introduce an automated, efficient, and elegant model to combine all pieces of evidence (e.g., expected retention times, peak shapes, isotope distributions, fragment-to-parent ratio) obtained from liquid chromatography-tandem mass spectrometry (LC-MS/MS/MS) data for screening purposes. Combining all these pieces of evidence requires a careful assessment of the uncertainties in the analytical system as well as all possible outcomes. To-date, the majority of the existing algorithms are highly dependent on user input parameters. Additionally, the screening process is tackled as a deterministic problem. In this work we present a Bayesian framework to deal with the combination of all these pieces of evidence. Contrary to conventional algorithms, the information is treated in a probabilistic way, and a final probability assessment of the presence/absence of a compound feature is computed. Additionally, all the necessary parameters except the chromatographic band broadening for the method are learned from the data in training and learning phase of the algorithm, avoiding the introduction of a large number of user-defined parameters. The proposed method was validated with a large data set and has shown improved sensitivity and specificity in comparison to a threshold-based commercial software package. PMID:27391247

  16. Induced radioactivity of a GSO scintillator by secondary fragments in carbon ion therapy and its effects on in-beam OpenPET imaging.

    PubMed

    Hirano, Yoshiyuki; Nitta, Munetaka; Nishikido, Fumihiko; Yoshida, Eiji; Inadama, Naoko; Yamaya, Taiga

    2016-07-01

    The accumulation of induced radioactivity within in-beam PET scanner scintillators is of concern for its long-term clinical usage in particle therapy. To estimate the effects on OpenPET which we are developing for in-beam PET based on GSOZ (Zi doped Gd2SiO5), we measured the induced radioactivity of GSO activated by secondary fragments in a water phantom irradiation by a (12)C beam with an energy of 290 MeV u(-1). Radioisotopes of Na, Ce, Eu, Gd, Nd, Pm and Tb including positron emitters were observed in the gamma ray spectra of the activated GSO with a high purity Ge detector and their absolute radioactivities were calculated. We used the Monte Carlo simulation platform, Geant4 in which the observed radioactivity was assigned to the scintillators of a precisely reproduced OpenPET and the single and coincidence rates immediately after one treatment and after one-year usage were estimated for the most severe conditions. Comparing the highest coincidence rate originating from the activated scintillators (background) and the expected coincidence rate from an imaging object (signal), we determined the expected signal-to-noise ratio to be more than 7 within 3 min and more than 10 within 1 min from the scan start time. We concluded the effects of scintillator activation and their accumulation on the OpenPET imaging were small and clinical long-term usage of the OpenPET was feasible. PMID:27280308

  17. Induced radioactivity of a GSO scintillator by secondary fragments in carbon ion therapy and its effects on in-beam OpenPET imaging

    NASA Astrophysics Data System (ADS)

    Hirano, Yoshiyuki; Nitta, Munetaka; Nishikido, Fumihiko; Yoshida, Eiji; Inadama, Naoko; Yamaya, Taiga

    2016-07-01

    The accumulation of induced radioactivity within in-beam PET scanner scintillators is of concern for its long-term clinical usage in particle therapy. To estimate the effects on OpenPET which we are developing for in-beam PET based on GSOZ (Zi doped Gd2SiO5), we measured the induced radioactivity of GSO activated by secondary fragments in a water phantom irradiation by a 12C beam with an energy of 290 MeV u‑1. Radioisotopes of Na, Ce, Eu, Gd, Nd, Pm and Tb including positron emitters were observed in the gamma ray spectra of the activated GSO with a high purity Ge detector and their absolute radioactivities were calculated. We used the Monte Carlo simulation platform, Geant4 in which the observed radioactivity was assigned to the scintillators of a precisely reproduced OpenPET and the single and coincidence rates immediately after one treatment and after one-year usage were estimated for the most severe conditions. Comparing the highest coincidence rate originating from the activated scintillators (background) and the expected coincidence rate from an imaging object (signal), we determined the expected signal-to-noise ratio to be more than 7 within 3 min and more than 10 within 1 min from the scan start time. We concluded the effects of scintillator activation and their accumulation on the OpenPET imaging were small and clinical long-term usage of the OpenPET was feasible.

  18. Collision-induced dissociation of aminophospholipids (PE, MMPE, DMPE, PS): an apparently known fragmentation process revisited.

    PubMed

    Pittenauer, Ernst; Rehulka, Pavel; Winkler, Wolfgang; Allmaier, Günter

    2015-07-01

    A new type of low-mass substituted 4-oxazolin product ions of [M + H](+) precursor ions of aminophospholipids (glycerophosphatidylethanolamine, glycerophosphatidyl-N-methylethanolamine, glycerophosphatidyl-N,N-dimethylethanolamine, glycerophosphatidylserine) resulting from high-energy collision-induced dissociation (matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry) and low-energy collision-induced dissociation (e.g., electrospray ionization quadrupole reflectron time-of-flight mass spectrometry) with accurate mass determination is described; these were previously misidentified as CHO-containing radical cationic product ions. The mechanism for the formation of these ions is proposed to be via rapid loss of water followed by cyclization to an 11-membered-ring transition state for the sn-1 fatty acid substituent and to a ten-membered-ring transition state for the sn-2 fatty acid substituent, and via final loss of monoacylglycerol phosphate, leading to substituted 4-oxazolin product ions. The minimum structural requirement for this interesting skeletal rearrangement fragmentation is an amino group linked to at least one hydrogen atom (i.e., ethanolamine, N-methylethanolamine, serine). Therefore, N,N-dimethylethanolamine derivates do not exhibit this type of fragmentation. The analytical value of these product ions is given by the fact that by post source decay and particularly high-energy collision-induced dissociation achieved via matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry, the sn-2-related substituted 4-oxazolin product ion is always significantly more abundant than the sn-1-related one, which is quite helpful for detailed structural analysis of complex lipids. All other important product ions found are described in detail (following our previously published glycerophospholipid product ion nomenclature; Pittenauer and Allmaier, Int. J. Mass. Spectrom

  19. UV fragmentation and ultrafast dynamics of trinuclear silver/1-methylthymine and silver/1-methyluracil metal-base pairs in an ion trap

    NASA Astrophysics Data System (ADS)

    Nosenko, Yevgeniy; Riehn, Christoph; Klopper, Wim

    2016-08-01

    We report on gas phase UV action spectroscopy and photodynamics of [Ag3(1MT-H/1MU-H)2]+ comprised of a linear silver string and two deprotonated 1-methyl-thymine/uracil (1MT/1MU) ligands. We applied pump-probe femtosecond laser photofragmentation in an electrospray ion trap mass spectrometer and high-level ab initio calculations at the level of approximate coupled-cluster singles-doubles theory. The experimental UV band at 283/275 nm is assigned to a red shifted 1ππ∗ nucleobase located transition. Relaxation of the 1ππ∗ state occurs with time constants of 0.2/1.1 ps and 0.2/4.2 ps for the 1MT and 1MU complexes, respectively, on a similar ultrafast time scale as non-metalated uracil derivatives.

  20. The fragmentation of 510 MeV/nucleon iron-56 in polyethylene. I. Fragment fluence spectra

    NASA Technical Reports Server (NTRS)

    Zeitlin, C.; Miller, J.; Heilbronn, L.; Frankel, K.; Gong, W.; Schimmerling, W.

    1996-01-01

    The fragmentation of 510 MeV/nucleon iron ions in several thicknesses of polyethylene has been measured. Non-interacting primary beam particles and fragments have been identified and their LETs calculated by measuring ionization energy loss in a stack of silicon detectors. Fluences, normalized to the incident beam intensity and corrected for detector effects, are presented for each fragment charge and target. Histograms of fluence as a function of LET are also presented. Some implications of these data for measurements of the biological effects of heavy ions are discussed.

  1. Preferred Modes of Decay in Nuclear Fragmentation

    NASA Astrophysics Data System (ADS)

    Aranda, Alfredo; López, Jorge A.; Wu, Zehua

    1997-04-01

    Recent experiments show a characteristic energy dependence of the different fragmentation modes in heavy ion reactions at intermediate energies. In this work we study this effect and find that, in nuclear fragmentation, like in binary fission, some modes of decay are more probable than the rest. We argue that these high probability mass partitions are ultimately responsible for the observed energy dependence. This work was supported by the National Science Foundation grant PHY-9600038 and Artemio de la Vega Foundation.

  2. CF3+ fragmentation by electron impact ionization of perfluoro-propyl-vinyl-ethers, C5F10O, in gas phase

    NASA Astrophysics Data System (ADS)

    Kondo, Yusuke; Ishikawa, Kenji; Hayashi, Toshio; Miyawaki, Yudai; Takeda, Keigo; Kondo, Hiroki; Sekine, Makoto; Hori, Masaru

    2015-04-01

    The gas phase fragmentations of perfluoro-propyl-vinyl ether (PPVE, C5F10O) are studied experimentally. Dominant fragmentations of PPVE are found to be the result of a dissociative ionization reaction, i.e., CF3+ via direct bond cleavage, and C2F3O- and C3F7O- via electron attachment. Regardless of the appearance energy of around 14.5 eV for the dissociative ionization of CF3+, the observed ion efficiency for the CF3+ ion was extremely large the order of 10-20 cm-2, compared with only 10-21 cm-2 for the other channels. PPVE characteristically generated CF3+ as the largest abundant ion are advantageous for use of feedstock gases in plasma etching processes.

  3. Ion imaging studies of Cl(2P3/2) fragments arising in the visible photolysis of BrCl: Measurement of orientation, alignment, and alignment-free anisotropy parameters

    NASA Astrophysics Data System (ADS)

    Wouters, Eloy R.; Beckert, Marco; Russell, Lucy J.; Rosser, Keith N.; Orr-Ewing, Andrew J.; Ashfold, Michael N. R.; Vasyutinskii, Oleg S.

    2002-08-01

    The photodissociation dynamics of jet-cooled BrCl molecules have been investigated at four different wavelengths in the range 425-485 nm by high-resolution velocity map ion imaging. Four images of the Cl(2P3/2) atomic fragments are recorded at each photolysis wavelength with the probe laser polarization, respectively, linearly aligned and vertical (i.e., perpendicular to the detection axis), right circularly polarized, horizontally linearly polarized (i.e., parallel to the detection axis) and left circularly polarized on successive laser shots, thereby ensuring automatic mutual self-normalization. Appropriate linear combinations of these images allow quantification of the angular momentum alignment of the Cl(2P3/2)o fragments [i.e., the correlation between their recoil velocity (v) and their electronic angular momentum (J)] in terms of the alignment anisotropy parameters s2, alpha2, eta2, and gamma2, and determination of the "alignment-free" recoil anisotropy parameter, beta0, as a function of parent excitation wavelength. Both incoherent and coherent contributions to the alignment are identified, with both simultaneous parallel and perpendicular excitations to the B 3Pi(0+) and C 1Pi(1 states and excitations to the Omega]=[plus-or-minus1 components of the C state contributing to the latter. The deduced values of the alignment-free beta parameters indicate (wavelength dependent) contributions from both parallel and perpendicular parent absorptions in this wavelength range. Such a conclusion accords with approximate deconvolutions of the parent absorption spectrum that are currently available, and with determinations of the orientation parameter gamma1' obtained by fitting the difference image obtained when using left and right circularly polarized radiation to probe the ground state Cl atoms arising in the 480.63 nm photodissociation of BrCl when the photolysis laser radiation is polarized linearly at 45deg to the detection axis.

  4. Fragmentation reactions of deprotonated peptides containing proline. The proline effect.

    PubMed

    Harrison, Alex G; Young, Alex B

    2005-09-01

    The collision-induced dissociation (CID) fragmentation reactions of a variety of deprotonated peptides containing proline have been studied in detail using MS(2) and MS(3) experiments, deuterium labelling and accurate mass measurements when necessary. The [M--H--CO(2)](-) (a(2)) ion derived from H-Pro-Xxx-OH dipeptides shows an unusual fragmentation involving loss of C(2)H(4); this fragmentation reaction is not observed for larger peptides. The primary fragmentation reactions of deprotonated tripeptides with an N-terminal proline are formation of a(3) and y(1) ions. When proline is in the central position of tripeptides, a(3), y(2) and y(1) ions are the primary fragmentation products of [M--H](-), while when the proline is in the C-terminal position, a(3)and y(1) ions are the major primary products. In the latter case, the a(3) ion fragments primarily to the ''b(2) ion; further evidence is presented that the ''b(2) ions have a deprotonated oxazolone structure. Larger deprotonated peptides having at least two amino acid residues N-terminal to proline show a distinct preference for cleavage of the amide bond N-terminal to proline to form, mainly, the appropriate y ion. This proline effect is compared and contrasted with the similar proline effect observed in the fragmentation of protonated peptides containing proline. PMID:16041740

  5. Computer Model Of Fragmentation Of Atomic Nuclei

    NASA Technical Reports Server (NTRS)

    Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.

    1995-01-01

    High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.

  6. Life history strategy influences parasite responses to habitat fragmentation.

    PubMed

    Froeschke, Götz; van der Mescht, Luther; McGeoch, Melodie; Matthee, Sonja

    2013-12-01

    Anthropogenic habitat use is a major threat to biodiversity and is known to increase the abundance of generalist host species such as rodents, which are regarded as potential disease carriers. Parasites have an intimate relationship with their host and the surrounding environment and it is expected that habitat fragmentation will affect parasite infestation levels. We investigated the effect of habitat fragmentation on the ecto- and endoparasitic burdens of a broad niche small mammal, Rhabdomys pumilio, in the Western Cape Province, South Africa. Our aim was to look at the effects of fragmentation on different parasite species with diverse life history characteristics and to determine whether general patterns can be found. Sampling took place within pristine lowland (Fynbos/Renosterveld) areas and at fragmented sites surrounded and isolated by agricultural activities. All arthropod ectoparasites and available gastrointestinal endoparasites were identified. We used conditional autoregressive models to investigate the effects of habitat fragmentation on parasite species richness and abundance of all recovered parasites. Host density and body size were larger in the fragments. Combined ecto- as well as combined endoparasite taxa showed higher parasite species richness in fragmented sites. Parasite abundance was generally higher in the case of R. pumilio individuals in fragmented habitats but it appears that parasites that are more permanently associated with the host's body and those that are host-specific show the opposite trend. Parasite life history is an important factor that needs to be considered when predicting the effects of habitat fragmentation on parasite and pathogen transmission. PMID:23954434

  7. Mineralogy and petrology of basaltic fragments from the Luna 24 drill core

    NASA Technical Reports Server (NTRS)

    Coish, R. A.; Taylor, L. A.

    1978-01-01

    The petrology of rock fragments and monomineralic grains from Luna 24 samples is described, and a petrogenetic scheme for the derivation of Mare Crisium basalts is presented. Components of the rock fragments include subophitic basalts, metabasalts, late-stage fragments, olivine vitrophyres, and non-mare lithic fragments of possible cumulate origin. Among the monomineralic grains (which are much more abundant than the rock fragments) are pyroxene, plagioclase, olivine, ilmenite and native Fe.

  8. Selectable fragmentation warhead

    DOEpatents

    Bryan, Courtney S.; Paisley, Dennis L.; Montoya, Nelson I.; Stahl, David B.

    1993-01-01

    A selectable fragmentation warhead capable of producing a predetermined number of fragments from a metal plate, and accelerating the fragments toward a target. A first explosive located adjacent to the plate is detonated at selected number of points by laser-driven slapper detonators. In one embodiment, a smoother-disk and a second explosive, located adjacent to the first explosive, serve to increase acceleration of the fragments toward a target. The ability to produce a selected number of fragments allows for effective destruction of a chosen target.

  9. Selectable fragmentation warhead

    SciTech Connect

    Bryan, C.S.; Paisley, D.L.; Montoya, N.I.; Stahl, D.B.

    1992-12-31

    This report discusses a selectable fragmentation warhead which is capable of producing a predetermined number of fragments from a metal plate, and accelerating the fragments toward a target. A first explosive located adjacent to the plate is detonated at selected number of points by laser-driven slapper detonators. In one embodiment, a smoother-disk and a second explosive, located adjacent to the first explosive, serve to increase acceleration of the fragments toward a target. The ability to produce a selected number of fragments allows for effective destruction of a chosen target.

  10. Bimodal Behavior of the Heaviest Fragment Distribution in Projectile Fragmentation

    SciTech Connect

    Bonnet, E.; Borderie, B.; Rivet, M. F.; Dayras, R.; Gagnon-Moisan, F.; Guinet, D.; Lautesse, P.; Parlog, M.; Rosato, E.; Vigilante, M.

    2009-08-14

    The charge distribution of the heaviest fragment detected in the decay of quasiprojectiles produced in intermediate energy heavy-ion collisions has been observed to be bimodal. This feature is expected as a generic signal of phase transition in nonextensive systems. In this Letter, we present new analyses of experimental data from Au on Au collisions at 60, 80, and 100 MeV/nucleon showing that bimodality is largely independent of the data selection procedure and of entrance channel effects. An estimate of the latent heat of the transition is extracted.

  11. Universality of fragment shapes.

    PubMed

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-01-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

  12. Universality of fragment shapes

    PubMed Central

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-01-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

  13. Universality of fragment shapes

    NASA Astrophysics Data System (ADS)

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-03-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism.

  14. Structural characterization of phospholipids by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Marto, J A; White, F M; Seldomridge, S; Marshall, A G

    1995-11-01

    Matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry provides for structural analysis of the principal biological phospholipids: glycerophosphatidylcholine, -ethanolamine, -serine, and -inositol. Both positive and negative molecular or quasimolecular ions are generated in high abundance. Isolated molecular ions may be collisionally activated in the source side of a dual trap mass analyzer, yielding fragments serving to identify the polar head group (positive ion mode) and fatty acid side chains (negative ion mode). Azimuthal quadrupolar excitation following collisionally activated dissociation refocuses productions close to the solenoid axis; subsequent transfer of product ions to the analyzer ion trap allows for high-resolution mass analysis. Cyro-cooling of the sample probe with liquid nitrogen greatly reduces matrix adduction encountered in the negative ion mode. PMID:8633761

  15. Light ion components of the galactic cosmic rays: Nuclear interactions and transport theory

    NASA Astrophysics Data System (ADS)

    Cucinotta, F. A.; Townsend, L. W.; Wilson, J. W.; Shinn, J. L.; Badhwar, G. D.; Dubey, R. R.

    Light nuclei are present in the primary galactic cosmic rays (GCR) and are produced in thick targets due to projectile or target fragmentation from both nucleon and heavy induced reactions. In the primary GCR, He-4 is the most abundant nucleus after H-1. However, there are also a substantial fluxes of H-2 and He-3. In this paper we describe theoretical models based on quantum multiple scattering theory for the description of light ion nuclear interactions. The energy dependence of the light ion fragmentation cross section is considered with comparisons of inclusive yields and secondary momentum distributions to experiments described. We also analyze the importance of a fast component of lights ions from proton and neutron induced target fragementation. These theoretical models have been incorporated into the cosmic ray transport code HZETRN and will be used to analyze the role of shielding materials in modulating the production and the energy spectrum of light ions.

  16. Light ion components of the galactic cosmic rays: Nuclear interactions and transport theory

    NASA Technical Reports Server (NTRS)

    Cucinotta, F. A.; Townsend, L. W.; Wilson, J. W.; Shinn, J. L.; Badhwar, G. D.; Dubey, R. R.

    1996-01-01

    Light nuclei are present in the primary galactic cosmic rays (GCR) and are produced in thick targets due to projectile or target fragmentation from both nucleon and heavy induced reactions. In the primary GCR, He-4 is the most abundant nucleus after H-1. However, there are also a substantial fluxes of H-2 and He-3. In this paper we describe theoretical models based on quantum multiple scattering theory for the description of light ion nuclear interactions. The energy dependence of the light ion fragmentation cross section is considered with comparisons of inclusive yields and secondary momentum distributions to experiments described. We also analyze the importance of a fast component of lights ions from proton and neutron induced target fragementation. These theoretical models have been incorporated into the cosmic ray transport code HZETRN and will be used to analyze the role of shielding materials in modulating the production and the energy spectrum of light ions.

  17. Fragmentation properties of metals

    SciTech Connect

    Grady, D.E.; Kipp, M.E.

    1996-06-01

    In the present study we are developing an experimental fracture material property test method specific to dynamic fragmentation. Spherical test samples of the metals of interest are subjected to controlled impulsive stress loads by acceleration to high velocities with a light-gas launcher facility and subsequent normal impact on thin plates. Motion, deformation and fragmentation of the test samples are diagnosed with multiple flash radiography methods. The impact plate materials are selected to be transparent to the x-ray method so that only test metal material is imaged. Through a systematic series of such tests, both strain-to-failure and fragmentation resistance properties are determined through this experimental method. Fragmentation property data for several steels, copper, aluminum, tantalum and titanium have been obtained to date. Aspects of the dynamic data have been analyzed with computational methods to achieve a better understanding of the processes leading to failure and fragmentation, and to test an existing computational fragmentation model.

  18. Insights into 2-Chloropyrimidine fragmentation through a thermochemical analysis of the ionic fragments

    NASA Astrophysics Data System (ADS)

    Castrovilli, Mattea Carmen; Bolognesi, Paola; Casavola, Annarita; Cartoni, Antonella; Catone, Daniele; O'Keeffe, Patrick; Avaldi, Lorenzo

    2014-09-01

    In the present work we have studied the photoinduced ion chemistry of the 2Cl-pyrimidine molecule in the energy region 9-14 eV. The theoretical gas phase enthalpies of formation of the main fragments calculated using the G3B3 and G2 ab initio methods are compared to the experimental values, derived by the measured appearance energy of the fragments. This approach provides new insights into both the geometric structure of the ionic fragments and the basic mechanisms governing the molecular fragmentation. Contribution to the Topical Issue "Nano-scale Insights into Ion-beam Cancer Therapy", edited by Andrey V. Solov'yov, Nigel Mason, Paulo Limão-Vieira and Malgorzata Smialek-Telega.

  19. MALDI-TOF/TOF CID Study of Poly(1,4-dihydroxybenzene terephthalate) Fragmentation Reactions

    PubMed Central

    Gies, Anthony P.; Stow, Sarah M.; McLean, John A.; Hercules, David M.

    2015-01-01

    MALDI-TOF/TOF collision-induced dissociation (CID) experiments were conducted on model aromatic polyester oligomers. CID fragmentation studies identified initial fracture of the ester bond and subsequent CO loss as a major pathway, consistent with the general fragmentation mechanism used to explain the origin of poly(p-phenylenediamine terephthalamide) (PPD-T) fragment ions. Specifically, both charge-remote and charge-site fragmentation were observed. Different parent-ion species were observed, the major ones being carboxyl-hydroxyl, di-carboxyl, di-hydroxyl, and phenyl-carboxyl terminated. One species observed was hydroxyl-diethylamine terminated caused by reaction of carboxyl groups with triethylamine added to the synthesis reaction mixture. Fragment ions reflected the end groups of the parent oligomers. Some MALDI fragment-ion spectra were obtained for species showing exchange between Li and H at the carboxyl end group. Bond energy calculations provide further insight into suggested fragmentation mechanisms. PMID:26195848

  20. Abundance variations in solar energetic particles

    NASA Technical Reports Server (NTRS)

    Cane, H. V.; Reames, D. V.; Von Rosenvinge, T. T.

    1991-01-01

    Abundance variations are examined in a large number of events including smaller nonimpulsive events not previously considered. Whereas a comparison at equal energy per nucleon is appropriate for heavy ions this is not the case when including H. The best representation is either in terms of rigidity or energy per charge depending on the type of event under consideration. For the majority of large events, where particles are primarily accelerated at interplanetary shocks, if abundances relative to H are evaluated at equal energy per charge then abundance ratios are compatible with solar wind values and spectral shapes agree. Furthermore the behavior of H is then compatible with that of other high FIP elements.

  1. Solar Energetic Particles: Sampling Coronal Abundances

    NASA Astrophysics Data System (ADS)

    Reames, Donald V.

    1998-05-01

    In the large solar energetic particle (SEP) events, coronal mass ejections (CMEs) drive shock waves out through the corona that accelerate elements of the ambient material to MeV energies in a fairly democratic, temperature-independent manner. These events provide the most complete source of information on element abundances in the corona. Relative abundances of 22 elements from H through Zn display the well-known dependence on the first ionization potential (FIP) that distinguishes coronal and photospheric material. For most elements, the main abundance variations depend upon the gyrofrequency, and hence on the charge-to-mass ratio, Q/A, of the ion. Abundance variations in the dominant species, H and He, are not Q/A dependent, presumably because of non-linear wave-particle interactions of H and He during acceleration. Impulsive flares provide a different sample of material that confirms the Ne:Mg:Si and He/C abundances in the corona.

  2. Fragments and Coherence

    ERIC Educational Resources Information Center

    Watson, Anne

    2008-01-01

    Can teachers contact the inner coherence of mathematics while working in a context fragmented by always-new objectives, criteria, and initiatives? How, more importantly, can learners experience the inner coherence of mathematics while working in a context fragmented by testing, modular curricular, short-term learning objectives, and lessons that…

  3. Fragmentation pathways of ethylene after core ionization

    NASA Astrophysics Data System (ADS)

    Gaire, B.; Bocharova, I.; Sturm, F. P.; Gehrken, N.; Haxton, D. J.; Belkacem, A.; Weber, Th.; Zohrabi, M.; Ben-Itzhak, I.; Gatton, A.; Williams, J.; Reedy, D.; Nook, C.; Landers, A.; Gassert, H.; Zeller, S.; Voigtsberger, J.; Jahnke, T.; Doerner, R.

    2014-05-01

    We have measured the Auger electrons in coincidence with the recoil ions, resulting from the core ionization of ethylene molecules, by employing the COLd Target Recoil Ion Momentum Spectroscopy (COLTRIMS) method. The Auger-electron and recoil-ion energy maps are used to identify the fragmentation pathways and they are compared to the valence photo-double-ionization of ethylene. The dicationic electronic states favored by the propensity rules are identified and their role on the fragmentation pathways is discussed. The molecular-frame Auger electron angular distribution provides further insight into the breakup of this molecule after core ionization. Supported by the Director, Office of Science, Office of Basic Energy Sciences, and by the Division of Chemical Sciences, Geosciences, and Biosciences of the U.S. Department of Energy at LBNL under Contract No. DE-AC02-05CH11231.

  4. Solar abundance of osmium

    PubMed Central

    Jacoby, George; Aller, Lawrence H.

    1976-01-01

    The abundance parameter, log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance (by numbers of atoms with respect to hydrogen), has been derived for three lines of osmium by a method of spectrum synthesis. An apparent discordance of the derived abundance with that found from the carbonaceous chondrites is probably to be attributed primarily to errors in the f-values, and blending with unknown contributors. PMID:16592314

  5. Habitat fragmentation, tree diversity, and plant invasion interact to structure forest caterpillar communities.

    PubMed

    Stireman, John O; Devlin, Hilary; Doyle, Annie L

    2014-09-01

    Habitat fragmentation and invasive species are two of the most prominent threats to terrestrial ecosystems. Few studies have examined how these factors interact to influence the diversity of natural communities, particularly primary consumers. Here, we examined the effects of forest fragmentation and invasion of exotic honeysuckle (Lonicera maackii, Caprifoliaceae) on the abundance and diversity of the dominant forest herbivores: woody plant-feeding Lepidoptera. We systematically surveyed understory caterpillars along transects in 19 forest fragments over multiple years in southwestern Ohio and evaluated how fragment area, isolation, tree diversity, invasion by honeysuckle and interactions among these factors influence species richness, diversity and abundance. We found strong seasonal variation in caterpillar communities, which responded differently to fragmentation and invasion. Abundance and richness increased with fragment area, but these effects were mitigated by high levels of honeysuckle, tree diversity, landscape forest cover, and large recent changes in area. Honeysuckle infestation was generally associated with decreased caterpillar abundance and diversity, but these effects were strongly dependent on other fragment traits. Effects of honeysuckle on abundance were moderated when fragment area, landscape forest cover and tree diversity were high. In contrast, negative effects of honeysuckle invasion on caterpillar diversity were most pronounced in fragments with high tree diversity and large recent increases in area. Our results illustrate the complex interdependencies of habitat fragmentation, plant diversity and plant invasion in their effects on primary consumers and emphasize the need to consider these processes in concert to understand the consequences of anthropogenic habitat change for biodiversity. PMID:25015121

  6. Selectable fragmentation warhead

    SciTech Connect

    Bryan, C.S.; Paisley, D.L.; Montoya, N.I.; Stahl, D.B.

    1993-07-20

    A selectable fragmentation warhead is described comprising: a case having proximal and distal ends; a fragmenting plate mounted in said distal end of said casing; first explosive means cast adjacent to said fragmenting plate for creating a predetermined number of fragments from said fragmenting plate; three or more first laser-driven slapper detonators located adjacent to said first explosive means for detonating said first explosive means in a predetermined pattern; smoother-disk means located adjacent to said first means for accelerating said fragments; second explosive means cast adjacent to said smoother-disk means for further accelerating said fragments; at least one laser-driven slapper detonators located in said second explosive means; a laser located in said proximal end of said casing; optical fibers connecting said laser to said first and second laser-driven slapper detonators; and optical switch means located in series with said optical fibers connected to said plurality of first laser-driven slapper detonators for blocking or passing light from said laser to said plurality of first laser-driven slapper detonators.

  7. Detection of gaseous organophosphorus compounds using secondary ion mass spectrometry

    SciTech Connect

    Groenewold, G.S.; Todd, P.J.

    1985-04-01

    Molecular secondary ion mass spectrometry (SIMS) has been investigated for sensitivity and selectivity in the analysis of gaseous organophosphorus compounds. Abundant analyte ions were observed when the gaseous organophosphorus compounds were admitted into the secondary ion source, where a matrix was under primary ion bombardment. The best matrix for the detection of dimethyl methylphosphonate (DMMP), trimethyl phosphate (TMP), and diisopropyl methylphosphonate (DIMP) was determined to be polyphosphoric acid. The abundance of secondary analyte ions was observed to be linear with the introduction rate of gaseous analyte. The introduction rate necessary to produce a 3:1 signal-to-noise ratio in the intensity of secondary protonated molecular ions from DMMP was estimated to be 4 x 10/sup -11/ mols/sup -1/. Substantially more analyte fragmentation is observed by using SIMS than by using methane chemical ionization mass spectrometry. Ten compounds representative of other compound classes were investigated in the same manner as the organic phosphonates; characteristic secondary protonated molecular ions were detected from amines only.

  8. Stratification of gallstone fragments: the key to more effective fragmentation.

    PubMed

    Alderfer, J T; Laufer, I; Wisniewski, F; Malet, P F

    1992-04-01

    During previous experiments with in vitro fragmentation in a simulated gallbladder, we noticed that stone fragments tended to stratify with the dust and smaller fragments settled to the dependent portion, while the larger fragments settled on top. We reviewed the oral cholecystogram (OCG) of 10 patients examined 6 months following gallstone lithotripsy. In all cases with adequate visualization of stone fragments, the stratification phenomenon was observed. We hypothesized that adjusting the shock wave focus to target on these large fragments would improve the efficiency of fragmentation. To test this hypothesis, we fragmented three matched pairs of gallstones in vitro. For each pair, the stones were removed from the same gallbladder and the stone weights of the two stones were within 10%. The smaller member of each pair was fragmented using the "old method" with the focus on the fragment line. The larger stone was fragmented with the "new method" with the focus in the acoustic shadow deep to the echogenic line caused by the dust and small fragments in the dependent portion. The distribution of fragments was analyzed by passing the fragments through a series of filters. With the new method of targeting, the proportion of fragments less than 1.5 mm was doubled while the fragments greater than 5 mm were eliminated. The new method of targeting, taking into account the stratification of stone fragments, produces more effective fragmentation and should lead to more rapid clearance of fragments from the gallbladder. PMID:10149180

  9. The Origin of Element Abundance Variations in Solar Energetic Particles

    NASA Astrophysics Data System (ADS)

    Reames, Donald V.

    2016-08-01

    Abundance enhancements, during acceleration and transport in both gradual and impulsive solar energetic particle (SEP) events, vary approximately as power laws in the mass-to-charge ratio [A/Q] of the ions. Since the Q-values depend upon the electron temperature of the source plasma, this has allowed a determination of this temperature from the pattern of element-abundance enhancements and a verification of the expected inverse-time dependence of the power of A/Q for diffusive transport of ions from the SEP events, with scattering mean free paths found to be between 0.2 and 1 AU. SEP events derived from plasma of different temperatures map into different regions in typical cross-plots of abundances, spreading the distributions. In comparisons of SEP events with temperatures above 2 MK, impulsive events show much broader non-thermal variation of abundances than do gradual events. The extensive shock waves accelerating ions in gradual events may average over much of an active region where numerous but smaller magnetic reconnections, "nanojets", produce suprathermal seed ions, thus averaging over varying abundances, while an impulsive SEP event only samples one local region of abundance variations. Evidence for a reference He/O-abundance ratio of 91, rather than 57, is also found for the hotter plasma. However, while this is similar to the solar-wind abundance of He/O, the solar-wind abundances otherwise provide an unacceptably poor reference for the SEP-abundance enhancements, generating extremely large errors.

  10. The Origin of Element Abundance Variations in Solar Energetic Particles

    NASA Astrophysics Data System (ADS)

    Reames, Donald V.

    2016-07-01

    Abundance enhancements, during acceleration and transport in both gradual and impulsive solar energetic particle (SEP) events, vary approximately as power laws in the mass-to-charge ratio [ A/Q] of the ions. Since the Q-values depend upon the electron temperature of the source plasma, this has allowed a determination of this temperature from the pattern of element-abundance enhancements and a verification of the expected inverse-time dependence of the power of A/Q for diffusive transport of ions from the SEP events, with scattering mean free paths found to be between 0.2 and 1 AU. SEP events derived from plasma of different temperatures map into different regions in typical cross-plots of abundances, spreading the distributions. In comparisons of SEP events with temperatures above 2 MK, impulsive events show much broader non-thermal variation of abundances than do gradual events. The extensive shock waves accelerating ions in gradual events may average over much of an active region where numerous but smaller magnetic reconnections, "nanojets", produce suprathermal seed ions, thus averaging over varying abundances, while an impulsive SEP event only samples one local region of abundance variations. Evidence for a reference He/O-abundance ratio of 91, rather than 57, is also found for the hotter plasma. However, while this is similar to the solar-wind abundance of He/O, the solar-wind abundances otherwise provide an unacceptably poor reference for the SEP-abundance enhancements, generating extremely large errors.

  11. Parton Propagation and Fragmentation in QCD Matter

    SciTech Connect

    Alberto Accardi, Francois Arleo, William Brooks, David D'Enterria, Valeria Muccifora

    2009-12-01

    We review recent progress in the study of parton propagation, interaction and fragmentation in both cold and hot strongly interacting matter. Experimental highlights on high-energy hadron production in deep inelastic lepton-nucleus scattering, proton-nucleus and heavy-ion collisions, as well as Drell-Yan processes in hadron-nucleus collisions are presented. The existing theoretical frameworks for describing the in-medium interaction of energetic partons and the space-time evolution of their fragmentation into hadrons are discussed and confronted to experimental data. We conclude with a list of theoretical and experimental open issues, and a brief description of future relevant experiments and facilities.

  12. Angular momentum dependence of complex fragment emission

    SciTech Connect

    Sobotka, L.G.; Sarantites, D.G.; Li, Z.; Dines, E.L.; Halbert, M.L.; Hensley, D.C.; Lisle, J.C.; Schmitt, R.P.; Majka, Z.; Nebbia, G.

    1987-12-01

    The angular momentum dependence of large fragment production in long-lived reactions is studied by measurements of fragment cross sections from reactions with substantially different angular momentum distributions and the coincident ..gamma..-ray multiplicity distributions. The results indicate that the primary l-wave distributions move to larger mean values and decrease in width and skewness with increasing mass symmetry in the decay channel. The results also confirm that the partition of angular momentum kinetic energy relaxed heavy-ion reactions is that expected for a rigidly rotating intermediate.

  13. Fragment capture device

    DOEpatents

    Payne, Lloyd R.; Cole, David L.

    2010-03-30

    A fragment capture device for use in explosive containment. The device comprises an assembly of at least two rows of bars positioned to eliminate line-of-sight trajectories between the generation point of fragments and a surrounding containment vessel or asset. The device comprises an array of at least two rows of bars, wherein each row is staggered with respect to the adjacent row, and wherein a lateral dimension of each bar and a relative position of each bar in combination provides blockage of a straight-line passage of a solid fragment through the adjacent rows of bars, wherein a generation point of the solid fragment is located within a cavity at least partially enclosed by the array of bars.

  14. Extraribosomal cyclic tetradepsipeptides beauverolides: profiling and modeling the fragmentation pathways.

    PubMed

    Jegorov, Alexandr; Paizs, Bela; Kuzma, Marek; Zabka, Martin; Landa, Zdenek; Sulc, Miroslav; Barrow, Mark P; Havlicek, Vladimir

    2004-08-01

    Profiling of cyclic tetradepsipeptides beauverolides was tested as a chemotaxonomic tool for fungal strain identification/discrimination. Two new tetradepsipeptides, beauverolides Q and R, were characterized by tandem mass spectrometry. Specific elimination of 113 atomic mass units from both protonated and sodiated molecules of beauverolides is ubiquitous for all 12 most dominant congeners evaluated in this profiling study. Reconstruction of the total ion chromatogram, according to this neutral fragment release, was used for data filtering and selectivity enhancement. Selective ring opening and fragment ion formation of beauverolide I are discussed in detail utilizing high-level theoretical modeling of the fragmentation pathways. PMID:15329847

  15. Fracture tooth fragment reattachment

    PubMed Central

    Maitin, Nitin; Maitin, Shipra Nangalia; Rastogi, Khushboo; Bhushan, Rajarshi

    2013-01-01

    Coronal fractures of the anterior teeth are a common form of dental trauma and its sequelae may impair the establishment and accomplishment of an adequate treatment plan. Among the various treatment options, reattachment of a crown fragment is a conservative treatment that should be considered for crown fractures of anterior teeth. This clinical case reports the management of two coronal tooth fracture cases that were successfully treated using tooth fragment reattachment using glass-fibre-reinforced composite post. PMID:23853012

  16. Stream Hydrological Fragmentation Drives Bacterioplankton Community Composition

    PubMed Central

    Fazi, Stefano; Vázquez, Eusebi; Casamayor, Emilio O.; Amalfitano, Stefano; Butturini, Andrea

    2013-01-01

    In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow re-convergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain), at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter) tightly shaping the bacterioplankton community composition. PMID:23741302

  17. Hydrogen Attachment/Abstraction Dissociation (HAD) of Gas-Phase Peptide Ions for Tandem Mass Spectrometry.

    PubMed

    Takahashi, Hidenori; Sekiya, Sadanori; Nishikaze, Takashi; Kodera, Kei; Iwamoto, Shinichi; Wada, Motoi; Tanaka, Koichi

    2016-04-01

    Dissociation of gas-phase peptide ions through interaction with low-energy hydrogen (H) radical (∼0.15 eV) was observed with a quadrupole ion trap mass spectrometry. The H radical generated by thermal dissociation of H2 molecules passing through a heated tungsten capillary (∼2000 °C) was injected into the ion trap containing target peptide ions. The fragmentation spectrum showed abundant c-/z- and a-/x-type ions, attributable to H attachment/abstraction to/from peptide ion. Because the low-energy neutral H radical initiated the fragmentation, the charge state of the precursor ion was maintained during the dissociation. As a result, precursor ions of any charge state, including singly charged positive and negative ions, could be analyzed for amino acid sequence. The sequence coverage exceeding 90% was obtained for both singly protonated and singly deprotonated substance P peptide. This mass spectrometry also preserved labile post-translational modification bonds. The modification sites of triply phosphorylated peptide (kinase domain of insulin receptor) were identified with the sequence coverage exceeding 80%. PMID:27002918

  18. Ecological correlates of abundance in the Tana mangabey (Cercocebus galeritus).

    PubMed

    Wieczkowski, Julie

    2004-07-01

    I investigated the ecological correlates of abundance in the Tana mangabey (Cercocebus galeritus), one of the world's most endangered primates, with the goal of recommending management strategies. I systematically selected 31 forest fragments throughout the mangabey's 60-km distribution along the lower Tana River in southeastern Kenya. Within the 31 fragments, I measured vegetation structure, food abundance, and human forest product use in 107 belt transects, and conducted 370 mangabey surveys. I used a weighted multiple regression analysis to determine whether there was a dependence between the selected forest attributes and the mean number of mangabey groups per fragment. Fragment area and density of trees > or =10 cm diameter at breast height (DBH) were the only variables that significantly correlated with the variation in mangabey abundance. No additional variables were significant when the analysis was limited to forest fragments inside the Tana River Primate National Reserve (TRPNR) or to fragments outside the TRPNR. When I estimated the resources available before recent human forest product use by adding nonharvested and harvested variables, the total basal area of the top 15 food species became significant. This was only within the TRPNR, however. Management, therefore, should focus on increasing forest area, density of trees > or =10 cm DBH, and coverage of food trees throughout the mangabey's distribution. Solutions must be found for the problem of forest clearing, and forest product use must be better managed to protect the habitat of this critically endangered primate. The significance of food abundance only within the TRPNR suggests a need to collect dietary data from mangabey groups in fragments toward the southern limit of the mangabey's distribution, where plant species composition differs from that in fragments in which dietary data have been previously collected. PMID:15258957

  19. Gas phase studies on terpenes by ion mobility spectrometry using different atmospheric pressure chemical ionization techniques

    NASA Astrophysics Data System (ADS)

    Borsdorf, H.; Stone, J. A.; Eiceman, G. A.

    2005-11-01

    The ionization pathways and drift behavior were determined for sets of constitutional isomeric and stereoisomeric non-polar hydrocarbons (unsaturated monocyclic terpenes, unsaturated and saturated bicyclic terpenes) using ion mobility spectrometry (IMS) with different techniques of atmospheric pressure chemical ionization (APCI) to assess how structural and stereochemical differences influence ion formation. Depending on the structural features, different ions were observed for constitutional isomers using ion mobility spectrometry with photoionization (PI) and corona discharge (CD) ionization. Photoionization provides ion mobility spectra containing one major peak for saturated compounds while at two peaks were observed for unsaturated compounds, which can be assigned to product ions related to monomer and dimer ions. However, differences in relative abundance of product ions were found depending on the position of the double bond. Although IMS using corona discharge ionization permits the most sensitive detection of non-polar hydrocarbons, the spectra are complex and differ from those obtained using photoionization. Additional cluster ions and fragment ions were detected. Only small differences in ion mobility spectra were observed for the diastereomers while the enantiomers provide identical spectra. The structure of the product ions formed was checked by investigations using the coupling of ion mobility spectrometry with mass spectrometry (IMS-MS).

  20. Dependence of Mass Spectrometric Fragmentation on the Bromine Substitution Pattern of Polybrominated Diphenyl Ethers

    NASA Astrophysics Data System (ADS)

    Wei, Hua; Zhang, Siyu; Wang, Yawei; Wang, Ying; Li, An; Negrusz, Adam; Yu, Gang

    2014-06-01

    This study investigates the link between the bromine substitution and the mass spectrometric fragmentation of polybrominated diphenyl ethers (PBDEs). The mass spectra of 180 PBDEs were obtained in both electron impact (EI) and electron capture negative ionization (ECNI) modes using a single quadrupole mass spectrometer (MS) as well as EI using a tandem MS (MS/MS). The major ions are M+, [M-2Br]+, [M-2Br]2+ and [M-nBr-28]+ in EI, and Br-, [HBr2]- and [C6BrnO]- in ECNI. In EI-MS, congeners without ortho bromine or having 2,3 substitution on one ring and no ortho bromines on the other were more robust than the others in each homolog. These congeners generated low [M-2Br]+ but relatively high [M-2Br]2+ in EI-MS and negligible [HBr2]- in ECNI-MS. In EI-MS/MS, the molecular ions of these congeners required higher collision energy to debrominate, and produced additional ions of [M-nBr]+ and [M-nBr-28]+. Full ortho substitution promotes C-O cleavage forming [C6BrnO]- in ECNI for congeners with >5 bromines. The relationship between the abundance of M+ and collision energy of the EI-MS/MS was well characterized with a logistic regression model. Principle component analysis found associations between the inflection point collision energy and a few molecular descriptors. Quantum chemistry simulations revealed different EI-induced fragmentation mechanisms among four dibrominated congeners, supporting the hypothesized formation of a stable dibenzofuran-like intermediate during the fragmentation of some congeners but not of others.

  1. Dependence of mass spectrometric fragmentation on the bromine substitution pattern of polybrominated diphenyl ethers.

    PubMed

    Wei, Hua; Zhang, Siyu; Wang, Yawei; Wang, Ying; Li, An; Negrusz, Adam; Yu, Gang

    2014-06-01

    This study investigates the link between the bromine substitution and the mass spectrometric fragmentation of polybrominated diphenyl ethers (PBDEs). The mass spectra of 180 PBDEs were obtained in both electron impact (EI) and electron capture negative ionization (ECNI) modes using a single quadrupole mass spectrometer (MS) as well as EI using a tandem MS (MS/MS). The major ions are M(+), [M-2Br](+), [M-2Br](2+) and [M-nBr-28](+) in EI, and Br(-), [HBr2](-) and [C6BrnO](-) in ECNI. In EI-MS, congeners without ortho bromine or having 2,3 substitution on one ring and no ortho bromines on the other were more robust than the others in each homolog. These congeners generated low [M-2Br](+) but relatively high [M-2Br](2+) in EI-MS and negligible [HBr2](-) in ECNI-MS. In EI-MS/MS, the molecular ions of these congeners required higher collision energy to debrominate, and produced additional ions of [M-nBr](+) and [M-nBr-28](+). Full ortho substitution promotes C-O cleavage forming [C6BrnO](-) in ECNI for congeners with >5 bromines. The relationship between the abundance of M(+) and collision energy of the EI-MS/MS was well characterized with a logistic regression model. Principle component analysis found associations between the inflection point collision energy and a few molecular descriptors. Quantum chemistry simulations revealed different EI-induced fragmentation mechanisms among four dibrominated congeners, supporting the hypothesized formation of a stable dibenzofuran-like intermediate during the fragmentation of some congeners but not of others. PMID:24692043

  2. Fast MS/MS acquisition without dynamic exclusion enables precise and accurate quantification of proteome by MS/MS fragment intensity

    PubMed Central

    Zhang, Shen; Wu, Qi; Shan, Yichu; Zhao, Qun; Zhao, Baofeng; Weng, Yejing; Sui, Zhigang; Zhang, Lihua; Zhang, Yukui

    2016-01-01

    Most currently proteomic studies use data-dependent acquisition with dynamic exclusion to identify and quantify the peptides generated by the digestion of biological sample. Although dynamic exclusion permits more identifications and higher possibility to find low abundant proteins, stochastic and irreproducible precursor ion selection caused by dynamic exclusion limit the quantification capabilities, especially for MS/MS based quantification. This is because a peptide is usually triggered for fragmentation only once due to dynamic exclusion. Therefore the fragment ions used for quantification only reflect the peptide abundances at that given time point. Here, we propose a strategy of fast MS/MS acquisition without dynamic exclusion to enable precise and accurate quantification of proteome by MS/MS fragment intensity. The results showed comparable proteome identification efficiency compared to the traditional data-dependent acquisition with dynamic exclusion, better quantitative accuracy and reproducibility regardless of label-free based quantification or isobaric labeling based quantification. It provides us with new insights to fully explore the potential of modern mass spectrometers. This strategy was applied to the relative quantification of two human disease cell lines, showing great promises for quantitative proteomic applications. PMID:27198003

  3. Coronal abundances determined from energetic particles

    NASA Technical Reports Server (NTRS)

    Reames, D. V.

    1995-01-01

    Solar energetic particles (SEPs) provide a measurement of coronal element abundances that is highly independent of the ionization states and temperature of the ions in the source plasma. The most complete measurements come from large 'gradual' events where ambient coronal plasma is swept up by the expanding shock wave from a coronal mass ejection. Particles from 'impulsive' flares have a pattern of acceleration-induced enhancements superimposed on the coronal abundances. Particles accelerated from high-speed solar wind streams at corotating shocks show a different abundance pattern corresponding to material from coronal holes. Large variations in He/O in coronal material are seen for both gradual and impulsive-flare events but other abundance ratios, such as Mg/Ne, are remarkably constant. SEP measurements now include hundreds of events spanning 15 years of high-quality measurement.

  4. Mass spectral study of hybrid peptides derived from (R)-aminoxy ester and [beta]-amino acids: The influence of aminoxy peptide bond (CO-NH-O) on peptide fragmentation under electrospray ionization conditions

    NASA Astrophysics Data System (ADS)

    Ramesh, V.; Ramesh, M.; Srinivas, R.; Sharma, G. V. M.; Manohar, V.

    2009-04-01

    A new class of Boc-protected aminoxy hybrid peptides containing repeats of [beta]-hAla-(R)-Ama-, and [beta]-Caa-(R)-Ama- ([beta]-hAla = [beta]3-(S)-hAlanine, (R)-Ama = (R)-aminoxy ester, and [beta]-Caa = (R)-C-linked carbo-[beta]3-amino acid) have been studied by electrospray ionization (ESI) ion-trap and quadrupole time-of-flight tandem mass spectrometry (Q-TOF MS/MS) of their protonated, cationized, and negative ions. MS3 CID of protonated aminoxy peptides of [beta]-hAla-(R)-Ama- yield intense [beta]-amino acid characteristic retro-Mannich fragmentation. The bn+ and [bn-methyl imine]+ (n = 3, 5) ions formed by cleavage of aminoxy peptide bond (CO-NH-O) are more intense than bn+ (n = 2, 4) formed by that of peptide bond (CO-NH-C) cleavage. Another characteristic ion observed is due to loss of H3NO from yn+ ions. The cationized (Li+, and Na+) peptides dissociate differently compared to protonated peptides. Intense cationized cn and zn ions are formed due to the cleavage of N-O bond. The deprotonated peptides also show abundant cn- and zn- ions (n = 1, 3, 5) and do not form any yn- ions. All these results clearly indicate the influence of aminoxy peptide bond on fragmentation of these hybrid peptides.

  5. Search for Methane Group Ions within Saturn

    NASA Astrophysics Data System (ADS)

    Sittler, E. C., Jr.; Hartle, R. E.; Cooper, J. F.; Johnson, R. E.; Smith, H. T.; Shappirio, M.; Simpson, D. G.; Waite, J. H., Jr.; Szego, K.

    2009-04-01

    In Hartle et al. [2006a,b] they presented evidence of CH4+ pickup ions within the mass loading region of the magnetospheric interaction with Titan. They also reported that keV water group ions W+ (i.e., O+) were present and dominated the magnetospheric heavy ion composition. The presence of methane group ions in outer magnetosphere, were also mentioned. These water group ions probably result from the emission of fast neutrals from the Enceladus torus via charge exchange reactions but still gravitationally bound to Saturn [see Johnson et al., 2005 and Sittler et al. 2006] and then become ionized in the outer magnetosphere where the pickup energies are ~ few keV. Methane ions would come from Titan. Since O+ and CH4+ have similar mass the primary discriminator is the O- fragment which appears at a different time-of-flight (TOF) than that for mass 16. Other discriminators have since been identified. If there is a methane torus as a consequence of the hydrodynamic model of Strobel [2008], then one expects the methane group ions to have comparable abundances relative to water group ions. Furthermore, CH3+ and not CH4+ should be the dominant methane group ion, since the methane dissociates to CH3 before they get ionized. Here we will be reporting on our continuing search for evidence of methane group ions within Saturn's outer magnetosphere. References: 1. Hartle, R. E., et al., Geophys. Res. Lett., 33, L08201, 2006a 2. Hartle, R. E., et al., Planet. Space Sci., 54, 1211, 2006b 3. Johnson. R.E., et. Astrophys. J. Letts, 644, L137-L139, 2005 4. Sittler, E. C., Jr., et al., JGR, 111, A09223, 2006 5. Strobel, D. F., Icarus, 193, 588, [2008

  6. OXYGEN ABUNDANCES IN CEPHEIDS

    SciTech Connect

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V. E-mail: serkor@skyline.od.ua E-mail: scan@deneb1.odessa.ua

    2013-07-01

    Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

  7. Laser mass spectrometry of biological molecular ions produced by matrix assisted laser desorption ionization (MALDI)

    NASA Astrophysics Data System (ADS)

    Jia, W. J.; Kosmidis, C.; Ledingham, K. W. D.; Scott, C. T. J.; Singhal, R. P.

    1996-10-01

    A tandem reflectron laser mass spectrometer is used for investigations of the photo fragmentation of molecular ions. The observed fragmentation patterns for 2,5-dihydrobenzoic acid and its fragments ions are analysed. PTH-trytophan and PTH-valine ions, generated by MALDI, are photodissociated and their fragmentation pattern is discussed.

  8. DNA fragmentation by charged particle tracks

    NASA Astrophysics Data System (ADS)

    Stenerlöw, B.; Höglund, E.; Carlsson, J.

    High-LET (linear energy transfer) charged particles induce DNA double-strand breaks (DSB) in a non-random fashion in mammalian cells. The clustering of DSB, probably determined by track structure as well as chromatin conformation, results in an excess of small- and intermediate-sized DNA fragments. DNA fragmentation in normal human fibroblasts (GM5758) was analyzed by pulsed-field gel electrophoresis after irradiation with photons ( 60Co) or 125 keV/μm nitrogen ions. Compared to conventional DSB analysis, i.e. assays only measuring the fraction of DNA smaller than a single threshold, the relative biological effectiveness (RBE) for DSB induction increased with 100%. Further, the size distribution of DNA fragments showed a significant dependence on radiation quality, with an excess of fragments up to 1 Mbp. Irradiation of naked genomic DNA without histone proteins increased the DSB yields 25 and 13 times for photons and nitrogen ions, respectively. The results suggest possible roles of both track structure and chromatin organization in the distribution of DNA double-strand breaks along the chromosome.

  9. Fragmentation of nitrogen-14 nuclei at 2.1 Gev per nucleon.

    NASA Technical Reports Server (NTRS)

    Heckman, H. H.; Greiner, D. E.; Lindstrom, P. J.; Bieser, F. S.

    1971-01-01

    An experiment has been carried out at the bevatron on the nuclear fragmentation of nitrogen-14 ions at an energy of 2.1 billion electron volts (Gev) per nucleon. Because of the near equality of the velocities of the nitrogen-14 beam and the fragmentation products at an angle of 0 deg, we find it possible to identify the nuclear fragments isotopically.

  10. Detection and Characterization of Low Abundance Glycopeptides Via Higher-Energy C-Trap Dissociation and Orbitrap Mass Analysis

    NASA Astrophysics Data System (ADS)

    Hart-Smith, Gene; Raftery, Mark J.

    2012-01-01

    Broad-scale mass spectrometric analyses of glycopeptides are constrained by the considerable complexity inherent to glycoproteomics, and techniques are still being actively developed to address the associated analytical difficulties. Here we apply Orbitrap mass analysis and higher-energy C-trap dissociation (HCD) to facilitate detailed insights into the compositions and heterogeneity of complex mixtures of low abundance glycopeptides. By generating diagnostic oxonium product ions at mass measurement errors of <5 ppm, highly selective glycopeptide precursor ion detections are made at sub-fmol limits of detection: analyses of proteolytic digests of a hen egg glycoprotein mixture detect 88 previously uncharacterized glycopeptides from 666 precursor ions selected for MS/MS, with only one false positive due to co-fragmentation of a non-glycosylated peptide with a glycopeptide. We also demonstrate that by (1) identifying multiple series of glycoforms using high mass accuracy single stage MS spectra, and (2) performing product ion scans at optimized HCD collision energies, the identification of peptide + N-acetylhexosamine (HexNAc) ions (Y1 ions) can be readily achieved at <5 ppm mass measurement errors. These data allow base peptide sequences and glycan compositional information to be attained with high confidence, even for glycopeptides that produce weak precursor ion signals and/or low quality MS/MS spectra. The glycopeptides characterized from low fmol abundances using these methods allow two previously unreported glycosylation sites on the Gallus gallus protein ovoglycoprotein (amino acids 82 and 90) to be confirmed; considerable glycan heterogeneities at amino acid 90 of ovoglycoprotein, and amino acids 34 and 77 of Gallus gallus ovomucoid are also revealed.

  11. Fragment generation, survival, and attachment of Dictyota spp. at Conch Reef in the Florida Keys, USA

    NASA Astrophysics Data System (ADS)

    Herren, L. W.; Walters, L. J.; Beach, K. S.

    2006-05-01

    During the past decade, the relative abundance of the brown macroalgae Dictyota spp. has been high in the Florida Keys. Recent studies have shown that members of this genus successfully reproduce via vegetative fragmentation. To investigate the importance of fragmentation on the reef community, this study examined: (1) the degree of epiphytism on benthic organisms, (2) the rate of fragment production through fish foraging activities, (3) the likelihood of fragment entanglement, and (4) the fragment attachment and success rate. It was found that reef fish contributed substantially to the fragment pool; furthermore, most fish-produced fragments produced rhizoids and attached to sand grains within 24 h in the field. Fragments of Dictyota spp. most commonly became entangled around and then attached themselves to the green alga Halimeda tuna, and other Dictyota spp. These results suggest that vegetative fragmentation of Dictyota spp. plays an important role in the changing community structure on the Florida Keys reef tract.

  12. Heavy fragment radioactivities

    SciTech Connect

    Price, P.B.

    1987-12-10

    This recently discovered mode of radioactive decay, like alpha decay and spontaneous fission, is believed to involve tunneling through the deformation-energy barrier between a very heavy nucleus and two separated fragments the sum of whose masses is less than the mass of the parent nucleus. In all known cases the heavier of the two fragments is close to doubly magic /sup 208/Pb, and the lighter fragment has even Z. Four isotopes of Ra are known to emit /sup 14/C nuclei; several isotopes of U as well as /sup 230/Th and /sup 231/Pa emit Ne nuclei; and /sup 234/U exhibits four hadronic decay modes: alpha decay, spontaneous fission, Ne decay and Mg decay.

  13. Fragment screening: an introduction.

    PubMed

    Leach, Andrew R; Hann, Michael M; Burrows, Jeremy N; Griffen, Ed J

    2006-09-01

    There are clearly many different philosophies associated with adapting fragment screening into mainstream Drug Discovery Lead Generation strategies. Scientists at Astex, for instance, focus entirely on strategies involving use of X-ray crystallography and NMR. However, AstraZeneca uses a number of different fragment screening strategies. One approach is to screen a 2000 compound fragment set (with close to "lead-like" complexity) at 100 microM in parallel with every HTS such that the data are obtained on the entire screening collection at 10 microM plus the extra samples at 100 microM; this provides valuable compound potency data in a concentration range that is usually unexplored. The fragments are then screen-specific "privileged structures" that can be searched for in the rest of the HTS output and other databases as well as having synthesis follow-up. A typical workflow for a fragment screen within AstraZeneca is shown below (Figure 24) and highlights the desirability (particularly when screening >100 microM) for NMR and X-ray information to validate weak hits and give information on how to optimise them. In this chapter, we have provided an introduction to the theoretical and practical issues associated with the use of fragment methods and lead-likeness. Fragment-based approaches are still in an early stage of development and are just one of many interrelated techniques that are now used to identify novel lead compounds for drug development. Fragment based screening has some advantages, but like every other drug hunting strategy will not be universally applicable. There are in particular some practical challenges associated with fragment screening that relate to the generally lower level of potency that such compounds initially possess. Considerable synthetic effort has to be applied for post-fragment screening to build the sort of potency that would be expected to be found from a traditional HTS. However, if there are no low-hanging fruit in a screening

  14. Coronal element abundances derived from solar energetic particles

    NASA Technical Reports Server (NTRS)

    Reames, Donald V.

    1994-01-01

    The large gradual solar-energetic-particle (SEP) events, where abundances are commonly measured, are produced when coronal mass ejections (CMEs) drive shock waves through the corona and the interplanetary medium. The shock accelerates particles from the highly-ionized, approximately 1.5 MK, plasma in a manner that depends only weakly upon the Q/A of the ion, except at very high energies. Averaging the approximately 1 MeV/amu abundances over many events compensates for the acceleration effects to produce abundances that appear to correspond directly to those in the coronal source for all observed elements, including H. The resulting abundances reflect the 4 x enhancement of ions with low values of first ionization potential (FIP) arising from ion-neutral fractionation that occurs as the atoms are transported up from the photosphere. A different pattern of fractionation is found for ions that are shock-accelerated from the high speed solar wind emerging from coronal holes.

  15. Molecular electrostatic potentials by systematic molecular fragmentation

    SciTech Connect

    Reid, David M.; Collins, Michael A.

    2013-11-14

    A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.

  16. Preferred modes of decay in nuclear fragmentation

    SciTech Connect

    Aranda, A.; Lopez, J.A.; Wu, Z.

    1997-02-01

    Recent experimental studies show a characteristic energy dependence of the different fragmentation modes in heavy-ion reactions at intermediate energies. In this work we study this dependence and find that, in multifragmentation, just like in low-energy fission, some modes of decay are more probable than the rest. We argue that these high-probability mass partitions are ultimately responsible for the observed energy dependence. {copyright} {ital 1997} {ital The American Physical Society}

  17. WITHDRAWN: Fragmentation of charged aqueous nanodroplets

    NASA Astrophysics Data System (ADS)

    Ichiki, Kengo

    2005-11-01

    The whole evaporating process of charged aqueous nanodroplets is studied by systematic molecular dynamics simulations until most of the solvent molecules are evaporated. % The solvent evaporation makes the droplet smaller and smaller, and at a certain point the repulsive force among ions causes an instability, where typically single ion and 10 to 20 water molecules are disintegrated from the main droplet. % This ion fragmentation occurs around 70 to 80% of the charge predicted by the Rayleigh theory [Lord Rayleigh, Phil. Mag. 14, 184 (1882)]. % The numerical results are summarized in the function R(z) which is the fragmentation radius at the charge z. From the fitting by the power law Rz^β, we find that at lower temperature T=350 and 370 K the result is close to the Rayleigh theory β= 2/3, while at higher temperature T=400 and 450 K it is like β= 1/2. % Another fitting on R(z) by the extended ion evaporation mechanism [M. Gamero-Castaño and J. Fern'andez de la Mora, Anal. Chim. Acta 406, 67 (2000)] works well for both cases. % The final state of the evaporation process is typically a single ion with several water molecules. If we put an alanine dipeptide in zwitterionic form at the beginning, two charges remain in some cases.

  18. Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer

    PubMed Central

    Gardner, Myles W.; Smith, Suncerae I.; Ledvina, Aaron R.; Madsen, James A.; Coon, Joshua J.; Schwartz, Jae C.; Stafford, George C.; Brodbelt, Jennifer S.

    2009-01-01

    A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells - the first a high pressure cell operated at nominally 5 × 10-3 Torr and the second a low pressure cell operated at nominally 3 × 10-4 Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y1 fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of ~100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra. PMID:19739654

  19. IMPACT fragmentation model developments

    NASA Astrophysics Data System (ADS)

    Sorge, Marlon E.; Mains, Deanna L.

    2016-09-01

    The IMPACT fragmentation model has been used by The Aerospace Corporation for more than 25 years to analyze orbital altitude explosions and hypervelocity collisions. The model is semi-empirical, combining mass, energy and momentum conservation laws with empirically derived relationships for fragment characteristics such as number, mass, area-to-mass ratio, and spreading velocity as well as event energy distribution. Model results are used for several types of analysis including assessment of short-term risks to satellites from orbital altitude fragmentations, prediction of the long-term evolution of the orbital debris environment and forensic assessments of breakup events. A new version of IMPACT, version 6, has been completed and incorporates a number of advancements enabled by a multi-year long effort to characterize more than 11,000 debris fragments from more than three dozen historical on-orbit breakup events. These events involved a wide range of causes, energies, and fragmenting objects. Special focus was placed on the explosion model, as the majority of events examined were explosions. Revisions were made to the mass distribution used for explosion events, increasing the number of smaller fragments generated. The algorithm for modeling upper stage large fragment generation was updated. A momentum conserving asymmetric spreading velocity distribution algorithm was implemented to better represent sub-catastrophic events. An approach was developed for modeling sub-catastrophic explosions, those where the majority of the parent object remains intact, based on estimated event energy. Finally, significant modifications were made to the area-to-mass ratio distribution to incorporate the tendencies of different materials to fragment into different shapes. This ability enabled better matches between the observed area-to-mass ratios and those generated by the model. It also opened up additional possibilities for post-event analysis of breakups. The paper will discuss

  20. Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation-Tandem Time-of-Flight Mass Spectrometry Approach

    PubMed Central

    Ibrahim, Yehia M.; Prior, David C.; Baker, Erin S.; Smith, Richard D.; Belov, Mikhail E.

    2010-01-01

    The confidence in peptide (and protein) identifications with ion mobility spectrometry time-of-flight mass spectrometry (IMS-TOFMS) is expected to drastically improve with the addition of information from an efficient ion dissociation step prior to MS detection. High throughput IMS-TOFMS analysis imposes a strong need for multiplexed ion dissociation approaches where multiple precursor ions yield complex sets of fragment ions that are often intermingled with each other in both the drift time and m/z domains. We have developed and evaluated an approach for collision-induced dissociation (CID) using IMS-TOFMS instrument. It has been shown that precursor ions activated inside an rf-device with an axial dc-electric field produce abundant fragment ions which are radially confined with the rf-field and collisionally cooled at an elevated pressure, resulting in high CID efficiencies comparable or higher than those measured in triple-quadrupole instruments. We have also developed an algorithm for deconvoluting these complex multiplexed tandem MS spectra by clustering both the precursor and fragment ions into matching drift time profiles and by utilizing the high mass measurement accuracy achievable with TOFMS. In a single IMS separation from direct infusion of tryptic digest of bovine serum albumin (BSA), we have reliably identified 20 unique peptides using a multiplexed CID approach downstream of the IMS separation. Peptides were identified based upon the correlation between the precursor and fragment drift time profiles and by matching the profile representative masses to those of in silico BSA tryptic peptides and their fragments. The false discovery rate (FDR) of peptide identifications from multiplexed MS/MS spectra was less than 1%. PMID:20596241

  1. Ultrafast ionization and fragmentation of molecular silane

    SciTech Connect

    Sayres, Scott G.; Ross, Matt W.; Castleman, A. W. Jr.

    2010-09-15

    The ionization and fragmentation of molecular silane is examined here with laser intensities ranging between 7x10{sup 12} and 1x10{sup 15} W/cm{sup 2} at 624 nm. The ionization potential of silane determined using both multiphoton ionization (MPI) and tunneling ionization (TI) models agrees with the vertical ionization potential of the molecule. In addition, the application of the tunneling ionization model is extended here to the fragments of silane to determine their appearance potentials. MPI values for SiH{sub 3}{sup +}, SiH{sub 2}{sup +}, SiH{sup +}, Si{sup +}, as well as H{sub 2}{sup +} and H{sup +} are consistent with vertical potentials, whereas the TI measurements are found to be in accord with adiabatic potentials. The tunneling appearance potentials observed for the fragments H{sub 2}{sup +} and H{sup +} are lower than reported for other techniques. In fact, the appearance potential measurements for these species resulting from silane are lower than their ionization potentials. The fragmentation rate of silane is determined to be nearly 20 times larger than the ionization rate. The main precursor for producing amorphous silicon (a-Si:H) thin films, SiH{sub 3}{sup +} is the dominant fragmentation product making up roughly a third of the total ion yield, a substantial increase from other techniques.

  2. Aromatic organosulfates in atmospheric aerosols: Synthesis, characterization, and abundance

    NASA Astrophysics Data System (ADS)

    Staudt, Sean; Kundu, Shuvashish; Lehmler, Hans-Joachim; He, Xianran; Cui, Tianqu; Lin, Ying-Hsuan; Kristensen, Kasper; Glasius, Marianne; Zhang, Xiaolu; Weber, Rodney J.; Surratt, Jason D.; Stone, Elizabeth A.

    2014-09-01

    Aromatic organosulfates are identified and quantified in fine particulate matter (PM2.5) from Lahore, Pakistan, Godavari, Nepal, and Pasadena, California. To support detection and quantification, authentic standards of phenyl sulfate, benzyl sulfate, 3- and 4-methylphenyl sulfate and 2-, 3-, and 4-methylbenzyl sulfate were synthesized. Authentic standards and aerosol samples were analyzed by ultra-performance liquid chromatography (UPLC) coupled to negative electrospray ionization (ESI) quadrupole time-of-flight (ToF) mass spectrometry. Benzyl sulfate was present in all three locations at concentrations ranging from 4 to 90 pg m-3. Phenyl sulfate, methylphenyl sulfates and methylbenzyl sulfates were observed intermittently with abundances of 4 pg m-3, 2-31 pg m-3, 109 pg m-3, respectively. Characteristic fragment ions of aromatic organosulfates include the sulfite radical (rad SO3-, m/z 80) and the sulfate radical (rad SO4-, m/z 96). Instrumental response factors of phenyl and benzyl sulfates varied by a factor of 4.3, indicating that structurally-similar organosulfates have significantly different instrumental responses and highlighting the need to develop authentic standards for absolute quantitation organosulfates. In an effort to better understand the sources of aromatic organosulfates to the atmosphere, chamber experiments with the precursor toluene were conducted under conditions that form biogenic organosulfates. Aromatic organosulfates were not detected in the chamber samples, suggesting that they form through different pathways, have different precursors (e.g. naphthalene or methylnaphthalene), or are emitted from primary sources.

  3. Isospin dependence of fragment spectra in heavy/super-heavy colliding nuclei at intermediate energies

    NASA Astrophysics Data System (ADS)

    Chugh, Rajiv; Kumar, Rohit; Vinayak, Karan Singh

    2016-05-01

    Using isospin-dependent quantum molecular dynamics (IQMD) approach, we performed a theoretical investigation of the evolution of various kinds of fragments in heavy and superheavy-ion reactions in the intermediate/medium energy domain. We demonstrated direct impact of symmetry energy and Coulomb interactions on the evolution of fragments. Final fragment spectra (yields) obtained from the analysis of various heavy/super-heavy ion reactions at different reaction conditions show high sensitivity towards Coulomb interactions and less significant sensitivity to symmetry energy forms. No inconsistent pattern of fragment structure is obtained in case of super-heavy ion involved reactions for all the parameterizations of density dependence of symmetry energy.

  4. Molecule fragmentation at the Dresden EBIS-Aa)

    NASA Astrophysics Data System (ADS)

    Kreller, M.; Zschornack, G.; Kentsch, U.; Heller, R.

    2008-02-01

    We report on molecule fragmentation measurements of propane in high dense electron beams of a room-temperature electron beam ion source, the so-called Dresden EBIS-A. After fragmentation of propane molecules in the electron beam the fragments were continuously extracted and q /A separated by a bifocal dipole magnet. Fragmentation spectra were measured at working gas pressures of 10-9mbar up to 10-8mbar, electron currents of 29mA up to 75mA, and electron energies of 11keV up to 15keV. Thereby all possible stoichiometric ratios of propane fragments were detected. At low electron beam currents the ion current output of the CHx+ (x =0-3) and the C2Hx+ (x=0-5) fragments is nearly identically. At higher electron currents the CHx+ (x =0-3) peaks dominate the spectra and the ratio between the C+ peak and CHx+ (x =0-3) peaks increases from 2:1 to 3:1. It was shown that the working gas pressure has no significant influence on the fragment distribution but on the total ion current.

  5. Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

    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 γ or δ 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 π 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.

  6. Fragmentation and hydration of tektites and microtektites

    USGS Publications Warehouse

    Glass, B.P.; Muenow, D.W.; Bohor, B.F.; Meeker, G.P.

    1997-01-01

    An examination of data collected over the last 30 years indicates that the percent of glass fragments vs. whole splash forms in the Cenozoic microtektite strewn fields increases towards the source crater (or source region). We propose that this is due to thermal stress produced when tektites and larger microtektites fall into water near the source crater while still relatively hot (>1150 ??C). We also find evidence (low major oxide totals, frothing when melted) for hydration of most of the North American tektite fragments and microtektites found in marine sediments. High-temperature mass spectrometry indicates that these tektite fragments and microtektites contain up to 3.8 wt% H2O. The H2O-release behavior during the high-temperature mass-spectrometric analysis, plus high Cl abundances (???0.05 wt%), indicate that the North. American tektite fragments and microtektites were hydrated in the marine environment (i.e., the H2O was not trapped solely on quenching from a melt). The younger Ivory Coast and Australasian microtektites do not exhibit much evidence of hydration (at least not in excess of 0.5 wt% H2O); this suggests that the degree of hydration increases with age. In addition, we find that some glass spherules (with 65 wt% SiO2 can undergo simple hydration in the marine environment, while impact glasses (with <65 wt% SiO2) can also undergo palagonitization.

  7. Solar abundance of platinum

    PubMed Central

    Burger, Harry; Aller, Lawrence H.

    1975-01-01

    Three lines of neutral platinum, located at λ 2997.98 Å, λ 3064.71 Å, and λ 3301.86 Å have been used to determine the solar platinum abundance by the method of spectral synthesis. On the scale, log A(H) = 12.00, the thus-derived solar platinum abundance is 1.75 ± 0.10, in fair accord with Cameron's value of log A(Pt) = 1.69 derived by Mason from carbonaceous chondrites and calculated on the assumption that log A(Si) = 7.55 in the sun. PMID:16592278

  8. Three-body fragmentation dynamics of carbon-dioxide dimers induced by intense femtosecond laser pulses

    NASA Astrophysics Data System (ADS)

    Fan, Yameng; Wu, Chengyin; Xie, Xiguo; Wang, Peng; Zhong, Xunqi; Shao, Yun; Sun, Xufei; Liu, Yunquan; Gong, Qihuang

    2016-06-01

    We experimentally studied three-body fragmentation dynamics of (CO2)23+ generated by intense femtosecond laser fields. Three-dimensional momentum vectors as well as kinetic energies were measured for correlated fragmental ions using the technology of coincidence measurement. The results demonstrate that sequential fragmentation channel dominates for three-body fragmentation of (CO2)23+, in which the weak van der Waals bond breaks first and then one strong covalent bond.

  9. Fragmentation of Lewis-type trisaccharides in the gas phase

    NASA Astrophysics Data System (ADS)

    Suzuki, Hiroaki; Yamagaki, Tohru; Tachibana, Kazuo; Fukui, Kazuhiko

    2008-11-01

    The mechanisms of fragmentation of the chlorinated Lewis-type trisaccharides Lewis a and Lewis X were studied by using experimental and theoretical methods. In the fragment ion spectra obtained by ESI-CID-MS, C- and Z-type fragmentations corresponding to 4- and 3-linked glycosyl bond cleavages of the N-acetylglucosamine moiety were observed. The relationships of the relative ion intensities of C- and Z-type fragmentations were Z > C in Lewis a and C > Z in Lewis X, suggesting that the relationships of the activation energies were C > Z in Lewis a and Z > C in Lewis X. Anomeric and acetoamide groups were assumed to be included in the mechanisms of C- and Z-type fragmentation; we therefore analyzed 3-fucosyllactose and methylated Lewis-type trisaccharides, which are the derivatives of Lewis-type trisaccharides. These analyses revealed that C-type fragmentation was little influenced by anomeric group and that Z-type fragmentation was influenced by both the anomeric and the acetoamide groups. Fragmentation mechanisms were proposed on the basis of the experimental results and were calculated at the HF/3-21G(d), HF/6-31G(d) levels. From the calculations, C-type fragmentation of the 4-linkage was considered to take place by electron transfer from the acetoamide group, and Z-type fragmentation at the 3-linkage was considered to take place in two steps: (i) elimination of the 3-linked saccharide moiety, and (ii) deprotonation of an anomeric proton by a chloride anion. The activation energies for C- and Z-type fragmentations, as determined by HF calculations, were consistent with the experimentally assumed trends.

  10. Multiphoton ionization-fragmentation patterns of tertiary amines

    NASA Astrophysics Data System (ADS)

    Parker, D. H.; Bernstein, R. B.; Lichtin, D. A.

    1981-09-01

    Multiphoton ionization (MPI)-fragmentation patterns are reported for a series of normal and caged tertiary amines. Ionization is enhanced by two-photon resonance with the 3s and 3p Rydberg states of trimethylamine, triethylamine, and the caged amines quinuclidine and triethylenediamine. Over the wavelength region λ = 400-530 nm, N(CH3)3 ionizes to the parent ion (P) and fragments only by the loss of a H atom to yield the P-H daughter ion; N(C2H5)3 ionizes to its parent ion and fragments by the loss of a methyl to form the P-CH3 ion. The branching ratio of daughter to parent ions is found to be essentially independent of laser intensity but strongly dependent on laser wavelength. The caged amines quinuclidine [N(C2H4)3CH, or ABCO] and triethylenediamine [N(C2H4)3N, or DABCO] fragment extensively over this λ range in a manner dependent on both laser wavelength and intensity. The extent of daughter ion formation in N(CH3)3 and N(C2H5)3 can be understood by consideration of the wavelength regions in which the total available energy from the initial three- or four-photon ionization event exceeds the appearance potential of the given daughter ion. For the caged amines direct observation of this mechanism is masked by fragmentation due to sequential absorption of photons (during the ˜5 ns pulse duration) by the parent and/or daughter ions. The present results show that even for molecules with broad, unstructured UV absorption and MPI spectra such as N(CH3)3 and N(C2H5)3, considerable information on photon-molecule and photon-ion interactions can still be gained by the MPI mass spectrometry technique.

  11. Gas-Phase Fragmentation Pathways of Mixed Addenda Keggin Anions: PMo12-nW nO 40 3- (n = 0-12).

    PubMed

    Gunaratne, K Don D; Prabhakaran, Venkateshkumar; Johnson, Grant E; Laskin, Julia

    2015-06-01

    We report a collision-induced dissociation (CID) investigation of the mixed addenda polyoxometalate (POM) anions, PMo(12-n)W(n)O(40)(3-) (n = 0-12). The anions were generated in solution using a straightforward single-step synthesis approach and introduced into the gas phase by electrospray ionization (ESI). Distinct differences in fragmentation patterns were observed for the range of mixed addenda POMs examined in this study. CID of molybdenum-rich anions, PMo(12-n)W(n)O(40)(3-) (n = 0-2), generates an abundant doubly charged fragment containing seven metal atoms (M) and 22 oxygen atoms (M(7)O(22)(2-)) and its complementary singly charged PM(5)O(18)(-) ion. In comparison, the doubly charged Lindqvist anion, (M(6)O(19)(2-)) and its complementary singly charged PM(6)O(21)(-) ion are the dominant fragments of Keggin POMs containing more than two tungsten atoms, PMo(12-n)W(n)O(40)(3-) (n = 3-12). The observed transition in the dissociation pathways with an increase in the number of W atoms in the POM may be attributed to the higher barrier of tungsten-rich anions towards isomerization. We present evidence that the observed distribution of Mo and W atoms in the major M(6)O(19)(2-) and M(7)O(22)(2-) fragment ions is different from that predicted by a random distribution, indicating substantial segregation of the addenda metal atoms in the POMs. Charge reduction of the triply charged precursor anion resulting in formation of doubly charged anions is also observed. This is a dominant pathway for mixed POMs having a majority (8-11) of W atoms and a minor channel for other precursors indicating a close competition between fragmentation and charge loss pathways in CID of POM anions. PMID:25832027

  12. Gas-Phase Fragmentation Pathways of Mixed Addenda Keggin Anions: PMo12-nWnO40 3- (n = 0-12)

    NASA Astrophysics Data System (ADS)

    Gunaratne, K. Don D.; Prabhakaran, Venkateshkumar; Johnson, Grant E.; Laskin, Julia

    2015-06-01

    We report a collision-induced dissociation (CID) investigation of the mixed addenda polyoxometalate (POM) anions, PMo12-nWnO40 3- (n = 0-12). The anions were generated in solution using a straightforward single-step synthesis approach and introduced into the gas phase by electrospray ionization (ESI). Distinct differences in fragmentation patterns were observed for the range of mixed addenda POMs examined in this study. CID of molybdenum-rich anions, PMo12-nWnO40 3- (n = 0-2), generates an abundant doubly charged fragment containing seven metal atoms (M) and 22 oxygen atoms (M7O22 2-) and its complementary singly charged PM5O18 - ion. In comparison, the doubly charged Lindqvist anion, (M6O19 2-) and its complementary singly charged PM6O21 - ion are the dominant fragments of Keggin POMs containing more than two tungsten atoms, PMo12-nWnO40 3- (n = 3-12). The observed transition in the dissociation pathways with an increase in the number of W atoms in the POM may be attributed to the higher barrier of tungsten-rich anions towards isomerization. We present evidence that the observed distribution of Mo and W atoms in the major M6O19 2- and M7O22 2- fragment ions is different from that predicted by a random distribution, indicating substantial segregation of the addenda metal atoms in the POMs. Charge reduction of the triply charged precursor anion resulting in formation of doubly charged anions is also observed. This is a dominant pathway for mixed POMs having a majority (8-11) of W atoms and a minor channel for other precursors indicating a close competition between fragmentation and charge loss pathways in CID of POM anions.

  13. Gas-Phase Fragmentation Pathways of Mixed-Addenda Keggin Anions: PMo12-nWnO403- (n = 0-12)

    SciTech Connect

    Gunaratne, Kalupathirannehelage Don D.; Prabhakaran, Venkateshkumar; Johnson, Grant E.; Laskin, Julia

    2015-06-01

    We report a collision-induced dissociation (CID) investigation of the mixed addenda polyoxometalate (POM) anions, PMo12-nWnO403- (n = 0-12). The anions were generated in solution using a straightforward single-step synthesis approach and introduced into the gas phase by electrospray ionization (ESI). Distinct differences in fragmentation patterns were observed for the range of mixed POMs examined in this study. CID of molybdenum-rich anions, PMo12- nWnO403- (n = 0-2), generates an abundant doubly charged fragment containing seven metal atoms (M) and twenty-two oxygen atoms (M7O222-) and its complementary singly charged PM5O18- ion, while the Lindqvist anion, (M6O192-) and its complementary PM6O21- ion are the dominant fragments of Keggin POMs containing more than two tungsten atoms, PMo12-nWnO403- (n = 3-12). The observed transition in the dissociation pathways with an increase in the number of W atoms may be attributed to the higher stability of tungsten-rich anions towards isomerization. We find that the observed distribution of Mo and W atoms in the major M6O192- and M7O222- fragment ions is different from that predicted by a random distribution indicating substantial segregation of the addenda metal atoms in the POMs. Electron detachment from the triply charged precursor anion resulting in formation of doubly charged anions is observed. This is a dominant dissociation pathway for mixed POMs having a majority (8-11) of W atoms and a minor channel for other precursors indicating a close competition between fragmentation and electron detachment pathways of POM anions.

  14. Abundances of light elements.

    PubMed Central

    Pagel, B E

    1993-01-01

    Recent developments in the study of abundances of light elements and their relevance to cosmological nucleosynthesis are briefly reviewed. The simplest model, based on standard cosmology and particle physics and assuming homogeneous baryon density at the relevant times, continues to stand up well. PMID:11607388

  15. Element abundances of classical novae

    NASA Astrophysics Data System (ADS)

    Andrea, J.; Drechsel, H.; Starrfield, S.

    1994-11-01

    Physical conditions and element abundances in the optically thin shells of 11 classical novae with outbursts between 1978 and 1989 were determined from an analysis of UV and optical spectra obtained during the nebular stage. Eight novae were studied on the basis of new optical and UV spectra. The accuracy of the element abundances depends on whether or not simultaneous UV spectra were available to determine individual ionization stage dependent gas temperatures. Generally, slightly higher than solar abundances of helium and pronounced overabundances of the heavier elements were found. QU Vul turned out to be an ONeMg nova, while the other objects belong to the class of CO novae. The nature of V2214 Oph could not be completely clarified. The novae V1668 Cyg (1978), V693 CrA (1981), and V1370 Aql (1982), for which published element abundances exist, were reanalyzed to check the consistency of our spectral analysis approach. Satisfactory agreement of the results was found. Photoionization calculations were carried out for PW Vul using the code of Aldrovandi, Pequignot, and Stasinska. A synthetic spectrum was generated for the parameters derived from the analysis of the UV and optical spectra, which is in very good agreement with the observations. The spectral analysis technique was then applied to the model spectrum and reproduced the model parameters well. Electron temperatures for the C(2+) and C(3+) ions between 7 500 and 12,000 K and for N(4+) betwen 12,000 and 16,000 K were derived. For PW Vul these temperatures remained relatively constant over several months. The decline in density of the ejected shells with time could be investigated for V842 Cen, QV Vul, V977 Sco, and V443 Sct, and was found to deviate from the relation Ne proportional to t-2 for free expansion of a shell in a different way for each object. A possible explanation may be the complex density structure of the shells. This suspicion is supported by high resolution spectra (ESO 3.6m telescope

  16. Effects of prairie fragmentation on the nest success of breeding birds in the midcontinental United States

    USGS Publications Warehouse

    Herkert, J.R.; Reinking, D.L.; Wiedenfeld, D.A.; Winter, M.; Zimmerman, J.L.; Jensen, W.E.; Finck, E.J.; Koford, Rolf R.; Wolfe, D.H.; Sherrod, S.K.; Jenkins, M.A.; Faaborg, J.; Robinson, S.K.

    2003-01-01

    Grassland fragmentation and habitat loss are hypothesized to be contributing to widespread grassland bird declines in North America due to the adverse effects of fragmentation on breeding bird abundance and reproductive success. To assess the effects of fragmentation on the reproductive success of grassland birds, we measured rates of nest predation and brood parasitism for four species of birds (Grasshopper Sparrow [Ammodramus savannaru], Henslow's Sparrow[Ammodramus henslowii], Eastern Meadowlark [Sturnella magna], and Dickcissel [Spiza Americana]) in 39 prairie fragments ranging from 24 to >40,000 ha in size in five states in the mid-continental United States. Throughout the region, nest-predation rates were significantly influenced by habitat fragmentation. Nest predation was highest in small (1000 ha) prairie fragments. Rates of brood parasitism by Brown-headed Cowbirds (Molothrus ater), however, were not consistently related to fragment size and instead were more strongly related to regional cowbird abundance, being significantly higher in regions with high cowbird abundance. Differences in nest-predation rates between large fragments (54-68% of all nests lost to predators) and small fragments (78-84% lost to predators) suggest that fragmentation of prairie habitats may be contributing to regional declines of grassland birds. Maintaining grassland bird populations, therefore, may require protection and restoration of large prairie areas.

  17. Abundance and chemistry of interstellar HOCO(+)

    NASA Technical Reports Server (NTRS)

    Minh, Y. C.; Brewer, M. K.; Irvine, W. M.; Friberg, P.; Johansson, L. E. B.

    1991-01-01

    Column densities of 10 to the 15th/sq cm toward the Galactic center and not more than 10 to the 12th/sq cm for cold dark clouds are derived from observations using an LVG model, and the chemical implications are discussed. The HOCO(+) 4(04)-3(03) line toward Sgr A is mapped. The fractional abundance of HOCO(+) in the Galactic center region was found to be three orders of magnitude larger than predicted by quiescent ion-molecule chemistry and an order of magnitude larger than predicted by an MHD shock model. It is suggested that the possibly high CO2 abundance, and consequently the observed HOCO(+) abundance in the Galactic center, may result from UV photolysis of grain mantles.

  18. Structural characterization of arginine-vasopressin and lysine-vasopressin by Fourier- transform ion cyclotron resonance mass spectrometry and infrared multiphoton dissociation.

    PubMed

    Bianco, Giuliana; Battista, Fabio; Buchicchio, Alessandro; Amarena, Concetta G; Schmitt-Kopplin, Philippe; Guerrieri, Antonio

    2015-01-01

    Arginine-vasopressin (AVP) and lysine-vasopressin (LVP) were analyzed by reversed-phase liquid chromatography/mass spectrometry (LC-MS) using Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) electrospray ionization (ESI) in the positive ion mode. LVP and AVP exhibited the protonated adduct [M+H](+) as the predominant ion at m/z 1056.43965 and at m/z 1084.44561, respectively. Infrared multiphoton dissociation (IRMPD), using a CO(2) laser source at a wavelength of 10.6 μm, was applied to protonated vasopressin molecules. The IRMPD mass spectra presented abundant mass fragments essential for a complete structural information. Several fragment ions, shared between two target molecules, are discussed in detail. Some previously unpublished fragments were identified unambiguously utilizing the high resolution and accurate mass information provided by the FT-ICR mass spectrometer. The opening of the disulfide loop and the cleavage of the peptide bonds within the ring were observed even under low-energy fragmentation conditions. Coupling the high-performance FT-ICR mass spectrometer with IRMPD as a contemporary fragmentation technique proved to be very promising for the structural characterization of vasopressin. PMID:26307701

  19. Fragmentation of cancer cells

    NASA Astrophysics Data System (ADS)

    Vanapalli, Siva; Kamyabi, Nabiollah

    Tumor cells have to travel through blood capillaries to be able to metastasize and colonize in distant organs. Among the numerous cells that are shed by the primary tumor, very few survive in circulation. In vivo studies have shown that tumor cells can undergo breakup at microcapillary junctions affecting their survival. It is currently unclear what hydrodynamic and biomechanical factors contribute to fragmentation and moreover how different are the breakup dynamics of highly and weakly metastatic cells. In this study, we use microfluidics to investigate flow-induced breakup of prostate and breast cancer cells. We observe several different modes of breakup of cancer cells, which have striking similarities with breakup of viscous drops. We quantify the breakup time and find that highly metastatic cancer cells take longer to breakup than lowly metastatic cells suggesting that tumor cells may dynamically modify their deformability to avoid fragmentation. We also identify the role that cytoskeleton and membrane plays in the breakup process. Our study highlights the important role that tumor cell fragmentation plays in cancer metastasis. Cancer Prevention and Research Institute of Texas.

  20. Electroeluting DNA fragments.

    PubMed

    Zarzosa-Alvarez, Ana L; Sandoval-Cabrera, Antonio; Torres-Huerta, Ana L; Bermudez-Cruz, Rosa M

    2010-01-01

    Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification kits. Thus, selecting a method will depend mostly of what is available in the laboratory. The electroelution procedure allows one to purify very clean DNA to be used in a large number of applications (sequencing, radiolabeling, enzymatic restriction, enzymatic modification, cloning etc). This procedure consists in placing DNA band-containing agarose or acrylamide slices into sample wells of the electroeluter, then applying current will make the DNA fragment to leave the agarose and thus be trapped in a cushion salt to be recovered later by ethanol precipitation. PMID:20834225

  1. Fracture, failure, and fragmentation

    SciTech Connect

    Dienes, J.K.

    1984-01-01

    Though continuum descriptions of material behavior are useful for many kinds of problems, particularly those involving plastic flow, a more general approach is required when the failure is likely to involve growth and coalescence of a large number of fractures, as in fragmentation. Failures of this kind appear frequently in rapid dynamic processes such as those resulting from impacts and explosions, particularly in the formation of spall fragments. In the first part of this paper an approach to formulating constitutive relations that accounts for the opening, shear and growth of an ensemble of cracks is discussed. The approach also accounts for plastic flow accompanying fragmentation. The resulting constitutive relations have been incorporated into a Lagrangean computer program. In the second part of this paper a theoretical approach to coalescence is described. The simplest formulation makes use of a linear Liouville equation, with crack growth limited by the mean free path of cracks, assumed constant. This approach allows for an anisotropic distribution of cracks. An alternative approach is also described in which the decrease of the mean free path with increasing crack size is accounted for, but the crack distribution is assumed isotropic. A reduction of the governing Liouville equation to an ordinary differential equation of third order is possible, and the result can be used to determine how mean-free-path decreases with increasing crack size.

  2. Nuclear fragmentation measurements for hadrontherapy and space radiation protection

    SciTech Connect

    De Napoli, M.; Agodi, C.; Blancato, A. A.; Cavallaro, M.; Cirrone, G. A. P.; Cuttone, G.; Sardina, D.; Scuderi, V.; Battistoni, G.; Bondi, M.; Cappuzzello, F.; Carbone, D.; Nicolosi, D.; Raciti, G.; Tropea, S.; Giacoppo, F.; Morone, M. C.; Pandola, L.; Rapisarda, E.; Romano, F.; and others

    2013-04-19

    Nuclear fragmentation measurements are necessary in hadrontherapy and space radiation protection, to predict the effects of the ion nuclear interactions within the human body. Nowadays, a very limited set of carbon fragmentation cross sections has been measured and in particular, to our knowledge, no double differential fragmentation cross sections at intermediate energies are available in literature. We have measured the double differential cross sections and the angular distributions of the secondary fragments produced in the {sup 12}C fragmentation at 62 AMeV on a thin carbon target. The experimental data have been also used to benchmark the prediction capability of the Geant4 Monte Carlo code at intermediate energies, where it was never tested before.

  3. Investigation of Fragmentation of Tryptophan Nitrogen Radical Cation

    NASA Astrophysics Data System (ADS)

    Piatkivskyi, Andrii; Happ, Marshall; Lau, Justin Kai-Chi; Siu, K. W. Michael; Hopkinson, Alan C.; Ryzhov, Victor

    2015-08-01

    This work describes investigation of the fragmentation mechanism of tryptophan N-indolyl radical cation, H3N+-TrpN• ( m/ z 204) studied via DFT calculations and several gas-phase experimental techniques. The main fragment ion at m/ z 131, shown to be a mixture of up to four isomers including 3-methylindole (3MI) π-radical cation, was found to undergo further loss of an H atom to yield one of the two isomeric m/ z 130 ions. 3-Methylindole radical cation generated independently (via CID of [CuII(terpy)3MI]•2+) displayed gas-phase reactivity partially similar to that of the m/ z 131 fragment, further confirming our proposed mechanism. CID of deuterated tryptophan N-indolyl radical cation ( m/ z 208) suggested that up to six H atoms are involved in the pathway to formation of the m/ z 131 ion, consistent with hydrogen atom scrambling during CID of protonated Trp.

  4. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    DOE PAGESBeta

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; et al

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

  5. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    SciTech Connect

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

  6. Analysis of neutral oligosaccharides for structural characterization by matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry.

    PubMed

    Ojima, Noriyuki; Masuda, Katsuyoshi; Tanaka, Koichi; Nishimura, Osamu

    2005-03-01

    We have acquired multi-stage mass spectra (MSn) of four branched N-glycans derived from human serum IgG by matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF-MS) in order to demonstrate high sensitivity structural analysis. [M+H]+ and [M+Na]+ ions were detected in the positive mode. The detection limit of [M+Na]+ in MS/MS and MS3 measurements for structural analysis was found to be 100 fmol, better than that for [M+H]+. The [M+H]+ ions subsequently fragmented to produce predominantly a Y series of fragments, whereas [M+Na]+ ions fragmented to give a complex mixture of B and Y ions together with some cross-ring fragments. Three features of MALDI-QIT-CID fragmentation of [M+Na]+ were cleared by the analysis of MS/MS, MS3 and MS4 spectra: (1) the fragment ions resulting from the breaking of a bond are more easily generated than that from multi-bond dissociation; (2) the trimannosyl-chitobiose core is either hardly dissociated, easily ionized or it is easy to break a bond between N-acetylglucosamine and mannose; (3) the fragmentation by loss of only galactose from the non-reducing terminus is not observed. We could determine the existence ratios of candidates for each fragment ion in the MS/MS spectrum of [M+Na]+ by considering these features. These results indicate that MSn analysis of [M+Na]+ ions is more useful for the analysis of complicated oligosaccharide structures than MS/MS analysis of [M+H]+, owing to the higher sensitivity and enhanced structural information. Furthermore, two kinds of glycans, with differing branch structures, could be distinguished by comparing the relative fragment ion abundances in the MS3 spectrum of [M+Na]+. These analyses demonstrate that the MSn technology incorporated in MALDI-QIT-TOF-MS can facilitate the elucidation of structure of complex branched oligosaccharides. PMID:15712371

  7. Hyperthermal Energy Collisions of CF3 + Ions with Modified Surfaces: Surface-Induced Dissociation

    SciTech Connect

    Rezayat, T.; Shukla, A.

    2004-01-01

    Collisions of low-energy ions, especially polyatomic ions, with surfaces have become an active area of research due to their numerous applications in chemistry, physics and material sciences. An interesting aspect of such collisions is the dissociation of ions which has been successfully exploited for the characterization of colliding ions, especially high mass ions from biological molecules. However, detailed studies of the energy transfer and dissociation have been performed only for a few simple systems and hence the mechanism(s) of ions’ excitation and dissociation are not as well understood even for small ions. We have therefore undertaken a study of the dissociation of a small polyatomic ion, CF3+, at several collision energies between 28.8 eV and 159 eV in collision with fluorinated alkyl thiol on gold 111 crystal and a LiF surface. These experiments were performed using a custom built tandem mass spectrometer where the energy and intensity distributions of the scattered fragment ions were measured as a function of the fragment ion mass and scattering angle. In contrast with the previous studies of the dissociation of ethanol and acetone cations where the inelastically scattered primary ions dominated the collision process (up to ~50 eV maximum energy used in those experiments), we did not observe a measurable abundance of inelastically scattered undissociated CF3+ ions at all energies studied here. We observed all fragment ions, CF2+, CF+, F+ and C+ at all energies studied with the relative intensity of the highest energy pathway, C+, increasing with collision energy. Also, the dissociation efficiency decreased significantly as the collision energy was increased from to 159 eV. The energy distributions of nearly all the fragment ions showed two distinct components, one corresponding to the loss of nearly all of the kinetic energy and scattered over a broad angular range while the other corresponding to smaller kinetic energy losses and scattered closer to

  8. Solar abundance of iridium

    PubMed Central

    Drake, Stephen; Aller, Lawrence H.

    1976-01-01

    By a method of spectrum synthesis, which yields log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance, an attempt is made to deduce the solar iridium abundance from one relatively unblended, but fairly weak IrI line, λ 3220.78 Å. If the Corliss-Bozman f-value for this line is adopted, we find log A(Ir) = 0.82 on the scale log A(H) = 12.00. The discordance with the value found from carbonaceous chondrites may arise from faulty f-values or from difficulties arising from line blending in this far ultraviolet domain of the solar spectrum. PMID:16578735

  9. Direct Photo Double Ionization of Water and Subsequent Fragmentation

    NASA Astrophysics Data System (ADS)

    Reedy, D.; Gaire, B.; Gatton, A.; Sartor, J.; Berry, B.; Weller, M.; Bauer, T.; Burzynski, P.; Henrichs, K.; Dorner, R.; Williams, J. B.; Weber, Th.; Landers, A. L.

    2016-05-01

    We have measured and imaged the dissociation of water in the gas phase following direct double photoionization by a 57 eV photon. The dissociation left the dication in a range of several energetically available excited states. The momenta of the resulting dication fragments and photoelectrons were measured in coincidence with Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS). The different states of the dication result in marked differences in photoelectron energies, kinetic energy release, and bond angle at the time of the fragmentation, as well as leaving the neutral oxygen fragment in one of several indirectly observed excited states.

  10. Titan's Topside Ionospheric Composition: Cassini Plasma Spectrometer Ion Mass spectrometer Measurements

    NASA Astrophysics Data System (ADS)

    Sittler, E. C., Jr.; Hartle, R. E.; Ali, A.; Cooper, J. F.; Lipatov, A. S.; Simpson, D. G.; Sarantos, M.; Chornay, D. J.

    2014-12-01

    In [1] the first quantitative evidence of ionospheric outflows (r > 10,000 km) coming from Titan was given using the Cassini Plasma Spectrometer (CAPS) Ion Mass Spectrometer (IMS) data for the T9 flyby. Later in [2] similar outflows were shown for T63 and T75. In [3] evidence for ionospheric outflows for T15 was given and [4] showed evidence of outflows for T41. Normally, the CAPS IMS cannot be used to measure Titan's relatively dense ionosphere because the IMS has high sensitivity to measure the more tenuous plasmas of Saturn's magnetosphere and its detectors will experience count rates beyond their maximum allowed rates, therefore the IMS is configured not to measure the ionospheric plasma. But, whenever there are high altitude Titan wake flybys the ion densities are low enough so the CAPS IMS can measure these ionospheric outflows and their corresponding composition characteristic of the topside ionosphere (i.e., composition freezes in above the exobase) using its unique compositional capabilities. For example, the IMS can distinguish against specific ion types such as hydrocarbon, nitrile and water group ions due fragmentation of molecular ions within the instrument (i.e., incident ions strikes ultra-thin carbon foils at 14.6 kV or higher with exiting fragments such C+,0,-, N+,0, O+,0,-1). The other ionospheric instruments only measure the ion mass-per-charge (M/Q), while the CAPS IMS measures both the ion M/Q and its fragments. Specific attention will be given to such ions as NH4+, N+, O+, CH4+, C2H5+, HCNH+ and C3H7+. These results may impose important constraints upon Titan's ionospheric water group, hydrocarbon and nitrile ion chemistry. Are NH4+ ions present as indicated by INMS at 1100 km altitude and/or water group ions? Our work has concentrated on the T15 flyby. Estimates of the NH4+, N+ and O+ abundances presently have upper values < 20% of the total ion density with actual abundances and their uncertainties to be given. [1] Sittler, E.C. Jr., et al

  11. Fragment-based lead design

    NASA Astrophysics Data System (ADS)

    Filz, O. A.; Poroikov, Vladimir V.

    2012-02-01

    State-of-the-art approaches to the fragment-based design of organic compounds with desired properties are considered. The review covers methods, which are used in different steps of the design, such as computational methods for fragment library design, experimental and computational methods for fragment discovery and methods for the generation of structures of organic compounds. Examples are given of drug candidates, which were constructed using the fragment-based approach. The bibliography includes 156 references.

  12. Overview of nuclear fragmentation models and needs

    NASA Technical Reports Server (NTRS)

    Townsend, L. W.; Cucinotta, F. A.; Wilson, J. W. (Principal Investigator)

    1996-01-01

    It has been known for some time that adequate assessment of spacecraft shield requirements and concomitant estimates of astronauts radiation exposures from galactic cosmic radiation requires accurate, quantitative methods for characterizing these radiation fields as they pass through thick absorbers. The main nuclear interaction processes involved are (1) nuclear elastic and inelastic collisions, and (2) nuclear breakup (fragmentation) and electromagnetic dissociation (EMD). Nuclear fragmentation and EMD are important because they alter the elemental and isotopic composition of the transported radiation fields. At present, there is no suitably accurate theory for predicting nuclear fragmentation cross sections for all collision pairs and energies of interest in space radiation protection. Typical cross-section differences between theory and experiment range from about 25 percent to a factor of two. The resulting errors in transported flux, for high linear energy transfer (LET) particles, are comparble to these cross-section errors. In this overview, theoretical models of heavy ion fragmentation currently used to generate input data bases for cosmic-ray transport and shielding codes are reviewed. Their shortcomings are discussed. Further actions needed to improve their accuracy and generality are presented.

  13. Methane Group Ions in Saturn's Outer Magnetosphere

    NASA Astrophysics Data System (ADS)

    Sittler, Edward C.; Hartle, R. E.; Cooper, J. F.; Johnson, R. E.; Smith, H. T.; Shappirio, M. D.; Simpson, D. J.

    2008-09-01

    In Hartle et al. [2006a,b] they reported evidence of keV methane group ions within Saturn's outer magnetosphere during Cassini's TA Titan flyby. They presented evidence of CH4+ pickup ions within the mass loading region of the magnetospheric interaction with Titan. They also reported that keV water group ions W+ (i.e., O+) were present and dominated the magnetospheric heavy ion composition. These water group ions probably result from the emission of fast neutrals from the Enceladus torus via charge exchange reactions but still gravitationally bound to Saturn [see Johnson et al., 2005 and Sittler et al. 2006] and then become ionized in the outer magnetosphere where the pickup energies are keV. Since O+ and CH4+ have similar mass the primary discriminator is the O- fragment which appears at a different time-of-flight (TOF) than that for mass 16. One way to separate the methane from the O+ is to measure the relative abundance of the mass 16 peak with the O- peak. If there is a methane torus as a consequence of the hydrodynamic model of Strobel [2008], then one expects the presence of CH3+ ions and not CH4+ ions, since the methane dissociates to CH3 before they get ionized. Here we will be reporting on a further search for evidence of methane group ions within Saturn's outer magnetosphere. References: Hartle, R. E., et al., Geophys. Res. Lett., 33, L08201, 2006a Hartle, R. E., et al., Planet. Space Sci., 54, 1211, 2006b Johnson. R.E., et. Astrophys. J. Letts, 644, L137-L139, 2005 Sittler, E. C., Jr., et al., JGR, 111, A09223, 2006 Strobel, D. F., Icarus, 193, 588, [2008

  14. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies

    PubMed Central

    Telonis, Aristeidis G.; Loher, Phillipe; Honda, Shozo; Jing, Yi; Palazzo, Juan; Kirino, Yohei; Rigoutsos, Isidore

    2015-01-01

    We analyzed transcriptomic data from 452 healthy men and women representing five different human populations and two races, and, 311 breast cancer samples from The Cancer Genome Atlas. Our studies revealed numerous constitutive, distinct fragments with overlapping sequences and quantized lengths that persist across dozens of individuals and arise from the genomic loci of all nuclear and mitochondrial human transfer RNAs (tRNAs). Surprisingly, we discovered that the tRNA fragments' length, starting and ending points, and relative abundance depend on gender, population, race and also on amino acid identity, anticodon, genomic locus, tissue, disease, and disease subtype. Moreover, the length distribution of mitochondrially-encoded tRNAs differs from that of nuclearly-encoded tRNAs, and the specifics of these distributions depend on tissue. Notably, tRNA fragments from the same anticodon do not have correlated abundances. We also report on a novel category of tRNA fragments that significantly contribute to the differences we observe across tissues, genders, populations, and races: these fragments, referred to as i-tRFs, are abundant in human tissues, wholly internal to the respective mature tRNA, and can straddle the anticodon. HITS-CLIP data analysis revealed that tRNA fragments are loaded on Argonaute in a cell-dependent manner, suggesting cell-dependent functional roles through the RNA interference pathway. We validated experimentally two i-tRF molecules: the first was found in 21 of 22 tested breast tumor and adjacent normal samples and was differentially abundant between health and disease whereas the second was found in all eight tested breast cancer cell lines. PMID:26325506

  15. Relative Abundance Measurements in Plumes and Interplumes

    NASA Astrophysics Data System (ADS)

    Guennou, C.; Hahn, M.; Savin, D. W.

    2015-07-01

    We present measurements of relative elemental abundances in plumes and interplumes. Plumes are bright, narrow structures in coronal holes that extend along open magnetic field lines far out into the corona. Previous work has found that in some coronal structures the abundances of elements with a low first ionization potential (FIP) <10 eV are enhanced relative to their photospheric abundances. This coronal-to-photospheric abundance ratio, commonly called the FIP bias, is typically 1 for elements with a high-FIP (>10 eV). We have used Extreme Ultraviolet Imaging Spectrometer observations made on 2007 March 13 and 14 over a ≈24 hr period to characterize abundance variations in plumes and interplumes. To assess their elemental composition, we used a differential emission measure analysis, which accounts for the thermal structure of the observed plasma. We used lines from ions of iron, silicon, and sulfur. From these we estimated the ratio of the iron and silicon FIP bias relative to that for sulfur. From the results, we have created FIP-bias-ratio maps. We find that the FIP-bias ratio is sometimes higher in plumes than in interplumes and that this enhancement can be time dependent. These results may help to identify whether plumes or interplumes contribute to the fast solar wind observed in situ and may also provide constraints on the formation and heating mechanisms of plumes.

  16. Virtual fragment preparation for computational fragment-based drug design.

    PubMed

    Ludington, Jennifer L

    2015-01-01

    Fragment-based drug design (FBDD) has become an important component of the drug discovery process. The use of fragments can accelerate both the search for a hit molecule and the development of that hit into a lead molecule for clinical testing. In addition to experimental methodologies for FBDD such as NMR and X-ray Crystallography screens, computational techniques are playing an increasingly important role. The success of the computational simulations is due in large part to how the database of virtual fragments is prepared. In order to prepare the fragments appropriately it is necessary to understand how FBDD differs from other approaches and the issues inherent in building up molecules from smaller fragment pieces. The ultimate goal of these calculations is to link two or more simulated fragments into a molecule that has an experimental binding affinity consistent with the additive predicted binding affinities of the virtual fragments. Computationally predicting binding affinities is a complex process, with many opportunities for introducing error. Therefore, care should be taken with the fragment preparation procedure to avoid introducing additional inaccuracies.This chapter is focused on the preparation process used to create a virtual fragment database. Several key issues of fragment preparation which affect the accuracy of binding affinity predictions are discussed. The first issue is the selection of the two-dimensional atomic structure of the virtual fragment. Although the particular usage of the fragment can affect this choice (i.e., whether the fragment will be used for calibration, binding site characterization, hit identification, or lead optimization), general factors such as synthetic accessibility, size, and flexibility are major considerations in selecting the 2D structure. Other aspects of preparing the virtual fragments for simulation are the generation of three-dimensional conformations and the assignment of the associated atomic point charges

  17. The electron-impact promoted fragmentation of aurone epoxides.

    NASA Technical Reports Server (NTRS)

    Brady, B. A.; O'Sullivan, W. I.; Duffield, A. M.

    1972-01-01

    The mass spectra of six aurone epoxides have been rationalized with the aid of high resolution mass spectrometry and metastable ion evidence. These compounds fragment in a well defined manner and mechanisms are proposed for the formation of their characteristic ions. Some similarity was observed between the mass spectra of 6-methoxyaurone epoxide (II), 4-hydroxy-7-methoxy-3-phenylcoumarin (VII) and 7-methoxyflavonol (IX). The possibility that VII and IX are intermediates in the fragmentation of epoxide II is discussed. Thermal rearrangement of aurone epoxide II was shown to yield the corresponding flavonol IX and coumarin VII.

  18. Core-shell resonant Auger-decay induced fragmentation of glycine molecule

    NASA Astrophysics Data System (ADS)

    Fang, Li; Xiong, Hui; Osipov, Timur; Petrovic, Vladimir; Guehre, Markus; Berrah, Nora

    2015-05-01

    We investigated the fragmentation of glycine molecular ions induced by resonant Auger decay with synchrotron light source. We measured the charge distribution and the kinetic energies of various fragment ions with photon energies at the oxygen and the carbon 1s electron excitation resonance, as well as at photon energies above the K-edge of the oxygen and carbon atoms. We studied the fragmentation pathways using ion-ion coincidence measurement with a velocity map imaging spectrometer. We observed closure of certain fragmentation pathways at the on-resonance photon energy and the opening-up of certain fragmentation pathways by ionization of certain atomic sites. We will present that resonant Auger leads to unique dissociation patterns. Department of Energy, Office of Science, Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences under grant N. DE-FG02-92ER14299.A002 and in part by the National Science Foundation under Grant No. 1404109.

  19. Laser ion source for isobaric heavy ion collider experiment

    NASA Astrophysics Data System (ADS)

    Kanesue, T.; Kumaki, M.; Ikeda, S.; Okamura, M.

    2016-02-01

    Heavy-ion collider experiment in isobaric system is under investigation at Relativistic Heavy Ion Collider. For this experiment, ion source is required to maximize the abundance of the intended isotope. The candidate of the experiment is 96Ru + 96Zr. Since the natural abundance of particular isotope is low and composition of isotope from ion source depends on the composites of the target, an isotope enriched material may be needed as a target. We studied the performance of the laser ion source required for the experiment for Zr ions.

  20. Laser ion source for isobaric heavy ion collider experiment.

    PubMed

    Kanesue, T; Kumaki, M; Ikeda, S; Okamura, M

    2016-02-01

    Heavy-ion collider experiment in isobaric system is under investigation at Relativistic Heavy Ion Collider. For this experiment, ion source is required to maximize the abundance of the intended isotope. The candidate of the experiment is (96)Ru + (96)Zr. Since the natural abundance of particular isotope is low and composition of isotope from ion source depends on the composites of the target, an isotope enriched material may be needed as a target. We studied the performance of the laser ion source required for the experiment for Zr ions. PMID:26931981

  1. Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin

    NASA Astrophysics Data System (ADS)

    Kleinnijenhuis, Anne J.; Mihalca, Romulus; Heeren, Ron M. A.; Heck, Albert J. R.

    2006-07-01

    Doubly protonated ions of the disulfide bond containing nonapeptide hormone oxytocin and oxytocin complexes with different transition metal ions, that have biological relevance under physiological conditions, were subjected to electron capture dissociation (ECD) to probe their structural features in the gas phase. Although, all the ECD spectra were strikingly different, typical ECD behavior was observed for complexes of the nonapeptide hormone oxytocin with Ni2+, Co2+ and Zn2+, i.e., abundant c/z' and a'/y backbone cleavages and ECD characteristic S-S and S-C bond cleavages were observed. We propose that, although in the oxytocin-transition metal ion complexes the metal ions serve as the main initial capture site, the captured electron is transferred to other sites in the complex to form a hydrogen radical, which drives the subsequent typical ECD fragmentations. The complex of oxytocin with Cu2+ displayed noticeably different ECD behavior. The fragment ions were similar to fragment ions typically observed with low-energy collision induced dissociation (CID). We propose that the electrons captured by the oxytocin-Cu2+ complex might be favorably involved in reducing the Cu2+ metal ion to Cu+. Subsequent energy redistribution would explain the observed low-energy CID-type fragmentations. Electron capture resulted also in quite different specific cleavage sites for the complexes of oxytocin with Ni2+, Co2+ and Zn2+. This is an indication for structural differences in these complexes possibly linked to their significantly different biological effects on oxytocin-receptor binding, and suggests that ECD may be used to study subtle structural differences in transition metal ion-peptide complexes.

  2. Tube Fragmentation of Multiple Materials

    SciTech Connect

    Thornhill, T. F.; Chhabildas, L. C.; Vogler, T. J.

    2006-07-28

    In the current study we are developing an experimental fracture material property test method specific to dynamic fragmentation. This test method allows the study of fracture fragmentation in a reproducible laboratory environment under well-controlled loading conditions. Motion and fragmentation of the specimen are diagnosed using framing camera, VISAR and soft recovery methods. Fragmentation properties of several steels, nitinol, tungsten alloy, copper, aluminum, and titanium have been obtained to date. The values for fragmentation toughness, and failure threshold will be reported, as well as effects in these values as the material strain-rate is varied through changes in wall thickness and impact conditions.

  3. Tube fragmentation of multiple materials.

    SciTech Connect

    Thornhill, Tom Finley, III; Vogler, Tracy John; Chhabildas, Lalit Chandra

    2003-07-01

    In the current study we are developing an experimental fracture material property test method specific to dynamic fragmentation. This test method allows the study of fracture fragmentation in a reproducible laboratory environment under well-controlled loading conditions. Motion and fragmentation of the specimen are diagnosed using framing camera, VISAR and soft recovery methods. Fragmentation properties of several steels, nitinol, tungsten alloy, copper, aluminum, and titanium have been obtained to date. The values for fragmentation toughness, and failure threshold will be reported, as well as effects in these values as the material strain-rate is varied through changes in wall thickness and impact conditions.

  4. New Scalings in Nuclear Fragmentation

    SciTech Connect

    Bonnet, E.; Bougault, R.; Galichet, E.; Gagnon-Moisan, F.; Guinet, D.; Lautesse, P.; Marini, P.; Parlog, M.

    2010-10-01

    Fragment partitions of fragmenting hot nuclei produced in central and semiperipheral collisions have been compared in the excitation energy region 4-10 MeV per nucleon where radial collective expansion takes place. It is shown that, for a given total excitation energy per nucleon, the amount of radial collective energy fixes the mean fragment multiplicity. It is also shown that, at a given total excitation energy per nucleon, the different properties of fragment partitions are completely determined by the reduced fragment multiplicity (i.e., normalized to the source size). Freeze-out volumes seem to play a role in the scalings observed.

  5. Scaling behavior of fragment shapes.

    PubMed

    Kun, F; Wittel, F K; Herrmann, H J; Kröplin, B H; Måløy, K J

    2006-01-20

    We present an experimental and theoretical study of the shape of fragments generated by explosive and impact loading of closed shells. Based on high speed imaging, we have determined the fragmentation mechanism of shells. Experiments have shown that the fragments vary from completely isotropic to highly anisotropic elongated shapes, depending on the microscopic cracking mechanism of the shell. Anisotropic fragments proved to have a self-affine character described by a scaling exponent. The distribution of fragment shapes exhibits a power-law decay. The robustness of the scaling laws is illustrated by a stochastic hierarchical model of fragmentation. Our results provide a possible improvement of the representation of fragment shapes in models of space debris. PMID:16486594

  6. Abundance of field galaxies

    NASA Astrophysics Data System (ADS)

    Klypin, Anatoly; Karachentsev, Igor; Makarov, Dmitry; Nasonova, Olga

    2015-12-01

    We present new measurements of the abundance of galaxies with a given circular velocity in the Local Volume: a region centred on the Milky Way Galaxy and extending to distance ˜10 Mpc. The sample of ˜750 mostly dwarf galaxies provides a unique opportunity to study the abundance and properties of galaxies down to absolute magnitudes MB ≈ -10 and virial masses M_vir= 109{ M_{⊙}}. We find that the standard Λ cold dark matter (ΛCDM) model gives remarkably accurate estimates for the velocity function of galaxies with circular velocities V ≳ 70 kms-1 and corresponding virial masses M_vir≳ 5× 10^{10}{ M_{⊙}}, but it badly fails by overpredicting ˜5 times the abundance of large dwarfs with velocities V = 30-40 kms-1. The warm dark matter (WDM) models cannot explain the data either, regardless of mass of WDM particle. Just as in previous observational studies, we find a shallow asymptotic slope dN/dlog V ∝ Vα, α ≈ -1 of the velocity function, which is inconsistent with the standard ΛCDM model that predicts the slope α = -3. Though reminiscent to the known overabundance of satellite problem, the overabundance of field galaxies is a much more difficult problem. For the standard ΛCDM model to survive, in the 10 Mpc radius of the Milky Way there should be 1000 not yet detected galaxies with virial mass M_vir≈ 10^{10}{ M_{⊙}}, extremely low surface brightness and no detectable H I gas. So far none of this type of galaxies have been discovered.

  7. Solar abundances as derived from solar energetic particles

    NASA Technical Reports Server (NTRS)

    Stone, E. C.

    1989-01-01

    Recent studies have shown that there are well defined average abundances of heavy (Z above 2) solar energetic particles (SEPs), with variations in the acceleration and propagation producing a systematic flare-to-flare fractionation that depends on the charge per unit mass of the ion. Correcting the average SEP abundances for this fractionation yields SEP-derived coronal abundances for 20 elements. High-resolution SEP studies have also provided isotopic abundances for five elements. SEP-derived abundances indicate that elements with high first ionization potentials (greater than 10 eV) are depleted in the corona relative to the photosphere and provide new information on the solar abundance of C and Ne-22.

  8. Nuclear fragmentation database for GCR transport code development

    NASA Astrophysics Data System (ADS)

    Zeitlin, C.; Guetersloh, S.; Heilbronn, L.; Miller, J.; Fukumura, A.; Iwata, Y.; Murakami, T.; Sihver, L.

    2010-09-01

    A critical need for NASA is the ability to accurately model the transport of heavy ions in the Galactic Cosmic Rays (GCR) through matter, including spacecraft walls, equipment racks, etc. Nuclear interactions are of great importance in the GCR transport problem, as they can cause fragmentation of the incoming ion into lighter ions. Since the radiation dose delivered by a particle is proportional to the square of (charge/velocity), fragmentation reduces the dose delivered by incident ions. The other mechanism by which dose can be reduced is ionization energy loss, which can lead to some particles stopping in the shielding. This is the conventional notion of shielding, but it is not applicable to human spaceflight since the particles in the GCR tend to be too energetic to be stopped in the relatively thin shielding that is possible within payload mass constraints. Our group has measured a large number of fragmentation cross sections, intended to be used as input to, or for validation of, NASA's radiation transport models. A database containing over 200 charge-changing cross sections and over 2000 fragment production cross sections has been compiled. In this report, we examine in detail the contrast between fragment measurements at large acceptance and small acceptance. We use output from the PHITS Monte Carlo code to test our assumptions using as an example 40Ar data (and simulated data) at a beam energy of 650 MeV/nucleon. We also present preliminary analysis in which isotopic resolution was attained for beryllium fragments produced by beams of 10B and 11B. Future work on the experimental data set will focus on extracting and interpreting production cross sections for light fragments.

  9. Late embryogenesis abundant proteins

    PubMed Central

    Olvera-Carrillo, Yadira; Reyes, José Luis

    2011-01-01

    Late Embryogenesis Abundant (LEA) proteins accumulate at the onset of seed desiccation and in response to water deficit in vegetative plant tissues. The typical LEA proteins are highly hydrophilic and intrinsically unstructured. They have been classified in different families, each one showing distinctive conserved motifs. In this manuscript we present and discuss some of the recent findings regarding their role in plant adaptation to water deficit, as well as those concerning to their possible function, and how it can be related to their intrinsic structural flexibility. PMID:21447997

  10. Fragment oriented molecular shapes.

    PubMed

    Hain, Ethan; Camacho, Carlos J; Koes, David Ryan

    2016-05-01

    Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here, we introduce and evaluate fragment oriented molecular shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of shape constraints, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search. PMID:27085751

  11. Comet 67P/Churyumov-Gerasimenko: Close-up on Dust Particle Fragments

    NASA Astrophysics Data System (ADS)

    Hilchenbach, M.; Kissel, J.; Langevin, Y.; Briois, C.; von Hoerner, H.; Koch, A.; Schulz, R.; Silén, J.; Altwegg, K.; Colangeli, L.; Cottin, H.; Engrand, C.; Fischer, H.; Glasmachers, A.; Grün, E.; Haerendel, G.; Henkel, H.; Höfner, H.; Hornung, K.; Jessberger, E. K.; Lehto, H.; Lehto, K.; Raulin, F.; Le Roy, L.; Rynö, J.; Steiger, W.; Stephan, T.; Thirkell, L.; Thomas, R.; Torkar, K.; Varmuza, K.; Wanczek, K.-P.; Altobelli, N.; Baklouti, D.; Bardyn, A.; Fray, N.; Krüger, H.; Ligier, N.; Lin, Z.; Martin, P.; Merouane, S.; Orthous-Daunay, F. R.; Paquette, J.; Revillet, C.; Siljeström, S.; Stenzel, O.; Zaprudin, B.

    2016-01-01

    The COmetary Secondary Ion Mass Analyser instrument on board ESA's Rosetta mission has collected dust particles in the coma of comet 67P/Churyumov-Gerasimenko. During the early-orbit phase of the Rosetta mission, particles and particle agglomerates have been imaged and analyzed in the inner coma at distances between 100 km and 10 km off the cometary nucleus and at more than 3 AU from the Sun. We identified 585 particles of more than 14 μm in size. The particles are collected at low impact speeds and constitute a sample of the dust particles in the inner coma impacting and fragmenting on the targets. The sizes of the particles range from 14 μm up to sub-millimeter sizes and the differential dust flux size distribution is fitted with a power law exponent of -3.1. After impact, the larger particles tend to stick together, spread out or consist of single or a group of clumps, and the flocculent morphology of the fragmented particles is revealed. The elemental composition of the dust particles is heterogeneous and the particles could contain typical silicates like olivine and pyroxenes, as well as iron sulfides. The sodium to iron elemental ratio is enriched with regard to abundances in CI carbonaceous chondrites by a factor from ˜1.5 to ˜15. No clear evidence for organic matter has been identified. The composition and morphology of the collected dust particles appear to be similar to that of interplanetary dust particles.

  12. Intranuclear cascade with emission of light fragment code implemented in the transport code system PHITS

    NASA Astrophysics Data System (ADS)

    Sawada, Y.; Uozumi, Y.; Nogamine, S.; Yamada, T.; Iwamoto, Y.; Sato, T.; Niita, K.

    2012-11-01

    The Intranuclear Cascade with Emission of Light Fragment (INC-ELF) code has been developed and implemented in the Particle and Heavy Ion Transport code System (PHITS). The INC-ELF code explicitly includes nucleon correlations within the framework of the INC model to describe light fragment emissions from nuclear spallation reactions by using the model in Phys. Rev. C 84, (2011) 064617. In addition to the degrees of freedom of nucleons, the developed code also accounts for pions, Δs, and N∗s, and can cover energy ranges up to 3 GeV. The predictive capabilities of the ELF/PHITS system have been verified through comparison with a diverse set of experimental observations. In particular, the verification was conducted with abundant double-differential cross-section data covering a wide range of reactions (e.g., (p, p'x), (p, nx), (p, dx), (p, 3Hex), (p, αx) and (p, πx) reactions) over a wide energy range (between 400 MeV and 1.5 GeV). As a result, our ELF/PHITS code has demonstrated strong predictive capability for all of these data, although areas requiring future study remain due to the lack of experimental data on high-energy cluster production.

  13. Flare Plasma Iron Abundance

    NASA Technical Reports Server (NTRS)

    Dennis, Brian R.; Dan, Chau; Jain, Rajmal; Schwartz, Richard A.; Tolbert, Anne K.

    2008-01-01

    The equivalent width of the iron-line complex at 6.7 keV seen in flare X-ray spectra suggests that the iron abundance of the hottest plasma at temperatures >approx.10 MK may sometimes be significantly lower than the nominal coronal abundance of four times the photospheric value that is commonly assumed. This conclusion is based on X-ray spectral observations of several flares seen in common with the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Solar X-ray Spectrometer (SOXS) on the second Indian geostationary satellite, GSAT-2. The implications of this will be discussed as it relates to the origin of the hot flare plasma - either plasma already in the corona that is directly heated during the flare energy release process or chromospheric plasma that is heated by flare-accelerated particles and driven up into the corona. Other possible explanations of lower-than-expected equivalent widths of the iron-line complex will also be discussed.

  14. Geographic variation in cowbird distribution, abundance, and parasitism

    USGS Publications Warehouse

    Morrison, M.L.; Hahn, D.C.

    2002-01-01

    We evaluated geographical patterns in the abundance and distribution of Brown-headed Cowbirds (Molothrus ater), and in the frequency of cowbird parasitism, across North America in relation to habitat fragmentation. We found no distinctive parasitism patterns at the national or even regional scales, but the species is most abundant in the Great Plains, the heart of their original range, and least common in the southeastern U.S. This situation is dynamic, because both the Brown-headed and two other cowbird species are actively expanding their ranges in the southern U.S. We focused almost entirely in this paper on the Brown-headed Cowbird, because it is the only endemic North American cowbird, its distribution is much wider, and it has been much more intensively studied. We determined that landscape is the most meaningful unit of scale for comparing cowbird parasitism patterns as, for example, in comparisons of northeastern and central hardwood forests within agricultural matrices, and suburbanized areas versus western coniferous forests. We concluded that cowbird parasitism patterns were broadly similar within all landscapes. Even comparisons between prominently dissimilar landscapes, such as hardwoods in agriculture and suburbia versus coniferous forest, display a striking similarity in the responses of cowbirds. Our review clearly indicated that proximity of feeding areas is the key factor influencing presence and parasitism patterns within the landscape. We considered intensity of landscape fragmentation from forest-dominated landscapes altered in a forest management context to fragmentation characterized by mixed suburbanization or agricultural development. Our review consistently identified an inverse relationship between extent of forest cover across the landscape and cowbird presence. Invariably, the variation seen in parasitism frequencies within a region was at least partially explained as a response to changes in forest cover. The most salient geographic

  15. Bird communities in two fragments of Cerrado in Itirapina, Brazil.

    PubMed

    Telles, M; Dias, M M

    2010-08-01

    The Cerrado domain is a mosaic of vegetation types at the local scale, and this environmental heterogeneity leads to high regional bird diversity. Therefore, we aimed to survey quantitative and qualitatively the bird fauna of two fragments of Cerrado and to compare them with an adjacent protected area (Estação Ecológica de Itirapina), in order to assess the heterogeneity of bird diversity in the region. The present study was conducted during 12 months from October 2006 to September 2007 in the municipality of Itirapina, Southeastern Brazil. Altogether we recorded 210 bird species. Fifty-six of them had never been detected in Estação Ecológica de Itirapina, and eleven species are new records for the whole Itirapina region. The list also includes six species that are endangered in Sao Paulo State and five endemic species of the Cerrado domain. Most species were recorded in less than 50% of the visits and exhibited low relative abundance. Primarily insectivorous species were the most common, followed by omnivores. Frugivorous birds were poorly represented. Carnivores were more abundant than usually observed in fragments. The similarity among fragments was higher than between fragments and the protected area. Considering the vegetation heterogeneity in the Cerrado domain, our results reinforce the importance of conserving fragments in order to sample this diversity. PMID:20730340

  16. HZEFRG1 - SEMIEMPIRICAL NUCLEAR FRAGMENTATION MODEL

    NASA Technical Reports Server (NTRS)

    Townsend, L. W.

    1994-01-01

    The high charge and energy (HZE), Semiempirical Nuclear Fragmentation Model, HZEFRG1, was developed to provide a computationally efficient, user-friendly, physics-based program package for generating nuclear fragmentation databases. These databases can then be used in radiation transport applications such as space radiation shielding and dosimetry, cancer therapy with laboratory heavy ion beams, and simulation studies of detector design in nuclear physics experiments. The program provides individual element and isotope production cross sections for the breakup of high energy heavy ions by the combined nuclear and Coulomb fields of the interacting nuclei. The nuclear breakup contributions are estimated using an energy-dependent abrasion-ablation model of heavy ion fragmentation. The abrasion step involves removal of nucleons by direct knockout in the overlap region of the colliding nuclei. The abrasions are treated on a geometric basis and uniform spherical nuclear density distributions are assumed. Actual experimental nuclear radii obtained from tabulations of electron scattering data are incorporated. Nuclear transparency effects are included by using an energy-dependent, impact-parameter-dependent average transmission factor for the projectile and target nuclei, which accounts for the finite mean free path of nucleons in nuclear matter. The ablation step, as implemented by Bowman, Swiatecki, and Tsang (LBL report no. LBL-2908, July 1973), was treated as a single-nucleon emission for every 10 MeV of excitation energy. Fragmentation contributions from electromagnetic dissociation (EMD) processes, arising from the interacting Coulomb fields, are estimated by using the Weiszacker-Williams theory, extended to include electric dipole and electric quadrupole contributions to one-nucleon removal cross sections. HZEFRG1 consists of a main program, seven function subprograms, and thirteen subroutines. Each is fully commented and begins with a brief description of its

  17. Photodissociation at various wavelengths: fragmentation studies of oxazine 170 using nanosecond laser pulses.

    PubMed

    Gernert, Claus; Grotemeyer, Jürgen

    2015-01-01

    The fragmentation of oxazine 170, a rhodamine-type dye, has been investigated by means of collisions and photodissociation with visible and ultraviolet radiation in a Fourier transform ion cyclotron resonance mass spectrometer. Because of an improved experimental setup, the photodissociation processes of stored ions are measured with high intensity with respect to the absorbed photons. By isotope labelling and quantum chemical calculations, the various fragmentation mechanisms are investigated. It is shown that the most important intermediate ion structure leading to the various ionic products is an even-electron azarine cation. Several new fragmentation mechanisms have been unveiled for the first time. PMID:26307739

  18. Comparison of Data Acquisition Strategies on Quadrupole Ion Trap Instrumentation for Shotgun Proteomics

    NASA Astrophysics Data System (ADS)

    Canterbury, Jesse D.; Merrihew, Gennifer E.; MacCoss, Michael J.; Goodlett, David R.; Shaffer, Scott A.

    2014-12-01

    The most common data collection in shotgun proteomics is via data-dependent acquisition (DDA), a process driven by an automated instrument control routine that directs MS/MS acquisition from the highest abundant signals to the lowest. An alternative to DDA is data-independent acquisition (DIA), a process in which a specified range in m/ z is fragmented without regard to prioritization of a precursor ion or its relative abundance in the mass spectrum, thus potentially offering a more comprehensive analysis of peptides than DDA. In this work, we evaluate both DDA and DIA on three different linear ion trap instruments: an LTQ, an LTQ modified with an electrodynamic ion funnel, and an LTQ Velos. These instruments represent both older (LTQ) and newer (LTQ Velos) ion trap designs (i.e., linear versus dual ion traps, respectively), and allow direct comparison of peptide identifications using both DDA and DIA analysis. Further, as the LTQ Velos has an enhanced "S-lens" ion guide to improve ion flux, we found it logical to determine if the former LTQ model could be leveraged by improving sensitivity by modifying with an electrodynamic ion guide of significantly different design to the S-lens. We find that the ion funnel enabled LTQ identifies more proteins in the insoluble fraction of a yeast lysate than the other two instruments in DIA mode, whereas the faster scanning LTQ Velos performs better in DDA mode. We explore reasons for these results, including differences in scan speed, source ion optics, and linear ion trap design.

  19. Oxygen abundance and convection

    NASA Astrophysics Data System (ADS)

    Van't Veer, C.; Cayrel, R.

    The triplet IR lines of O I near 777 nm are computed with the Kurucz's code, modified to accept several convection models. The program has been run with the MLT algorithm, with l/H = 1.25 and 0.5, and with the Canuto-Mazzitelli and Canuto-Goldman-Mazzitelli approaches, on a metal-poor turnoff-star model atmosphere with Teff=6200 K, log g = 4.3, [Fe/H]= -1.5. The results show that the differences in equivalent widths for the 4 cases do not exceed 2 per cent (0.3 mA). The convection treatment is therefore not an issue for the oxygen abundance derived from the permitted lines.

  20. The Multiple Impacts of Tropical Forest Fragmentation on Arthropod Biodiversity and on their Patterns of Interactions with Host Plants

    PubMed Central

    Benítez-Malvido, Julieta; Dáttilo, Wesley; Martínez-Falcón, Ana Paola; Durán-Barrón, César; Valenzuela, Jorge; López, Sara; Lombera, Rafael

    2016-01-01

    Tropical rain forest fragmentation affects biotic interactions in distinct ways. Little is known, however, about how fragmentation affects animal trophic guilds and their patterns of interactions with host plants. In this study, we analyzed changes in biotic interactions in forest fragments by using a multitrophic approach. For this, we classified arthropods associated with Heliconia aurantiaca herbs into broad trophic guilds (omnivores, herbivores and predators) and assessed the topological structure of intrapopulation plant-arthropod networks in fragments and continuous forests. Habitat type influenced arthropod species abundance, diversity and composition with greater abundance in fragments but greater diversity in continuous forest. According to trophic guilds, coleopteran herbivores were more abundant in continuous forest and overall omnivores in fragments. Continuous forest showed a greater diversity of interactions than fragments. Only in fragments, however, did the arthropod community associated with H aurantiaca show a nested structure, suggesting novel and/or opportunistic host-arthropod associations. Plants, omnivores and predators contributed more to nestedness than herbivores. Therefore, Heliconia-arthropod network properties do not appear to be maintained in fragments mainly caused by the decrease of herbivores. Our study contributes to the understanding of the impact of fragmentation on the structure and dynamics of multitrophic arthropod communities associated with a particular plant species of the highly biodiverse tropical forests. Nevertheless, further replication of study sites is needed to strengthen the conclusion that forest fragmentation negatively affects arthropod assemblages. PMID:26731271

  1. The Multiple Impacts of Tropical Forest Fragmentation on Arthropod Biodiversity and on their Patterns of Interactions with Host Plants.

    PubMed

    Benítez-Malvido, Julieta; Dáttilo, Wesley; Martínez-Falcón, Ana Paola; Durán-Barrón, César; Valenzuela, Jorge; López, Sara; Lombera, Rafael

    2016-01-01

    Tropical rain forest fragmentation affects biotic interactions in distinct ways. Little is known, however, about how fragmentation affects animal trophic guilds and their patterns of interactions with host plants. In this study, we analyzed changes in biotic interactions in forest fragments by using a multitrophic approach. For this, we classified arthropods associated with Heliconia aurantiaca herbs into broad trophic guilds (omnivores, herbivores and predators) and assessed the topological structure of intrapopulation plant-arthropod networks in fragments and continuous forests. Habitat type influenced arthropod species abundance, diversity and composition with greater abundance in fragments but greater diversity in continuous forest. According to trophic guilds, coleopteran herbivores were more abundant in continuous forest and overall omnivores in fragments. Continuous forest showed a greater diversity of interactions than fragments. Only in fragments, however, did the arthropod community associated with H aurantiaca show a nested structure, suggesting novel and/or opportunistic host-arthropod associations. Plants, omnivores and predators contributed more to nestedness than herbivores. Therefore, Heliconia-arthropod network properties do not appear to be maintained in fragments mainly caused by the decrease of herbivores. Our study contributes to the understanding of the impact of fragmentation on the structure and dynamics of multitrophic arthropod communities associated with a particular plant species of the highly biodiverse tropical forests. Nevertheless, further replication of study sites is needed to strengthen the conclusion that forest fragmentation negatively affects arthropod assemblages. PMID:26731271

  2. Chapter 4 embedded metal fragments.

    PubMed

    Kalinich, John F; Vane, Elizabeth A; Centeno, Jose A; Gaitens, Joanna M; Squibb, Katherine S; McDiarmid, Melissa A; Kasper, Christine E

    2014-01-01

    The continued evolution of military munitions and armor on the battlefield, as well as the insurgent use of improvised explosive devices, has led to embedded fragment wounds containing metal and metal mixtures whose long-term toxicologic and carcinogenic properties are not as yet known. Advances in medical care have greatly increased the survival from these types of injuries. Standard surgical guidelines suggest leaving embedded fragments in place, thus individuals may carry these retained metal fragments for the rest of their lives. Nursing professionals will be at the forefront in caring for these wounded individuals, both immediately after the trauma and during the healing and rehabilitation process. Therefore, an understanding of the potential health effects of embedded metal fragment wounds is essential. This review will explore the history of embedded fragment wounds, current research in the field, and Department of Defense and Department of Veterans Affairs guidelines for the identification and long-term monitoring of individuals with embedded fragments. PMID:25222538

  3. Diverse Effects of a Seven-Year Experimental Grassland Fragmentation on Major Invertebrate Groups.

    PubMed

    Braschler, Brigitte; Baur, Bruno

    2016-01-01

    Habitat fragmentation is a major driver of biodiversity loss, but observed effects vary and may depend on the group examined. Time since fragmentation may explain some differences between taxonomical groups, as some species and thus species composition respond with a delay to changes in their environment. Impacts of drivers of global change may thus be underestimated in short-term studies. In our study we experimentally fragmented nutrient-poor dry calcareous grasslands and studied the response of species richness, individual density and species composition of various groups of invertebrates (gastropods, ants, ground beetles, rove beetles, orthoptera, spiders, woodlice) in 12 small (1.5 m * 1.5 m) and 12 large (4.5 m * 4.5 m) fragments and their corresponding control plots after 7 years. We further examined responses to fragmentation in relation to body size and habitat preferences. Responses to fragmentation varied between taxonomical groups. While spider species richness and individual density were lower in fragments, the opposite was true for an orthopteran species and woodlice. Species composition and β-diversity differed between fragments and control plots for some groups. However, the interaction treatment*plot size was rarely significant. Species with high occupancy rates in undisturbed control plots responded more negatively to the fragmentation, while species with large body size were relatively more abundant in fragments in some groups. No effect of the fragmentation was found for ants, which may have the longest lag times because of long-lived colonies. However, relationships between abundance and the species' preferences for environmental factors affected by edge effects indicate that ant diversity too may be affected in the longer-term. Our results show the importance of considering different groups in conservation management in times of widespread fragmentation of landscapes. While species richness may respond slowly, changes in abundance related to

  4. Does Tropical Forest Fragmentation Increase Long-Term Variability of Butterfly Communities?

    PubMed Central

    Leidner, Allison K.; Haddad, Nick M.; Lovejoy, Thomas E.

    2010-01-01

    Habitat fragmentation is a major driver of biodiversity loss. Yet, the overall effects of fragmentation on biodiversity may be obscured by differences in responses among species. These opposing responses to fragmentation may be manifest in higher variability in species richness and abundance (termed hyperdynamism), and in predictable changes in community composition. We tested whether forest fragmentation causes long-term hyperdynamism in butterfly communities, a taxon that naturally displays large variations in species richness and community composition. Using a dataset from an experimentally fragmented landscape in the central Amazon that spanned 11 years, we evaluated the effect of fragmentation on changes in species richness and community composition through time. Overall, adjusted species richness (adjusted for survey duration) did not differ between fragmented forest and intact forest. However, spatial and temporal variation of adjusted species richness was significantly higher in fragmented forests relative to intact forest. This variation was associated with changes in butterfly community composition, specifically lower proportions of understory shade species and higher proportions of edge species in fragmented forest. Analysis of rarefied species richness, estimated using indices of butterfly abundance, showed no differences between fragmented and intact forest plots in spatial or temporal variation. These results do not contradict the results from adjusted species richness, but rather suggest that higher variability in butterfly adjusted species richness may be explained by changes in butterfly abundance. Combined, these results indicate that butterfly communities in fragmented tropical forests are more variable than in intact forest, and that the natural variability of butterflies was not a buffer against the effects of fragmentation on community dynamics. PMID:20224772

  5. Does tropical forest fragmentation increase long-term variability of butterfly communities?

    PubMed

    Leidner, Allison K; Haddad, Nick M; Lovejoy, Thomas E

    2010-01-01

    Habitat fragmentation is a major driver of biodiversity loss. Yet, the overall effects of fragmentation on biodiversity may be obscured by differences in responses among species. These opposing responses to fragmentation may be manifest in higher variability in species richness and abundance (termed hyperdynamism), and in predictable changes in community composition. We tested whether forest fragmentation causes long-term hyperdynamism in butterfly communities, a taxon that naturally displays large variations in species richness and community composition. Using a dataset from an experimentally fragmented landscape in the central Amazon that spanned 11 years, we evaluated the effect of fragmentation on changes in species richness and community composition through time. Overall, adjusted species richness (adjusted for survey duration) did not differ between fragmented forest and intact forest. However, spatial and temporal variation of adjusted species richness was significantly higher in fragmented forests relative to intact forest. This variation was associated with changes in butterfly community composition, specifically lower proportions of understory shade species and higher proportions of edge species in fragmented forest. Analysis of rarefied species richness, estimated using indices of butterfly abundance, showed no differences between fragmented and intact forest plots in spatial or temporal variation. These results do not contradict the results from adjusted species richness, but rather suggest that higher variability in butterfly adjusted species richness may be explained by changes in butterfly abundance. Combined, these results indicate that butterfly communities in fragmented tropical forests are more variable than in intact forest, and that the natural variability of butterflies was not a buffer against the effects of fragmentation on community dynamics. PMID:20224772

  6. Diverse Effects of a Seven-Year Experimental Grassland Fragmentation on Major Invertebrate Groups

    PubMed Central

    Braschler, Brigitte; Baur, Bruno

    2016-01-01

    Habitat fragmentation is a major driver of biodiversity loss, but observed effects vary and may depend on the group examined. Time since fragmentation may explain some differences between taxonomical groups, as some species and thus species composition respond with a delay to changes in their environment. Impacts of drivers of global change may thus be underestimated in short-term studies. In our study we experimentally fragmented nutrient-poor dry calcareous grasslands and studied the response of species richness, individual density and species composition of various groups of invertebrates (gastropods, ants, ground beetles, rove beetles, orthoptera, spiders, woodlice) in 12 small (1.5 m * 1.5 m) and 12 large (4.5 m * 4.5 m) fragments and their corresponding control plots after 7 years. We further examined responses to fragmentation in relation to body size and habitat preferences. Responses to fragmentation varied between taxonomical groups. While spider species richness and individual density were lower in fragments, the opposite was true for an orthopteran species and woodlice. Species composition and β-diversity differed between fragments and control plots for some groups. However, the interaction treatment*plot size was rarely significant. Species with high occupancy rates in undisturbed control plots responded more negatively to the fragmentation, while species with large body size were relatively more abundant in fragments in some groups. No effect of the fragmentation was found for ants, which may have the longest lag times because of long-lived colonies. However, relationships between abundance and the species’ preferences for environmental factors affected by edge effects indicate that ant diversity too may be affected in the longer-term. Our results show the importance of considering different groups in conservation management in times of widespread fragmentation of landscapes. While species richness may respond slowly, changes in abundance related

  7. Aromatic organosulfates in atmospheric aerosols: synthesis, characterization, and abundance

    PubMed Central

    Staudt, Sean; Kundu, Shuvashish; Lehmler, Hans-Joachim; He, Xianran; Cui, Tianqu; Lin, Ying-Hsuan; Kristensen, Kasper; Glasius, Marianne; Zhang, Xiaolu; Weber, Rodney J.; Surratt, Jason D.; Stone1, Elizabeth A.

    2014-01-01

    Aromatic organosulfates are identified and quantified in fine particulate matter (PM2.5) from Lahore, Pakistan, Godavari, Nepal, and Pasadena, California. To support detection and quantification, authentic standards of phenyl sulfate, benzyl sulfate, 3-and 4-methylphenyl sulfate and 2-, 3-, and 4-methylbenzyl sulfate were synthesized. Authentic standards and aerosol samples were analyzed by ultra-performance liquid chromatography (UPLC) coupled to negative electrospray ionization (ESI) quadrupole time-of-flight (ToF) mass spectrometry. Benzyl sulfate was present in all three locations at concentrations ranging from 4 – 90 pg m−3. Phenyl sulfate, methylphenyl sulfates and methylbenzyl sulfates were observed intermittently with abundances of 4 pg m−3, 2-31 pg m−3, 109 pg m−3, respectively. Characteristic fragment ions of aromatic organosulfates include the sulfite radical (•SO3−, m/z 80) and the sulfate radical (•SO4−,m/z 96). Instrumental response factors of phenyl and benzyl sulfates varied by a factor of 4.3, indicating that structurally-similar organosulfates may have significantly different instrumental responses and highlighting the need to develop authentic standards for absolute quantitation organosulfates. In an effort to better understand the sources of aromatic organosulfates to the atmosphere, chamber experiments with the precursor toluene were conducted under conditions that form biogenic organosulfates. Aromatic organosulfates were not detected in the chamber samples, suggesting that they form through different pathways, have different precursors (e.g. naphthalene or methylnaphthalene), or are emitted from primary sources. PMID:24976783

  8. NUCFRG2: An evaluation of the semiempirical nuclear fragmentation database

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Tripathi, R. K.; Cucinotta, F. A.; Shinn, J. L.; Badavi, F. F.; Chun, S. Y.; Norbury, J. W.; Zeitlin, C. J.; Heilbronn, L.; Miller, J.

    1995-01-01

    A semiempirical abrasion-ablation model has been successful in generating a large nuclear database for the study of high charge and energy (HZE) ion beams, radiation physics, and galactic cosmic ray shielding. The cross sections that are generated are compared with measured HZE fragmentation data from various experimental groups. A research program for improvement of the database generator is also discussed.

  9. Recent results from the Argonne Fragment Mass Analyzer

    SciTech Connect

    Davids, C.N.; Back, B.; Carpenter, M.P.; Henderson, D.J.; Henry, R.G.; Janssens, R.V.F.; Khoo, T.L.; Lauritsen, T.; Liang, Y.; Bindra, K. |; Chung, W. |; Soramel, F. |; Bearden, I.G.; Daly, P.J.; Fornal, B.; Grabowski, Z.W.; Mayer, R.H.; Nisius, D.; Broda, R. |; Bingham, C.R.; Moltz, D.M.; Ramayya, A.V.; Robertson, J.D.; Scarlassara, F.; Spolaore, P.; Toth, K.S.; Walters, W.B.

    1992-12-31

    The Fragment Mass Analyzer (FMA) at the ATLAS accelerator has been operational for about one year. During that period a number of test runs and experiments have been carried out. The test runs have verified that the ion optics of the FMA are essentially as calculated. A brief facility description is followed by recent experimental results.

  10. Recent results from the Argonne Fragment Mass Analyzer

    SciTech Connect

    Davids, C.N.; Back, B.; Carpenter, M.P.; Henderson, D.J.; Henry, R.G.; Janssens, R.V.F.; Khoo, T.L.; Lauritsen, T.; Liang, Y. ); Bindra, K. Vanderbilt Univ., Nashville, TN ); Chung, W. Notre Dame Univ., IN ); Soramel, F. (Argonne National Lab., IL (

    1992-01-01

    The Fragment Mass Analyzer (FMA) at the ATLAS accelerator has been operational for about one year. During that period a number of test runs and experiments have been carried out. The test runs have verified that the ion optics of the FMA are essentially as calculated. A brief facility description is followed by recent experimental results.

  11. Percolation Theory for the Distribution and Abundance of Species

    NASA Astrophysics Data System (ADS)

    He, Fangliang; Hubbell, Stephen P.

    2003-11-01

    We develop and test new models that unify the mathematical relationships among the abundance of a species, the spatial dispersion of the species, the number of patches occupied by the species, the edge length of the occupied patches, and the scale on which the distribution of species is mapped. The models predict that species distributions will exhibit percolation critical thresholds, i.e., critical population abundances at which the fragmented patches (as measured by the number of patches and edge length) start to coalesce to form large patches.

  12. Detection and sequencing of Okazaki fragments in S. cerevisiae

    PubMed Central

    Smith, Duncan J.; Yadav, Tejas; Whitehouse, Iestyn

    2016-01-01

    SUMMARY We have previously demonstrated that lagging-strand synthesis in budding yeast is coupled with chromatin assembly on newly synthesized DNA. Using a strain of S. cerevisiae in which DNA ligase I can be conditionally depleted, we can enrich and purify Okazaki fragments. We delineate a method to extract, end-label and visualize Okazaki fragments using denaturing agarose gel electrophoresis. Furthermore, we describe an ion-exchange chromatographic method for purification of fragments and preparation of strand-specific sequencing libraries. Deep sequencing of Okazaki fragments generates a comprehensive, genomic map of DNA synthesis, starting from a single asynchronous culture. Altogether this approach represents a tractable system to investigate key aspects of DNA replication and chromatin assembly. PMID:25916711

  13. Time sequence and time scale of intermediate mass fragment emission

    SciTech Connect

    De Filippo, E.; Pagano, A.; Cardella, G.; Lanzano, G.; Papa, M.; Pirrone, S.; Politi, G.; Wilczynski, J.

    2005-04-01

    Semiperipheral collisions in the {sup 124}Sn+{sup 64}Ni reaction at 35 MeV/nucleon were studied using the forward part of the Charged Heavy Ion Mass and Energy Resolving Array. Nearly completely determined ternary events involving projectilelike fragments (PLF), targetlike fragments (TLF), and intermediate mass fragments (IMF) were selected. A new method of studying the reaction mechanism, focusing on the analysis of the correlations between relative velocities in the IMF+PLF and IMF+TLF subsystems, is proposed. The relative velocity correlations provide information on the time sequence and time scale of the neck fragmentation processes leading to production of IMFs. It is shown that the majority of light IMFs are produced within 40-80 fm/c after the system starts to reseparate. Heavy IMFs are formed at times of about 120 fm/c or later and can be viewed as resulting from two-step (sequential) neck rupture processes.

  14. Calibrations for studies of neutron-rich precursor fragments

    NASA Astrophysics Data System (ADS)

    Mazza, Maria; Parkhurst, Rachel; Wilensky, Samuel; Mosby, Michelle; Stephenson, Sharon; Rogers, Warren; MoNA Collaboration Collaboration

    2015-10-01

    Heavy ion collisions at relativistic energies produce the radioactive beams used at nuclear structure facilities worldwide. However, there are still unanswered questions about the reaction mechanism of projectile fragmentation and the specific roles that ablation, evaporation, and abrasion play. Using the projectile fragmentation of a 32Mg beam at 86 MeV/u on a natural Beryllium target at the National Superconducting Cyclotron Laboratory (NSCL), our experimental goal is to better understand the excitation energy and the momentum distribution of the precursors of the observed final fragments (neon, sodium, and fluorine). A suite of charged particle detectors in conjunction with the Modular Neutron Array (MoNA) allows us to analyze both the charged final fragments as well as the coincident neutrons. Detector calibration results and preliminary results will be presented. This material is based upon work supported by the National Science Foundation under Grants PHY-1205537.

  15. Electroproduction in the Target Fragmentation Region

    NASA Astrophysics Data System (ADS)

    Avagyan, Harut

    2014-09-01

    The Semi-Inclusive DIS process in the Target Fragmentation Region (TFR), when the hadron is produced in the fragmentation process of the target remnants, can be described through the so-called Fracture Functions (FFs). They represent the joint probability of producing the final hadron from the target remnants, when a parton of the target nucleon is struck by the virtual photon in a hard scattering process. Like the ordinary parton distribution functions, the FFs are universal objects, thus they can be measured in one experiment at a given hard scale and then used to make predictions for other experiments, at another hard scale. Measurements of the Lambda multiplicities and polarization asymmetries in TFR, in particular, will provide information on corresponding Fracture Functions. The study of its Q2 dependence at JLab and EIC also will test the perturbative framework implied by Fracture Functions, simultaneously encoding the information on the interacting parton and on the fragmentation of the spectator system. We will present ongoing studies of electroproduction in TFR at Jefferson Lab, and proposed future measurement at upgraded JLab and Electron Ion Collider.

  16. Three-body fragmentation of CO{sub 2} driven by intense laser pulses

    SciTech Connect

    Wu, Chengyin Liu, Yunquan; Gong, Qihuang; Wu, Cong; Fan, Yameng; Xie, Xiguo; Wang, Peng; Deng, Yongkai

    2015-03-28

    Dissociative ionization dynamics were studied experimentally for CO{sub 2} driven by intense laser pulses. Three-dimensional momentum vectors of correlated atomic ions were obtained for each three-body fragmentation event using triple ion coincidence measurement. Newton diagram demonstrated that three-body fragmentation of CO{sub 2}{sup n+} (n = 3-6) can occur through Coulomb explosion process and sequential fragmentation process depending on the fragmentation channels. The experimental data from these two processes were disentangled by using correlation diagram of correlated ions. Based on the accurate Coulomb explosion data, we reconstructed the bond angle distributions of CO{sub 2}{sup n+} at the moment of fragmentation, which are close to that of neutral CO{sub 2} before laser irradiation.

  17. Actinide abundances in ordinary chondrites

    NASA Technical Reports Server (NTRS)

    Hagee, B.; Bernatowicz, T. J.; Podosek, F. A.; Johnson, M. L.; Burnett, D. S.

    1990-01-01

    Measurements of actinide and light REE (LREE) abundances and of phosphate abundances in equilibrated ordinary chondrites were obtained and were used to define the Pu abundance in the solar system and to determine the degree of variation of actinide and LREE abundances. The results were also used to compare directly the Pu/U ratio with the earlier obtained ratio determined indirectly, as (Pu/Nd)x(Nd/U), assuming that Pu behaves chemically as a LREE. The data, combined with high-accuracy isotope-dilution data from the literature, show that the degree of gram-scale variability of the Th, U, and LREE abundances for equilibrated ordinary chondrites is a factor of 2-3 for absolute abundances and up to 50 percent for relative abundances. The observed variations are interpreted as reflecting the differences in the compositions and/or proportions of solar nebula components accreted to ordinary chondrite parent bodies.

  18. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of EUVE spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous Advanced Satellite for Cosmology and Astrophysics (ASCA) data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated. With these new models applied to the ASCA spectrum, better fits were obtained. Findings are that: (1) ASCA and EUVE spectra are both dominated by a region at 6 x 10(exp 6) K. (2) The high energy cut-off of the ASCA spectrum is consistent with emission from the highest ionization stages of EUVE, namely Fe XXIV. (3) EUVE requires a continuous emission measure distribution with more than two temperatures. (4) The ASCA spectra are of such high statistical significance that systematic uncertainties dominate, including atomic physics issues and calibration issues. (5) While the ASCA spectral fits achieve lower Chi(exp 2 with two-temperature fits, the EUVE-derived emission measure distribution models are also consistent with the spectra. (6) The Fe/H ratio obtained from the ASCA fit is within 20 % of the Fe/H abundance obtained from the summed spectra of Capella over 5 EUVE pointings, as well as the 1996 EUVE data. This result confirms our claims that quasi-continua composed of weak emission lines in the short wavelength spectrometer of EUVE are not major contributors to the measured Capella continuum. Other abundance ratios are also determined from the ASCA data, using models derived with EUVE. Si, Si, and Mg appear to be close to solar photospheric values, while the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined

  19. Spatial patterns in the abundance of the coastal horned lizard

    USGS Publications Warehouse

    Fisher, R.N.; Suarez, A.V.; Case, T.J.

    2002-01-01

    Coastal horned lizards (Phrynosoma coronatum) have undergone severe declines in southern California and are a candidate species for state and federal listing tender the Endangered Species Act. Quantitative data on their habitat use, abundance, and distribution are lacking, however. We investigated the determinants of abundance for coastal horned lizards at multiple spatial scales throughout southern California. Specifically, we estimated lizard distribution and abundance by establishing 256 pitfall trap arrays clustered within 21 sites across four counties. These arrays were sampled bimonthly for 2-3 years. At each array we measured 26 "local" site descriptors and averaged these values with other "regional" measures to determine site characteristics. Our analyses were successful at identifying factors within and among sites correlated with the presence and abundance of coastal horned lizards. These factors included the absence of the invasive Argentine ant (Linepithema humile) (and presence of native ant species eaten by the lizards), the presence of chaparral community plants, and the presence of sandy substrates. At a regional scale the relative abundance of Argentine ants was correlated with the relative amount of developed edge around a site. There was no evidence for spatial autocorrelation, even at the scale of the arrays within sites, suggesting that the determinants of the presence or absence and abundance of horned lizard can vary over relatively small spatial scales (hundreds of meters). Our results suggest that a gap-type approach may miss some of the fine-scale determinants of species abundance in fragmented habitats.

  20. Tandem-in-space and tandem-in-time mass spectrometry: Triple quadrupoles and quadrupole ion traps

    SciTech Connect

    Johnson, J.V.; Yost, R.A. ); Kelley, P.E.; Bradford, D.C. )

    1990-10-15

    Tandem-in-time and tandem-in-space MS/MS on quadrupole ion trap (ITMS) and triple quadrupole (TQMS) tandem mass spectrometers, respectively, were compared by evaluating the MS/MS daughter spectra, efficiencies of collision-induced dissociation (CID), limits of detection, and dynamic ranges obtained for the methane positive chemical ionization (PCI)-CID of two alkylphosphonates. Although the yield of daughter ions is dependent upon a number of instrumental parameters on both instruments, with judicious selection of parameters the ITMS and TQMS both yielded daughter ions of similar relative abundances. The ITMS had greater efficiencies of fragmentation, collection, and mass selection and transmission of the daughter ions to the detector. With PCI-MS/MS analysis of diisopropyl methylphosphonate standards introduced via capillary gas chromatography, full daughter spectra could be obtained for as little as 15 pg and 1.5 ng injected for the ITMS and the TQMS, respectively.

  1. The determination of electron abundances in interstellar clouds

    NASA Technical Reports Server (NTRS)

    Wootten, A.; Snell, R.; Glassgold, A. E.

    1979-01-01

    An independent method is proposed for the determination of electron abundances in dense clouds based upon the abundance ratio of HCO(+) and CO. The method is derived from a simple application of gas phase ion molecule interstellar chemistry. It is noted that unlike the fractionation of deuterated molecules, it applies to warm as well as to cool clouds. The method is illustrated with the results of the recent abundance survey of Wooten et al. (1978). Finally, it is shown that in cases where deuterium enhancement is measured, an upper limit can be obtained for the cosmic ray ionization rate.

  2. A Semi-automated Abundance Survey of Ap Stars

    NASA Astrophysics Data System (ADS)

    Hall, Martin P.; Kurtz, Don; Elkin, Vladimir; Bruntt, Hans

    2015-08-01

    We have carried out an abundance analysis on the high-resolution spectra of approximately 350 Ap stars collected between 2007 and 2010 on the FEROS Echelle (Fibre-led, Extended Range, Echelle ) spectrograph housed at the 2.2-m telescope at European Southern Observatory at La Silla, Chile. We employed the VWA package (vsin I, wavelength shift, abundance analysis) for preliminary selection of spectral lines, and a semi-automated set of routines which we developed in the programming language IDL, to calculate the equivalent widths and abundances of ions of Iron and the rare earth elements Neodymium and Praseodymium using the WIDTH program and NEMO model atmospheres. Initial results are presented, which reinforce the correlation between iron abundance and effective temperature, from an over-abundance in the late Bp stars, to under-abundant in the early F stars. Results also suggest that the disequilibrium in abundances of the first and second ionisation stages of these ions in the rapidly oscillating Ap (roAp) stars may a consequence of the relatively cool temperatures of those stars, rather than a signature of pulsation.

  3. Fragment-based drug design.

    PubMed

    Feyfant, Eric; Cross, Jason B; Paris, Kevin; Tsao, Désirée H H

    2011-01-01

    Fragment-based drug design (FBDD), which is comprised of both fragment screening and the use of fragment hits to design leads, began more than 15 years ago and has been steadily gaining in popularity and utility. Its origin lies on the fact that the coverage of chemical space and the binding efficiency of hits are directly related to the size of the compounds screened. Nevertheless, FBDD still faces challenges, among them developing fragment screening libraries that ensure optimal coverage of chemical space, physical properties and chemical tractability. Fragment screening also requires sensitive assays, often biophysical in nature, to detect weak binders. In this chapter we will introduce the technologies used to address these challenges and outline the experimental advantages that make FBDD one of the most popular new hit-to-lead process. PMID:20981527

  4. Identification of Low Abundant Isomeric N-Glycan Structures in Biological Therapeutics by LC/MS.

    PubMed

    Zhao, Jia; Li, Siyang; Li, Chen; Wu, Shiaw-Lin; Xu, Wei; Chen, Yuetian; Shameem, Mohammed; Richardson, Douglas; Li, Huijuan

    2016-07-19

    An effective LC-MS based method for online characterization of low abundant structural isomers of N-linked glycans in biological therapeutics was developed. N-linked glycans of a recombinant monoclonal antibody were released by PNGase F and labeled with 2-aminobenzamide (2-AB) fluorescent tag. The labeled glycans were analyzed by online ultraperformance liquid chromatography-hydrophilic interaction liquid chromatography (UPLC-HILIC) coupled with mass spectrometry (MS). The glycan structure was characterized by MS(n) fragmentation in negative ion mode followed by identification of the signature D ions. The assignment included monosaccharide sequence and linkage information. The developed method successfully characterized structural isomers of A1G1F (assigned as terminal sialic acid attached in the 1,6 branch at 2,3 position), and A1G1F' (assigned as terminal sialic acid attached in the 1,3 branch at 2,3 position). Moreover, using the same approach, previously unknown low abundant species were identified unambiguously. One such structural isomer at low level, terminal GlcNAc of G1F+GlcNAc, was identified to be linked at the 1,6 branch. Additionally, another low level structural isomer, previously assigned as Man8 glycan, was found to be Man7+Glc glycan as its 1,3 branch containing three mannoses and one terminal glucose. The identification was further confirmed by a purified α-1,2-endomannosidase enzyme to generate the cleavage of α-1,3 linked terminal disaccharides (Man+glucose). Using this approach, different lots or different CHO produced mAbs was thoroughly examined and found that the newly identified "Man8" (Man7+Glc) was also present in different batches and in some commercially available therapeutic mAbs. PMID:27291648

  5. Comparison of Data Acquisition Strategies on Quadrupole Ion Trap Instrumentation for Shotgun Proteomics

    PubMed Central

    Canterbury, Jesse D.; Merrihew, Gennifer E.; Goodlett, David R.; MacCoss, Michael J.; Shaffer, Scott A.

    2015-01-01

    A common strategy in mass spectrometry analyses of complex protein mixtures is to digest the proteins to peptides, separate the peptides by microcapillary liquid chromatography and collect tandem mass spectra (MS/MS) on the eluting, complex peptide mixtures, a process commonly termed “shotgun proteomics”. For years, the most common way of data collection was via data-dependent acquisition (DDA), a process driven by an automated instrument control routine that directs MS/MS acquisition from the highest abundant signals to the lowest, a process often leaving lower abundant signals unanalyzed and therefore unidentified in the experiment. Advances in both instrumentation duty cycle and sensitivity allow DDA to probe to lower peptide abundance and therefore enable mapping proteomes to a more significant depth. An alternative to acquiring data by DDA is by data-independent acquisition (DIA), in which a specified range in m/z is fragmented without regard to prioritization of a precursor ion or its relative abundance in the mass spectrum. As a consequence, DIA acquisition potentially offers more comprehensive analysis of peptides than DDA and in principle can yield tandem mass spectra of all ionized molecules following their conversion to the gas-phase. In this work, we evaluate both DDA and DIA on three different linear ion trap instruments: an LTQ, an LTQ modified in-house with an electrodynamic ion funnel, and an LTQ-Velos. These instruments were chosen as they are representative of both older (LTQ) and newer (LTQ-Velos) ion trap designs i.e., linear ion trap and dual ion traps, respectively, and allow direct comparison of peptide identification using both DDA and DIA analysis. Further, as the LTQ-Velos has an improved “S-lens” ion guide in the high-pressure region to improve ion flux, we found it logical to determine if the former LTQ model could be leveraged by improving sensitivity by modifying with an electrodynamic ion guide of significantly different

  6. Fragmentation Mechanisms Associated with Lacustrine Lava-Water Explosions

    NASA Astrophysics Data System (ADS)

    Fitch, E. P.; Fagents, S. A.; Thordarson, T.; Hamilton, C.

    2015-12-01

    Rootless cones form when degassed lava interacts explosively with water contained in the near-surface substrate, and represents an end-member system that can elucidate mechanisms of magma-water interactions due to the absence of primary degassing-induced fragmentation. The proportion of finely fragmented ejecta (i.e. ash), generated in rootless explosions, even if the volume is small relative to coarser ejecta, may contribute significantly to the explosion energy release. Explosive melt-water experiments indicate that the degree of melt-water mixing and energy release are proportional to the abundance of blocky grains, fragmented by brittle disintegration, which effectively contribute thermal energy to the explosive lava-water interaction. In order to determine the state of the lava at the point of ash-grade fragmentation in rootless explosions we examined grain morphology over the following size ranges: 0.5-0 ϕ (1.41-1 mm, very coarse ash), 1.5-2 ϕ (0.354-0.250 mm, medium ash), and 3.5-4 ϕ (0.088-0.062 mm, very fine ash). We found that rootless ash is composed of blocky, mossy, and fluidal grains with a minor component of aggregates (≤ 2%) and glassy shards (< 35%). Typically, (1) very coarse ash contains blocky (9-58%), mossy (8-36%) and fluidal (28-67%) grains only, (2) medium ash contains blocky (32-76%), mossy (9-39%) and fluidal (15-43%) grains with a minor abundance of glassy shards (≤ 8%), and (3) very fine ash is dominated by blocky clasts (53-80%), with lower shard (12-34%) and fluidal (4-24%) components. We observe that the abundance of fluidal grains decreases while the abundance of blocky grains increases with decreasing grain size. Also, the abundance of blocky grains decreases with increasing stratigraphic height, indicating that as rootless explosions progressed, brittle fragmentation of lava is less pronounced, suggesting that the efficiency of lava-water mixing dropped, most likely due to reduced availability of external water. However, we

  7. To what extent does urbanisation affect fragmented grassland functioning?

    PubMed

    van der Walt, L; Cilliers, S S; Kellner, K; Du Toit, M J; Tongway, D

    2015-03-15

    grassland fragments, as well as to determine the potential for the use of LFA in decision-making involving the conservation of grassland fragments. The results indicated that the occurrence, size and characteristics of vegetated patches, and especially the presence of litter abundances, were the main factors determining differences in the LFA indices. Furthermore, mowing resulted in the overall fine-scale biophysical indices being higher for some of the urban grassland fragments. This implied that it is not necessarily the influence of urbanisation entailing high or low resource conserving patchiness and patch quality, but rather the management practices associated with urban and exurban areas. Therefore, from a conservation point of view, the grassland fragments in the City of Potchefstroom are just as conservable (on a biophysical function level involving soil processes) than the more "natural" exurban grassland fragments. PMID:25616514

  8. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of ASCA spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous EUVE data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated, resulting in a paper in process by Liedahl and Brickhouse. With these new models applied to the ASCA spectrum, better fits were obtained. While solar abundance ratios are generally consistent with the ASCA data, the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined from these data. Detailed discussion has been provided to NASA in the most recent annual report (1997). Two poster presentations have been made regarding modeling requirements. A substantial paper is in the final revision form, following review by six co-authors. The results of this work have wide implications, since the newly calculated emission lines almost certainly contribute to other problems in fitting not only other stellar spectra, but also composite supernova remnants, galaxies, and cooling flow clusters of galaxies. Furthermore, Liedahl and Brickhouse have identified other species for which lines of a similar nature (high principal quantum number) will contribute significant flux. For moderate resolution X-ray spectra, lines left out of the models in relatively isolated bands, will be attributed to continuum flux by spectral fitting engines, causing errors in line-to-continuum ratios. Thus addressing the general theoretical problem is of crucial importance.

  9. Fragmentation of N-14 nuclei at 29 GeV - Inclusive isotope spectra at 0 deg.

    NASA Technical Reports Server (NTRS)

    Heckman, H. H.; Greiner, D. E.; Lindstrom, P. J.; Bieser, F. S.

    1972-01-01

    We report the first results of a Bevatron heavy-ion experiment on the inclusive spectra of isotopically identified nuclei 3(Z-range between 3 and 7), produced by the fragmentation of 29-GeV N-14 ions in carbon and hydrogen. The preliminary values of the partial differential cross sections at 0 deg give evidence that the modes of fragmentation of N-14 projectiles are independent of the target nucleus.

  10. Abundances in dwarf irregular galaxies

    NASA Technical Reports Server (NTRS)

    Dufour, Reginald J.

    1986-01-01

    The results of abundance studies of dwarf irregular galaxies and similar objects are reviewed with special attention to variations in the CNO element group. Observations of the forbidden N II and semiforbidden C III lines in the most metal-poor galaxy known, IZw 18, are presented for the first time and CNO abundances are derived via a photoionization model and discussed in the context of the abundances found in other metal-poor H II regions and galaxies.

  11. Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes.

    PubMed

    Lefcheck, Jonathan S; Marion, Scott R; Lombana, Alfonso V; Orth, Robert J

    2016-01-01

    Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4-400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities. PMID:27244652

  12. Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes

    PubMed Central

    Marion, Scott R.; Lombana, Alfonso V.; Orth, Robert J.

    2016-01-01

    Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4–400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities. PMID:27244652

  13. Structure and mechanism of formation of an important ion in doping control

    NASA Astrophysics Data System (ADS)

    Borges, Chad R.; Taccogno, James; Crouch, Dennis J.; Le, Ly; Truong, Thanh N.

    2005-12-01

    An ion with m/z 143 serves as a biomarker that is often continuously monitored in urine samples undergoing screening by electron ionization gas chromatography/mass spectrometry (EI GC/MS) for banned anabolic agents. The ion is known to arise from trimethylsilyl (TMS)-derivatized synthetic 17-hydroxy, 17-methyl steroids. The purpose of this work was to characterize, in detail, the origin(s), structure(s), and mechanism(s) of formation of such ions with m/z 143. High resolution mass spectrometry (HRMS) data revealed the elemental composition of the D-ring derived m/z 143 ion to be C7H15OSi. Analysis of dihydrotestosterone (DHT) and its 2-methyl substituted analog dromostanolone by HRMS revealed that an elementally equivalent ion of m/z 143 could be derived from the A-ring of TMS-derivatized 3-keto-enol steroids demonstrating that an abnormally intense peak in the m/z 143 extracted ion chromatogram of urine samples undergoing screening for banned anabolic agents does not necessarily indicate the presence of a 17-hydroxy, 17-methyl steroid. To gain information on ion structure, breakdown curves for the most abundant product ions of the m/z 143 ion were generated using both native and perdeutero-TMS derivatives, providing structures for second, third, and fourth generation product ions. An EI-mass spectrum of [16,16,17-2H3]-DHT (DHT-d3) demonstrated that one of the C-16 hydrogen atoms is removed prior to the formation of an ion that is highly analogous to the ion with m/z 143 strongly suggesting, in accord with all other evidence, one particular fragmentation pathway and resulting product: a resonance stabilized 3-(O-trimethylsilyl)but-1-ene ion.

  14. Analysis of the theory of high energy ion transport

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.

    1977-01-01

    Procedures for the approximation of the transport of high-energy ions are discussed on the basis of available data on ion nuclear reactions. A straightahead approximation appears appropriate for space applications. The assumption that the secondary-ion-fragment velocity is equal to that of the fragmenting nucleus is inferior to straightahead theory but is of sufficient accuracy if the primary ions display a broad energy spectrum. An iterative scheme for the solution of the inhomogenous integral transport equations holds promise for practical calculation. A model calculation shows that multiple charged ion fragments penetrate to greater depths in comparison with the free path of a primary heavy ion.

  15. Discrimination Between Peptide O-Sulfo- and O-Phosphotyrosine Residues by Negative Ion Mode Electrospray Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    Unambiguous differentiation between isobaric sulfated and phosphorylated tyrosine residues (sTyr and pTyr) of proteins by mass spectrometry is challenging, even using high resolution mass spectrometers. Here we show that upon negative ion mode collision-induced dissociation (CID), pTyr- and sTyr-containing peptides exhibit entirely different modification-specific fragmentation patterns leading to a rapid discrimination between the isobaric covalent modifications using the tandem mass spectral data. This study reveals that the ratio between the relative abundances of [M-H-80]- and [M-H-98]- fragment ions in ion-trap CID and higher energy collision dissociation (HCD) spectra of singly deprotonated +80 Da Tyr-peptides can be used as a reliable indication of the Tyr modification group nature. For multiply deprotonated +80 Da Tyr-peptides, CID spectra of sTyr- and pTyr-containing sequences can be readily distinguished based on the presence/absence of the [M-nH-79](n-1)- and [M-nH-79-NL]( n-1)- ( n = 2, 3) fragment ions (NL = neutral loss).

  16. Abundance coefficients, a new method for measuring microorganism relative abundance

    USGS Publications Warehouse

    Forester, R.M.

    1977-01-01

    A new method of measuring the relative abundance of microorganisms by using a set of interrelated coefficients, termed 'abundance coefficients' or 'AC', is proposed. These coefficients provide a means of recording abundance for geometric density categories, and each density measurement represents an approximation of the Poisson parameter ??t. The AC is the natural logarithm of a 'characteristic value,' which is a particular number for each geometric density category. The 'characteristic values' are based upon a probabilistic error statement derived from the Poisson formula, and they present evidence for separation of the geometric category boundaries by e = 2.71828. The proposed AC provide a means for recording species abundance in a manner suitable for arithmetic manipulation, for population structure studies, and for the determination of practical limits for defining the presence or absence of a species. Further, these coefficients provide for both intrasample and intersample abundance comparisons. ?? 1977 Plenum Publishing Corporation.

  17. Peptide Dimethylation: Fragmentation Control via Distancing the Dimethylamino Group

    NASA Astrophysics Data System (ADS)

    McShane, Adam J.; Shen, Yuanyuan; Castillo, Mary Joan; Yao, Xudong

    2014-10-01

    Direct reductive methylation of peptides is a common method for quantitative proteomics. It is an active derivatization technique; with participation of the dimethylamino group, the derivatized peptides preferentially release intense a1 ions. The advantageous generation of a1 ions for quantitative proteomic profiling, however, is not desirable for targeted proteomic quantitation using multiple reaction monitoring mass spectrometry; this mass spectrometric method prefers the derivatizing group to stay with the intact peptide ions and multiple fragments as passive mass tags. This work investigated collisional fragmentation of peptides whose amine groups were derivatized with five linear ω-dimethylamino acids, from 2-(dimethylamino)-acetic acid to 6-(dimethylamino)-hexanoic acid. Tandem mass spectra of the derivatized tryptic peptides revealed different preferential breakdown pathways. Together with energy resolved mass spectrometry, it was found that shutting down the active participation of the terminal dimethylamino group in fragmentation of derivatized peptides is possible. However, it took a separation of five methylene groups between the terminal dimethylamino group and the amide formed upon peptide derivatization. For the first time, the gas-phase fragmentation of peptides derivatized with linear ω-dimethylamino acids of systematically increasing alkyl chain lengths is reported.

  18. Peptide Dimethylation: Fragmentation Control via Distancing the Dimethylamino Group

    PubMed Central

    McShane, Adam J.; Shen, Yuanyuan; Castillo, Mary Joan; Yao, Xudong

    2014-01-01

    Direct reductive methylation of peptides is a common method for quantitative proteomics. It is an active derivatization technique; with participation of the dimethylamino group, the derivatized peptides preferentially release intense a1 ions. The advantageous generation of a1 ions for quantitative proteomic profiling, however, is not desirable for targeted proteomic quantitation using multiple reaction monitoring mass spectrometry; this mass spectrometric method prefers the derivatizing group to stay with the intact peptide ions and multiple fragments as passive mass tags. This work investigated collisional fragmentation of peptides whose amine groups were derivatized with five linear ω-dimethylamino acids, from 2-(dimethylamino)-acetic acid to 6-(dimethylamino)-hexanoic acid. Tandem mass spectra of the derivatized tryptic peptides revealed different preferential breakdown pathways. Together with energy resolved mass spectrometry, it was found that shutting down the active participation of the terminal dimethylamino group in fragmentation of derivatized peptides is possible. However, it took a separation of five methylene groups between the terminal dimethylamino group and the amide formed upon peptide derivatization. For the first time, the gas-phase fragmentation of peptides derivatized with linear ω-dimethylamino acids of systematically increasing alkyl chain lengths is reported. PMID:25091822

  19. Composition of cavity-nesting bird communities in montane aspen woodland fragments: The roles of landscape context and forest structure

    USGS Publications Warehouse

    Lawler, J.J.; Edwards, T.C., Jr.

    2002-01-01

    We compared cavity-nesting bird communities in aspen (Populus tremuloides) woodland fragments classified on the basis of vegetation structure (tree density) and landscape context (surrounding vegetation). We found very few cavity nesters in fragments predominantly surrounded by forests. Fragments adjacent to meadows contained more species and a greater abundance of cavity nesters. Species richness and abundance were higher in sparsely than in densely treed meadow fragments. Because secondary cavity nesters are often limited by cavity availability, we augmented natural cavities with nest boxes. Although only five boxes contained bird nests, these were all in sparse aspen fragments predominantly surrounded by meadows. However, we found 25 northern flying squirrel (Glaucomys sabrinus) nests in boxes, none of which were in sparse meadow fragments. In addition to high-lighting the importance of landscape context in avian and mammalian habitat relationships, our results suggest that predator or competitor interactions may help structure this cavity-nester community. ?? The Cooper Ornithological Society 2002.

  20. Source abundances of ultra heavy elements derived from UHCRE measurements.

    PubMed

    Domingo, C; Font, J; Baixeras, C; Fernandez, F

    1996-11-01

    A total of 205 tracks have been located, measured, and positively identified as originating from Ultra Heavy (Z > or = 65) cosmic ray ions with energies over 2 GeV/amu in the 10 UHCRE plastic track detector (mainly Lexan polycarbonate) stacks studied by our Group. About 40 values of reduced etch rate S have been obtained along each of these tracks. A method based on determining the gradient of S, together with calibration in accelerators, is used to determine the charge of each ion resulting in one of such tracks to obtain the charge spectrum of the recorded Ultra Heavy ions. The abundance ratio of ions with 87 < or = Z < or = 100 to those with 74 < or = Z < or = 86 as well as that of ions with 81 < or = Z < or = 86 to those with 74 < or = Z < or = 80 are calculated at 0.016 and 0.32, respectively, which agree with the values obtained from measurements in the HEAO-3 and Ariel-6 experiments. The abundance ratio of ions with 70 < or = Z < or = 73 to those with 74 < or = Z < or = 86 is also calculated, but its value (0.074) did not seem to be significant because of our detectors' low registration efficiency in the charge range 70 < or = Z < or = 73. A computer program developed by our Group, based on the Leaky Box cosmic ray propagation model, has been used to determine the source abundances of cosmic ray nuclei with Z > or = 65 inferred from the abundances measured in the UHCRE. It appeared that r-process synthesized elements were overabundant compared to the Solar System abundances, as predicted by other authors. PMID:11540515

  1. Structural characterization of intact proteins is enhanced by prevalent fragmentation pathways rarely observed for peptides.

    PubMed

    Cobb, Jennifer S; Easterling, Michael L; Agar, Jeffrey N

    2010-06-01

    While collisionally activated dissociation (CAD) pathways for peptides are well characterized, those of intact proteins are not. We systematically assigned CAD product ions of ubiquitin, myoglobin, and bovine serum albumin generated using high-yield, in-source fragmentation. Assignment of >98% of hundreds of product ions implies that the fragmentation pathways described are representative of the major pathways. Protein dissociation mechanisms were found to be modulated by both source declustering potential and precursor ion charge state. Like peptides, higher charge states of proteins fragmented at lower energies next to Pro, via mobile protons, while lower charge states fragmented at higher energies after Asp and Glu, via localized protons. Unlike peptides, however, predominant fragmentation channels of proteins occurred at intermediate charge states via non-canonical mechanisms and produced extensive internal fragmentation. The non-canonical mechanisms include prominent cleavages C-terminal to Pro and Asn, and N-terminal to Ile, Leu, and Ser; these cleavages, along with internal fragments, led to a 45% increase in sequence coverage, improving the specificity of top-down protein identification. Three applications take advantage of the different mechanisms of protein fragmentation. First, modulation of declustering potential selectively fragments different charge states, allowing the source region to be used as the first stage of a low-resolution tandem mass spectrometer, facilitating pseudo-MS(3) of product ions with known parent charge states. Second, development and integration of automated modulation of ion funnel declustering potential allows users access to a particular fragmentation mechanism, yielding facile cleavage on a liquid chromatography timescale. Third, augmentation of a top-down search engine improved protein characterization. PMID:20303285

  2. Fragmentation Function in Thermofield Dynamics

    NASA Astrophysics Data System (ADS)

    Ladrem, M.; Chekerker, M.; Khanna, F. C.; Santana, A. E.

    2013-04-01

    The fragmentation function at high energy experiments is introduced by using thermofield dynamics (TFD), a real-time finite-temperature quantum field formalism. Due to the structure of TFD, the results at T = 0 and T ≠ 0 are split in a direct way. As an application, we consider the temperature effect on the fragmentation function of a hadron leading to quark-antiquark pairs. Using a definition of Wilson-loop in real-time, we find that the fragmentation function decreases in magnitude with an increase in the temperature.

  3. Velocity fluctuations of fission fragments

    NASA Astrophysics Data System (ADS)

    Llanes-Estrada, Felipe J.; Carmona, Belén Martínez; Martínez, Jose L. Muñoz

    2016-02-01

    We propose event by event velocity fluctuations of nuclear fission fragments as an additional interesting observable that gives access to the nuclear temperature in an independent way from spectral measurements and relates the diffusion and friction coefficients for the relative fragment coordinate in Kramers-like models (in which some aspects of fission can be understood as the diffusion of a collective variable through a potential barrier). We point out that neutron emission by the heavy fragments can be treated in effective theory if corrections to the velocity distribution are needed.

  4. Distinguishing of Ile/Leu amino acid residues in the PP3 protein by (hot) electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Kjeldsen, Frank; Haselmann, Kim F; Sørensen, Esben S; Zubarev, Roman A

    2003-03