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Sample records for abundant fragment ions

  1. Mechanisms of fragmentation of cationic peptide ions

    NASA Astrophysics Data System (ADS)

    Zhao, Hong; Adams, Jeanette

    1993-06-01

    Fragmentation mechanisms for formation of several commonly occurring product ions in high-energy collision-induced induced decomposition spectra of either (M + Cat2+ - H)+ ions of peptides cationized with alkaline earth metal ions, (M + Ca+)+ ions cationized with alkali metal ions, or (M + H)+ ions are evaluated by using deuterium-labelled peptides. The different sources of hydrogen transferred in the reactions are identified. Our study supports some previously proposed mechanisms but also provides evidence for others.

  2. 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.

  3. 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.

  4. Fragmentation of ions in a low pressure linear ion trap.

    PubMed

    Collings, Bruce A

    2007-08-01

    The efficiency of in-trap fragmentation in a low-pressure linear ion trap (LIT), using dipolar excitation, is dependent upon the choice of both the excitation q and the drive frequency of the quadrupole. In the work presented here, fragmentation efficiencies have been measured as a function of excitation q for drive frequencies of 816 kHz and 1.228 MHz. The experiments were carried out by fragmenting reserpine (609.23-->448.20 Th and 397.21-->365.19 Th transitions) and caffeine (195-->138 Th and 138-->110 Th transitions). The data showed that the onset of efficient fragmentation occurred at a lower Mathieu q for the LIT operated at 1.228 MHz when compared with the LIT operated at 816 kHz. A comparison of the fragmentation efficiency curves as a function of pseudo-potential well depth showed that the onset of fragmentation is independent of the drive frequency. In addition, a comparison of the fragmentation efficiency curves showed that all four of the precursor ions fragmented within a range of four V of pseudo-potential well depth. The choice of an appropriate excitation q can then be determined based upon a minimum pseudo-potential well depth, quadrupole field radius, drive frequency, and the mass of interest. Fragmentation efficiencies were also found to be significantly greater when using the higher drive frequency.

  5. Ion sources for fission fragment accelerators

    NASA Astrophysics Data System (ADS)

    Köster, U.; Kester, O.; Habs, D.

    1998-03-01

    At the Grenoble and Munich high-flux reactors fission fragment accelerators are under design which will deliver beams of very neutron-rich fission products with a final energy between 3 and 6 MeV/u. In order to obtain an efficient acceleration in a compact accelerator, charge conversion of the 1+ ion beams from the in-pile ion source to a q/A⩾0.16 has to take place. In the chain from production to acceleration, ion sources are the key elements to reach high beam intensities of over 1010s-1. For the in-pile part the target-ion source assembly has not only to be very efficient, but should also be highly selective for the desired elements (which go from nickel to europium) on one hand and robust against the hostile environment (high neutron and gamma flux) on the other hand. Foreseen types are a surface ionization source, which could also be run as laser ion source for resonant photo ionization, and, for rare gases, a plasma ion source coupled via a transfer line to the target. For the charge state breeding several different schemes are considered: the combination of a Penning trap for bunching, cooling, and mass separation and an electron beam ion source (EBIS) as charge breeder, similar to REX-ISOLDE, an EBIS with direct injection of a dc beam of 1+ ions ("accu-EBIS") or an electron cyclotron resonance ion source (ECRIS) with either continuous or bunched extraction. The EBIS may provide higher charge states, whereas the ECRIS is able to work with much higher beam intensities and allows cw-operation. The advantage of each scheme is explained and some design requirements of the different sources are presented.

  6. Ion sources for fission fragment accelerators

    NASA Astrophysics Data System (ADS)

    Köster, U.; Kester, O.; Habs, D.

    1998-02-01

    At the Grenoble and Munich high-flux reactors fission fragment accelerators are under design which will deliver beams of very neutron-rich fission products with a final energy between 3 and 6 MeV/u. In order to obtain an efficient acceleration in a compact accelerator, charge conversion of the 1+ ion beams from the in-pile ion source to a q/A⩾0.16 has to take place. In the chain from production to acceleration, ion sources are the key elements to reach high beam intensities of over 1010s-1. For the in-pile part the target-ion source assembly has not only to be very efficient, but should also be highly selective for the desired elements (which go from nickel to europium) on one hand and robust against the hostile environment (high neutron and gamma flux) on the other hand. Foreseen types are a surface ionization source, which could also be run as laser ion source for resonant photo ionization, and, for rare gases, a plasma ion source coupled via a transfer line to the target. For the charge state breeding several different schemes are considered: the combination of a Penning trap for bunching, cooling, and mass separation and an electron beam ion source (EBIS) as charge breeder, similar to REX-ISOLDE, an EBIS with direct injection of a dc beam of 1+ ions ("accu-EBIS") or an electron cyclotron resonance ion source (ECRIS) with either continuous or bunched extraction. The EBIS may provide higher charge states, whereas the ECRIS is able to work with much higher beam intensities and allows cw-operation. The advantage of each scheme is explained and some design requirements of the different sources are presented.

  7. Ion induced fragmentation cross-sections of DNA constituents

    NASA Astrophysics Data System (ADS)

    Rudek, Benedikt; Arndt, Alexander; Bennett, Daniel; Wang, Mingjie; Rabus, Hans

    2015-10-01

    Proton collision with chemical analogs for the base, the sugar and the phosphor residue of the DNA, namely pyrimidine, tetrahydrofuran and trimethyl phosphate, respectively, has been investigated. The impact energies ranged from 300 keV up to 16 MeV. For the first time, relative fragmentation cross-sections for proton impact are reported for tetrahydrofuran and trimethyl phosphate; previously reported cross sections for pyrimidine are extended for energies beyond 2500 keV. Ionization of tetrahydrofuran leads to a ring break in about 80% of all events, trimethyl phosphate predominantly fragments by bond cleavage to one of the three methyl-groups and for pyrimidine the parent ion has the highest abundance. Such comparison supports earlier findings that the sugar is the weak spot for strand breaks.

  8. Ion Optics Simulation for Fragment Separator

    NASA Astrophysics Data System (ADS)

    Kawada, Yosuke; Nakamura, Takashi; Kubo, Toshiyuki; Takeda, Hiroyuki; Sumikama, Toshiyuki

    2009-10-01

    We have developed a Monte-Carlo simulation code for unstable-nuclear beam experiments using a fragment-separator. This code primarily aims at calculating beam traces in the fragment separator BigRIPS and ZeroDegree Spectrometer (ZDS) at RIBF(RIKEN RI-Beam Factory). This code uses externally given transfer-matrices of ion optics such as an output of COSY Infinity[1]. We have applied this code to recent campaign of experiments using ^48Ca at 345MeV/u as primary beam. In the experiments, two modes of ion optical settings , namely ``Standard'' and ``High Brho'' modes were used. The former is an ordinary used starndard setteing, which has a limit in the maximum rigidity (Bρ<9.2Tm). On the other hand, the ``High Brho'' setting has been developed for a secondary beam with higher rigidity, such as for very neutron rich nuclei ^22C (A/Z=3.67). In this talk, we compare properties of these two optics settings and evaluate beam traces, emittances, and transmissions.[4pt] [1] K. Makino, M. Berz Nucl. Instr. Meth. A 558 (2005)

  9. 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.

  10. 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.

  11. Fragmentation of multiply-charged intact protein ions using MALDI TOF-TOF mass spectrometry.

    PubMed

    Liu, Zhaoyang; Schey, Kevin L

    2008-02-01

    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 nonpreferential 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.

  12. 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.

  13. Fragmentation of biomolecules using slow highly charged ions

    NASA Astrophysics Data System (ADS)

    Ruehlicke, Christiane; Schneider, Dieter; DuBois, Robert; Balhorn, Rodney

    1997-02-01

    We present first results of biomolecular fragmentation studies with slow highly charged ions (HCI). A thin layer of the tripeptide RVA was deposited on gold targets and irradiated with slow (few 100 keV) ions, e.g. Xe50+ and Xe15+, extracted from the LLNL EBIT (electron beam ion trap). The secondary ions released upon ion impact were mass analyzed via Time-Of-Flight Secondary-Ion-Mass-Spectrometry (TOF-SIMS). The results show a strong dependence of the positive and negative ion yields on the charge state of the incident ion. We also found that incident ions with high charge states cause the ejection of fragments with a wide mass range as well as the intact molecule (345 amu). The underlying mechanisms are not yet understood but electron depletion of the target due to the high incident charge is likely to cause a variety of fragmentation processes.

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

    PubMed

    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 H(2)O, NH(3), CH(2)O (from serine), C2H4O (from threonine), and H(3)PO(4), 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.

  15. 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.

  16. 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.

  17. Fragment formula calculator (FFC): determination of chemical formulas for fragment ions in mass spectrometric data.

    PubMed

    Wegner, André; Weindl, Daniel; Jäger, Christian; Sapcariu, Sean C; Dong, Xiangyi; Stephanopoulos, Gregory; Hiller, Karsten

    2014-02-18

    The accurate determination of mass isotopomer distributions (MID) is of great significance for stable isotope-labeling experiments. Most commonly, MIDs are derived from gas chromatography/electron ionization mass spectrometry (GC/EI-MS) measurements. The analysis of fragment ions formed during EI, which contain only specific parts of the original molecule can provide valuable information on the positional distribution of the label. The chemical formula of a fragment ion is usually applied to derive the correction matrix for accurate MID calculation. Hence, the correct assignment of chemical formulas to fragment ions is of crucial importance for correct MIDs. Moreover, the positional distribution of stable isotopes within a fragment ion is of high interest for stable isotope-assisted metabolomics techniques. For example, (13)C-metabolic flux analyses ((13)C-MFA) are dependent on the exact knowledge of the number and position of retained carbon atoms of the unfragmented molecule. Fragment ions containing different carbon atoms are of special interest, since they can carry different flux information. However, the process of mass spectral fragmentation is complex, and identifying the substructures and chemical formulas for these fragment ions is nontrivial. For that reason, we developed an algorithm, based on a systematic bond cleavage, to determine chemical formulas and retained atoms for EI derived fragment ions. Here, we present the fragment formula calculator (FFC) algorithm that can calculate chemical formulas for fragment ions where the chemical bonding (e.g., Lewis structures) of the intact molecule is known. The proposed algorithm is able to cope with general molecular rearrangement reactions occurring during EI in GC/MS measurements. The FFC algorithm is able to integrate stable isotope labeling experiments into the analysis and can automatically exclude candidate formulas that do not fit the observed labeling patterns.1 We applied the FFC algorithm to create

  18. Associations of forest cover, fragment area, and connectivity with neotropical understory bird species richness and abundance.

    PubMed

    Martensen, Alexandre Camargo; Ribeiro, Milton Cezar; Banks-Leite, Cristina; Prado, Paulo Inácio; Metzger, Jean Paul

    2012-12-01

    Theoretical and empirical studies demonstrate that the total amount of forest and the size and connectivity of fragments have nonlinear effects on species survival. We tested how habitat amount and configuration affect understory bird species richness and abundance. We used mist nets (almost 34,000 net hours) to sample birds in 53 Atlantic Forest fragments in southeastern Brazil. Fragments were distributed among 3 10,800-ha landscapes. The remaining forest in these landscapes was below (10% forest cover), similar to (30%), and above (50%) the theoretical fragmentation threshold (approximately 30%) below which the effects of fragmentation should be intensified. Species-richness estimates were significantly higher (F= 3715, p = 0.00) where 50% of the forest remained, which suggests a species occurrence threshold of 30-50% forest, which is higher than usually occurs (<30%). Relations between forest cover and species richness differed depending on species sensitivity to forest conversion and fragmentation. For less sensitive species, species richness decreased as forest cover increased, whereas for highly sensitive species the opposite occurred. For sensitive species, species richness and the amount of forest cover were positively related, particularly when forest cover was 30-50%. Fragment size and connectivity were related to species richness and abundance in all landscapes, not just below the 30% threshold. Where 10% of the forest remained, fragment size was more related to species richness and abundance than connectivity. However, the relation between connectivity and species richness and abundance was stronger where 30% of the landscape was forested. Where 50% of the landscape was forested, fragment size and connectivity were both related to species richness and abundance. Our results demonstrated a rapid loss of species at relatively high levels of forest cover (30-50%). Highly sensitive species were 3-4 times more common above the 30-50% threshold than below it

  19. Interactions of fragment ions of tetradecane with solid surfaces

    NASA Astrophysics Data System (ADS)

    Takaoka, Gikan H.; Takeuchi, Mitsuaki; Ryuto, Hiromichi; Imanaka, Kousuke; Hayashi, Kyohei

    2014-12-01

    Vapors of tetradecane (C14H30) were ionized by electron bombardment. The generated fragment ions such as C3H7, C6H13, and C12H25 ions were separated by an E × B filter (Wien filter) and accelerated toward Si(1 0 0) substrates. Thickness measurements showed that thin films were deposited on the Si substrates by C3H7- and C6H13-ion irradiation, although the Si substrate surface was predominantly sputtered by C12H25 ions. Rutherford backscattering spectroscopy showed that the irradiation damage by the fragment-ion beams decreased with the increasing molecular weight of the fragment ions at the same acceleration voltage. Furthermore, Raman spectra as well as X-ray photoelectron spectroscopy measurements showed that DLC films were formed by C3H7- and C6H13-ion irradiation with the film thickness being larger in case of C3H7. On the contrary, for C12H25-ion irradiation, chemical sputtering occurred by surface reactions of hydrogen and methyl radicals with silicon atoms. The chemical reaction at the irradiated substrate surface could be enhanced by the higher temperatures achieved by the high energy-density irradiation effect of the polyatomic ions.

  20. 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.

  1. 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

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

    SciTech Connect

    Vasil'ev, Yury V.; Figard, Benjamin J.; Morre, Jeff; Deinzer, Max L.

    2009-07-28

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

  3. Cluster Ion Stopping and Fragmentation for ICF

    NASA Astrophysics Data System (ADS)

    Deutsch, C.; Tahir, N. A.

    Cluster ion beam with energy in the several tens of keV/a.m.u. range are considered as a novel direct driver for a simple fusion pellet made of Deuterium + Tritium fuel surrounded by a Lithium pusher. The driver-pellet interaction is calculated through the hypothesis of maximum multifragmentation followed by highly correlated ion debris motion. One thus gets enhanced stopping and ablation pressure in the hundreds Mbar range. An implosion is then completed in 5 nsec. Indirect drive is also considered.

  4. 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

  5. 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.

  6. 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.

  7. Low fragment polyatomic molecular ion source by using permanent magnets.

    PubMed

    Takeuchi, Mitsuaki; Hayashi, Kyouhei; Imanaka, Kousuke; Ryuto, Hiromichi; Takaoka, Gikan H

    2014-02-01

    Electron-ionization-type polyatomic molecular ion source with low fragment was developed by using a pair of ring-shaped Sm-Co magnets. The magnets were placed forward and backward side of ionization part to confine electrons extracted from a thermionic cathode. Calculated electron trajectory of the developed ion source was 20 times longer than that of an ordinary outer filament configuration that has no magnetic confinement. Mass spectra of the molecular ions generated from n-tetradecane (C14H30) gas exhibited 4 times larger intensity than that of the ordinary configuration in a range of mass/charge from 93 to 210 u. This indicates that suppression of fragment ion was obtained by increase of low energy electrons resulted from the electron confinement.

  8. Substituent effects on the gas-phase fragmentation reactions of sulfonium ion containing peptides.

    PubMed

    Sierakowski, James; Amunugama, Mahasilu; Roberts, Kade D; Reid, Gavin E

    2007-01-01

    The multistage mass spectrometric (MS/MS and MS3) gas-phase fragmentation reactions of methionine side-chain sulfonium ion containing peptides formed by reaction with a series of para-substituted phenacyl bromide (XBr where X=CH2COC6H4R, and R=--COOH, --COOCH3, --H, --CH3 and --CH2CH3) alkylating reagents have been examined in a linear quadrupole ion trap mass spectrometer. MS/MS of the singly (M+) and multiply ([M++nH](n+1)+) charged precursor ions results in exclusive dissociation at the fixed charge containing side chain, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility). However, loss of the methylphenacyl sulfide side-chain fragment as a neutral versus charged (protonated) species was observed to be highly dependent on the proton mobility of the precursor ion, and the identity of the phenacyl group para-substituent. Molecular orbital calculations were performed at the B3LYP/6-31+G** level of theory to calculate the theoretical proton affinities of the neutral side-chain fragments. The log of the ratio of neutral versus protonated side-chain fragment losses from the derivatized side chain were found to exhibit a linear dependence on the proton affinity of the side-chain fragmentation product, as well as the proton affinities of the peptide product ions. Finally, MS3 dissociation of the nominally identical neutral and protonated loss product ions formed by MS/MS of the [M++H]2+ and [M++2H]3+ precursor ions, respectively, from the peptide GAILM(X)GAILK revealed significant differences in the abundances of the resultant product ions. These results suggest that the protonated peptide product ions formed by gas-phase fragmentation of sulfonium ion containing precursors in an ion trap mass spectrometer do not necessarily undergo intramolecular proton 'scrambling' prior to their further dissociation, in contrast to that previously demonstrated for peptide ions introduced by external ionization sources.

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

    PubMed Central

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

    2016-01-01

    The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility-mass spectrometry (TW IM-MS)for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation (CID) 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 were being separated. Collision cross sections (CCSs) of the isomers in positive and negative fragmentation mode were estimated from TW IM-MS data using dextran glycans as calibrant. More complete CCS 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 (CID) spectra of all resolved isomers are discussed. PMID:26956389

  10. 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.

  11. Visualizing ion relaxation in the transport of short DNA fragments.

    PubMed Central

    Allison, S A; Wang, H; Laue, T M; Wilson, T J; Wooll, J O

    1999-01-01

    Ion relaxation plays an important role in a wide range of phenomena involving the transport of charged biomolecules. Ion relaxation is responsible for reducing sedimentation and diffusion constants, reducing electrophoretic mobilities, increasing intrinsic viscosities, and, for biomolecules that lack a permanent electric dipole moment, provides a mechanism for orienting them in an external electric field. Recently, a numerical boundary element method was developed to solve the coupled Navier-Stokes, Poisson, and ion transport equations for a polyion modeled as a rigid body of arbitrary size, shape, and charge distribution. This method has subsequently been used to compute the electrophoretic mobilities and intrinsic viscosities of a number of model proteins and DNA fragments. The primary purpose of the present work is to examine the effect of ion relaxation on the ion density and fluid velocity fields around short DNA fragments (20 and 40 bp). Contour density as well as vector field diagrams of the various scalar and vector fields are presented and discussed at monovalent salt concentrations of 0.03 and 0.11 M. In addition, the net charge current fluxes in the vicinity of the DNA fragments at low and high salt concentrations are briefly examined and discussed. PMID:10233066

  12. 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.

  13. 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.

  14. DNA Fragmentation in mammalian cells exposed to various light ions

    NASA Astrophysics Data System (ADS)

    Belli, M.; Cherubini, R.; Dalla Vecchia, M.; Dini, V.; Esposito, G.; Moschini, G.; Sapora, O.; Signoretti, C.; Simone, G.; Sorrentino, E.; Tabocchini, M. A.

    Elucidation of how effects of densely ionizing radiation at cellular level are linked to DNA damage is fundamental for a better understanding of the mechanisms leading to genomic damage (especially chromosome aberrations) and developing biophysical models to predict space radiation effects. We have investigated the DNA fragmentation patterns induced in Chinese hamster V79 cells by 31 keV/μm protons, 123 keV/μm helium-4 ions and γ-rays in the size range 0.023-5.7 Mbp, using calibrated Pulsed Field Gel Electrophoresis (PFGE). The frequency distributions of fragments induced by the charged particles were shifted towards smaller sizes with respct to that induced by comparable doses of γ-rays. The DSB yields, evaluated from the fragments induced in the size range studied, were higher for protons and helium ions than for γ-rays by a factor of about 1.9 and 1.2, respectively. However, these ratios do not adequately reflect the RBE observed on the same cells for inactivation and mutation induced by these beams. This is a further indication for the lack of correlation between the effects exerted at cellular level and the initial yield of DSB. The dependence on radiation quality of the fragmentation pattern suggests that it may have a role in damage reparability. We have analyzed these patterns with a "random breakage" model generalized in order to consider the initial non-random distribution of the DNA molecules. Our results suggest that a random breakage mechanism can describe with a reasonable approximation the DNA fragmentation induced by γ-rays, while the approximation is not so good for light ions, likely due to the interplay between ion tracks and chromatin organization at the loop level.

  15. A new copper containing MALDI matrix that yields high abundances of [peptide + Cu]+ ions.

    PubMed

    Wu, Zhaoxiang; Fernandez-Lima, Francisco A; Perez, Lisa M; Russell, David H

    2009-07-01

    The dinuclear copper complex (alpha-cyano-4-hydroxycinnamic acid (CHCA) copper salt (CHCA)(4)Cu(2)), synthesized by reacting CHCA with copper oxide (CuO), yields increased abundances of [M + xCu - (x-1)H](+) (x = 1-6) ions when used as a matrix for matrix-assisted laser desorption ionization (355 nm Nd:YAG laser). The yield of [M + xCu - (x-1)H](+) (x = 1 to approximately 6) ion is much greater than that obtained by mixing peptides with copper salts or directly depositing peptides onto oxidized copper surfaces. The increased ion yields for [M + xCu - (x-1)H](+) facilitate studies of biologically important copper binding peptides. For example, using this matrix we have investigated site-specific copper binding of several peptides using fragmentation chemistry of [M + Cu](+) and [M + 2Cu - H](+) ions. The fragmentation studies reveal interesting insight on Cu binding preferences for basic amino acids. Most notable is the fact that the binding of a single Cu(+) ion and two Cu(+) ions are quite different, and these differences are explained in terms of intramolecular interactions of the peptide-Cu ionic complex.

  16. Ammonium and sulfate ion release of histamine from lung fragments.

    PubMed

    Charles, J M; Menzel, D B

    1975-06-01

    In vitro studies with guinea pig lung fragments incubated with 10- to 200-mM concentrations of ammonium ion demonstrated the release of substanial quantities of histamine. Of the anions tested with ammonium ion, sulfate was the most potent, while nitrate and acetate ions were of intermediate potency and chloride was less potent. An osmotic effect is unlikely since equal concentrations of sodium chloride failed to release histamine. Isoproterenol, known to decrease anaphylactic histamine release, and acetycholine, known to increase histamine release, had no effect on the ammonium sulfate-mediated release of histamine. N-6 2'-O-Dibutyryladenosine 3',5' monophosphate (dibutyryl c-AMP) was also ineffective. These studies suggest that the inhalation irritation associated with certain sulfate and other salts, may be a function of their ability to release histamine in the presence of amonium ion.

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

    PubMed

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

    2015-01-01

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

  18. Soft-x-ray fragmentation studies of molecular ions

    NASA Astrophysics Data System (ADS)

    Wolf, Andreas; Pedersen, Henrik B.; Lammich, Lutz; Jordon-Thaden, Brandon; Altevogt, Simon; Domesle, Christian; Hergenhahn, Uwe; Förstel, Marko; Heber, Oded

    2010-10-01

    Imaging of photofragments from molecular ions after irradiation by soft x-ray photons has been realized at the ion beam infrastructure TIFF set up at the FLASH facility. Photodissociation of the two-electron system HeH+ at 38.7 eV revealed the electronic excitations and the charge-state ratios for the products of this process, reflecting the non-adiabatic dissociation dynamics through multiple avoided crossings among the HeH+ Rydberg potential curves. Dissociative ionization of the protonated water molecules H3O+ and H5O+2 at 90 eV revealed the main fragmentation pathways after the production of valence vacancies in these ionic species, which include a strong three-body channel with a neutral fragment (OH + H+ + H+) in H3O+ photolysis and a significant two-body fragmentation channel (H3O++ H2O+) in H5O+2 photolysis. The measurements yield absolute cross sections and fragment angular distributions. Increased precision and sensitivity of the technique were realized in recent developments, creating a tool for exploring x-ray excited molecular states under highly controlled target conditions challenging detailed theoretical understanding.

  19. Evidence for sequence scrambling in collision-induced dissociation of y-type fragment ions.

    PubMed

    Miladi, Mahsan; Harper, Brett; Solouki, Touradj

    2013-11-01

    Sequence scrambling from y-type fragment ions has not been previously reported. In a study designed to probe structural variations among b-type fragment ions, it was noted that y fragment ions might also yield sequence-scrambled ions. In this study, we examined the possibility and extent of sequence-scrambled fragment ion generation from collision-induced dissociation (CID) of y-type ions from four peptides (all containing basic residues near the C-terminus) including: AAAAHAA-NH2 (where "A" denotes carbon thirteen ((13)C1) isotope on the alanine carbonyl group), des-acetylated-α-melanocyte (SYSMEHFRWGKPV-NH2), angiotensin II antipeptide (EGVYVHPV), and glu-fibrinopeptide b (EGVNDNEEGFFSAR). We investigated fragmentation patterns of 32 y-type fragment ions, including y fragment ions with different charge states (+1 to +3) and sizes (3 to 12 amino acids). Sequence-scrambled fragment ions were observed from ~50 % (16 out of 32) of the studied y-type ions. However, observed sequence-scrambled ions had low relative intensities from ~0.1 % to a maximum of ~12 %. We present and discuss potential mechanisms for generation of sequence-scrambled fragment ions. To the best of our knowledge, results on y fragment dissociation presented here provide the first experimental evidence for generation of sequence-scrambled fragments from CID of y ions through intermediate cyclic "b-type" ions.

  20. Internal energy and fragmentation of ions produced in electrospray sources.

    PubMed

    Gabelica, Valérie; De Pauw, Edwin

    2005-01-01

    This review addresses the determination of the internal energy of ions produced by electrospray ionization (ESI) sources, and the influence of the internal energy on analyte fragmentation. A control of the analyte internal energy is crucial for several applications of electrospray mass spectrometry, like structural studies, construction of reproducible and exportable spectral libraries, analysis of non-covalent complexes. Sections II and III summarize the Electrospray mechanisms and source design considerations which are relevant to the problem of internal energy, and Section IV gives an overview of the inter-relationships between ion internal energy, reaction time scale, and analyte fragmentation. In these three sections we tried to make the most important theoretical elements understandable by all ESI users, and their understanding requires a minimal background in physical chemistry. We then present the different approaches used to experimentally determine the ion internal energy, as well as various attempts in modeling the internal energy uptake in electrospray sources. Finally, a tentative comparison between electrospray and other ionization sources is made. As the reader will see, although many reports appeared on the subject, the knowledge in the field of internal energy of ions produced by soft ionization sources is still scarce, because of the complexity of the system, and this is what makes this area of research so interesting. The last section presents some perspectives for future research.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

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

    PubMed Central

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

    2015-01-01

    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

  10. 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.

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

    SciTech Connect

    Engelage, J.; Crawford, H.J.; Greiner, L.; Kuo, C.

    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.

  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. Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap.

    PubMed

    Wassermann, Tobias N; Boyarkin, Oleg V; Paizs, Béla; Rizzo, Thomas R

    2012-06-01

    We have applied conformer-selective infrared-ultraviolet (IR-UV) double-resonance photofragment spectroscopy at low temperatures in an ion trap mass spectrometer for the spectroscopic characterization of peptide fragment ions. We investigate b- and a-type ions formed by collision-induced dissociation from protonated leucine-enkephalin. The vibrational analysis and assignment are supported by nitrogen-15 isotopic substitution of individual amino acid residues and assisted by density functional theory calculations. Under such conditions, b-type ions of different size are found to appear exclusively as linear oxazolone structures with protonation on the N-terminus, while a rearrangement reaction is confirmed for the a (4) ion in which the side chain of the C-terminal phenylalanine residue is transferred to the N-terminal side of the molecule. The vibrational spectra that we present here provide a particularly stringent test for theoretical approaches.

  14. Repeatability and reproducibility of product ion abundances in electron capture dissociation mass spectrometry of peptides.

    PubMed

    Ben Hamidane, Hisham; Vorobyev, Aleksey; Tsybin, Yury O

    2011-01-01

    Site-specific reproducibility and repeatability of electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) are of fundamental importance for product ion abundance (PIA)-based peptide and protein structure analysis. However, despite the growing interest in ECD PIA-based applications, these parameters have not yet been investigated in a consistent manner. Here, we first provide a detailed description of the experimental parameters for ECD-based tandem mass spectrometry performed on a hybrid linear ion trap (LTQ) FT-ICR MS. In the following, we describe the evaluation and comparison of ECD and infrared multiphoton dissociation (IRMPD) PIA methodologies upon variation of a number of experimental parameters, for example, cathode potential (electron energy), laser power, electron and photon irradiation periods and pre- irradiation delays, as well as precursor ion number. Ranges of experimental parameters that yielded an average PIA variation below 5% and 15% were determined for ECD and IRMPD, respectively. We report cleavage site-dependent ECD PIA variation below 20% and correlation coefficients between fragmentation patterns superior to 0.95 for experiments performed on three FT-ICR MS instruments. Overall, the encouraging results obtained for ECD PIA reproducibility and repeatability support the use of ECD PIA as a complementary source of information to m/z data in radical-induced dissociation applied for peptide and protein structure analysis.

  15. Sequence-specific fragmentation of matrix-assisted laser-desorbed protein/peptide ions.

    PubMed

    Brown, R S; Lennon, J J

    1995-11-01

    By utilizing delayed pulsed ion extraction of ions generated via the matrix-assisted laser desorption/ionization (MALDI) technique, fast (< 320 ns) metastable ion fragmentation is observed for both peptide and protein analytes in the ion source of a linear time-of-flight mass spectrometer. Small peptides such as the oxidized B chain of bovine insulin exhibit fragmentation at the amide linking bond between peptide residues. Overlapping sequence information is provided by fragmentation from both the C- and N-terminal ends of the peptide (cn-, yn-, and z*n-type fragment ions). Larger proteins can also exhibit a wealth of sequence specific fragment ions in favorable cases. One example is cytochrome c, which undergoes substantial (approximately 80%) fast fragmentation at the amide bonds along the amino acid backbone of the protein. Only amide bond cleavages initiating from the C-terminal end (cn fragments) are observed. The observed fragmentation pattern provides a significant amount of potential sequence information for these molecules. External mass calibration of the intact protonated molecular ions is demonstrated with mass accuracies typically around 100 ppm. Mass accuracies for the observed fragment ions ranged from +/- 0.20 Da for the smaller peptides studied (i.e., oxidized B chain of bovine insulin) to +/- 0.38 Da for the largest protein studied (cytochrome c), based upon the known sequences.

  16. Edge-interior differences in the species richness and abundance of drosophilids in a semideciduous forest fragment.

    PubMed

    Penariol, Leiza V; Madi-Ravazzi, Lilian

    2013-12-01

    Habitat fragmentation is the main cause of biodiversity loss, as remnant fragments are exposed to negative influences that include edge effects, prevention of migration, declines in effective population sizes, loss of genetic variability and invasion of exotic species. The Drosophilidae (Diptera), especially species of the genus Drosophila, which are highly sensitive to environmental variation, have been used as bioindicators. A twelve-month field study was conducted to evaluate the abundance and richness of drosophilids in an edge-interior transect in a fragment of semideciduous forest in São Paulo State, Brazil. One objective of the study was to evaluate the applied methodology with respect to its potential use in future studies addressing the monitoring and conservation of threatened areas. The species abundance along the transect showed a clear gradient, with species associated with disturbed environments, such as Drosophila simulans, Scaptodrosophila latifasciaeformis and Zaprionus indianus, being collected at the fragment edge and the species D. willistoni and D. mediostriata being found in the fragment's interior. Replacement of these species occurred at approximately 60 meters from the edge, which may be a reflection of edge effects on species abundance and richness because the species found within the habitat fragment are more sensitive to variations in temperature and humidity than those sampled near the edge. The results support the use of this methodology in studies on environmental impacts.

  17. 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.

  18. Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

    PubMed

    van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B

    2015-12-01

    Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.

  19. Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    van Agthoven, Maria A.; Barrow, Mark P.; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A.; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B.

    2015-12-01

    Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules.

  20. 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.

  1. 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.

  2. Fragmentation dynamics of CO(2)(3+) investigated by multiple electron capture in collisions with slow highly charged ions.

    PubMed

    Neumann, N; Hant, D; Schmidt, L Ph H; Titze, J; Jahnke, T; Czasch, A; Schöffler, M S; Kreidi, K; Jagutzki, O; Schmidt-Böcking, H; Dörner, R

    2010-03-12

    Fragmentation of highly charged molecular ions or clusters consisting of more than two atoms can proceed in a one step synchronous manner where all bonds break simultaneously or sequentially by emitting one ion after the other. We separated these decay channels for the fragmentation of CO(2)(3+) ions by measuring the momenta of the ionic fragments. We show that the total energy deposited in the molecular ion is a control parameter which switches between three distinct fragmentation pathways: the sequential fragmentation in which the emission of an O(+) ion leaves a rotating CO(2+) ion behind that fragments after a time delay, the Coulomb explosion and an in-between fragmentation--the asynchronous dissociation. These mechanisms are directly distinguishable in Dalitz plots and Newton diagrams of the fragment momenta. The CO(2)(3+) ions are produced by multiple electron capture in collisions with 3.2 keV/u Ar(8+) ions.

  3. In situ ion microprobe U-Pb dating and REE abundances of a carboniferous conodont

    NASA Astrophysics Data System (ADS)

    Sano, Yuji; Terada, Kentaro

    We report here in situ ion microprobe U-Pb dating of a conodont micro-fossil using an ion microprobe method. Thirteen spots on the single fragment of the Carboniferous conodont (size: approximately 800 µm × 100 µm) yield a 238U/206Pb isochron age of 323±36 Ma and a Tera-Wasserburg concordia intercept age of 332±44 Ma in a three-dimensional 238U/206Pb-207Pb/206 Pb-204Pb/206Pb diagram. These ages are consistent with the depositional and early diagenetic ages of the fossil in its host Mississippian sedimentary sequence within experimental error. The success of the method depends on the chemical fractionation of U from Pb within a hundred-µm length scale and the consequent variations in Pb isotopic compositions due to radioactive decay. Shale-normalized rare earth element (REE) abundances of two spots on the same sample show flat patterns from light REE to middle REE and decreases from middle REE to heavy REE with negative anomalies of both Ce and Eu. The REE characteristics are significantly different from those of Devonian conodonts reported by other workers, suggesting discrepant redox states and/or formation environments.

  4. Fragmentation of H2O Molecules by slow multiply charged Ions

    NASA Astrophysics Data System (ADS)

    Pešić, Z. D.; Hellhammer, R.; Sulik, B.; Stolterfoht, N.

    2008-12-01

    We used the method of fragment ion spectroscopy to study ion-induced fragmentation of water molecules. An overview of our results for the energy and angular distribution of ionic fragments following the interaction with keV ions, ranging from 5 keV He2+ to 2 and 90 keV Ne9+, is presented. Specific attention is paid to the strong dependence on the projectile charge state and energy. The interpretation of the experimental results is guided by a classical trajectory simulation based on a Coulomb explosion model. In particular, the model elucidates the forward-backward asymmetry of the energy and intensity of the H+ fragments. The integrated cross-sections over all fragmentation channels, determined on the absolute scale, compare well with the cross-sections derived using the classical over-barrier model.

  5. Jet energy loss and fragmentation in heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Kharzeev, Dmitri E.; Loshaj, Frashër

    2013-04-01

    Recent LHC results indicate a suppression of jet fragmentation functions in Pb-Pb collisions at intermediate values of ξ=ln⁡(1/z). This seems to contradict the picture of energy loss based on the induced QCD radiation that is expected to lead to the enhancement of in-medium fragmentation functions. We use an effective 1+1 dimensional quasi-Abelian model to describe the dynamical modification of jet fragmentation in the medium. We find that this approach describes the data, and argue that there is no contradiction between the LHC results and the picture of QCD radiation induced by the in-medium scattering of the jet. The physics that underlies the suppression of the in-medium fragmentation function at intermediate values of ξ=ln⁡(1/z) is the partial screening of the color charge of the jet by the comoving medium-induced gluon.

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

    PubMed

    Pyritz, Lennart W; Büntge, Anna B S; Herzog, Sebastian K; Kessler, Michael

    2010-10-01

    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.

  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. Neutrons produced by known energies of ions abundant in space

    NASA Technical Reports Server (NTRS)

    Wadman, W. W., III

    1972-01-01

    Particle accelerator radiation measurements are applied to the problem of calculating biological dose from radiation produced in the walls of a spacecraft by various ions in space. Neutrons, one of the products of the interactions of energetic ions with matter, are usually quite penetrating and have large values of Q.F. or R.B.E. Ions of helium, boron, carbon, nitrogen, and oxygen were accelerated and directed onto target materials of copper or tantalum. The secondary neutron production was determined. Studies were made of the angular distribution and an inferred neutron spectrum was calculated from activities of threshold reaction detectors.

  9. 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.

  10. 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.

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

    DOE PAGES

    Krutenkova, Anna P.; Abramov, B. M.; Alekseev, P. 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 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

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

    DOE PAGES

    Krutenkova, A. P.; Abramov, B. M.; Alekseev, P. N.; ...

    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

  13. 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.

  14. Combined Use of Post-Ion Mobility/Collision-Induced Dissociation and Chemometrics for b Fragment Ion Analysis

    NASA Astrophysics Data System (ADS)

    Zekavat, Behrooz; Miladi, Mahsan; Becker, Christopher; Munisamy, Sharon M.; Solouki, Touradj

    2013-09-01

    Although structural isomers may yield indistinguishable ion mobility (IM) arrival times and similar fragment ions in tandem mass spectrometry (MS), it is demonstrated that post-IM/collision-induced dissociation MS (post-IM/CID MS) combined with chemometrics can enable independent study of the IM-overlapped isomers. The new approach allowed us to investigate the propensity of selected b type fragment ions from AlaAlaAlaHisAlaAlaAla-NH2 (AAA(His)AAA) heptapeptide to form different isomers. Principle component analysis (PCA) of the unresolved post-IM/CID profiles indicated the presence of two different isomer types for b4 +, b5 +, and b6 + and a single isomer type for b7 + fragments of AAA(His)AAA. We employed a simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) to calculate the total IM profiles and CID mass spectra of b fragment isomers. The deconvoluted CID mass spectra showed discernible fragmentation patterns for the two isomers of b4 +, b5 +, and b6 + fragments. Under our experimental conditions, calculated percentages of the "cyclic" isomers (at the 95 % confidence level for n = 3) for b4 +, b5 +, and b6 + were 61 (± 5) %, 36 (± 5) %, and 48 (± 2) %, respectively. Results from the SIMPLISMA deconvolution of b5 + species resembled the CID MS patterns of fully resolved IM profiles for the two b5 + isomers. The "cyclic" isomers for each of the two-component b fragment ions were less susceptible to ion fragmentation than their "linear" counterparts.

  15. Orientation and alignment effects in ion-induced fragmentation of water: A triple coincidence study

    SciTech Connect

    Rajput, Jyoti; Safvan, C. P.

    2014-10-28

    The technique of recoil ion momentum spectroscopy is employed to determine the complete momentum vectors for three fragment dissociation channels, [D{sub 2}O]{sup (q+2)} → (D{sup +} + D{sup +} + O{sup q+}) with q = 1, 2, or 3 formed in collisions of isolated water molecules with 450 keV Xe{sup 9+} ions. The kinetic energy released in each of these dissociation channels is measured and angular correlations between the fragment momenta are determined. From the angular correlations of the three fragment ions with the direction of the incoming beam, a strong anisotropy in the emission of recoil fragments is reported. It is inferred that the molecular plane prefers to lie orthogonal to the incoming beam direction with certain orientations being more preferred than others and a clear signature of non-coplanar dissociation is also observed.

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

    USGS Publications Warehouse

    Laakkonen, Juha; Fisher, Robert N.; Case, Ted J.

    2001-01-01

    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.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.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.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.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.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 make both species

  17. 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.

  18. Fragmentation of phosphorylated and singly charged peptide ions via interaction with metastable atoms

    PubMed Central

    Berkout, Vadym D.; Doroshenko, Vladimir M.

    2008-01-01

    Fragmentation of phosphorylated peptide ions via interaction with electronically excited metastable argon atoms was studied in a linear trap – time-of-flight mass spectrometer. Doubly charged ions of phosphorylated peptides from an Enolase digest were produced by electrospray ionization and subjected to a metastable atom beam in the linear trap. The metastable argon atoms were generated using a glow-discharge source. An intensive series of c- and z- ions were observed in all cases, with the phosphorylation group intact. The formation of molecular radical cations with reduced charge indicated that an electron transfer from a highly excited metastable state of argon to the peptide cation occurred. Additionally, singly charged Bradykinin, Substance P and Fibrinopeptide A molecular ions were fragmented via interaction with electronically excited metastable helium atoms. The fragmentation mechanism was different in this case and involved Penning ionization. PMID:19956340

  19. Fragmentation of phosphorylated and singly charged peptide ions via interaction with metastable atoms.

    PubMed

    Berkout, Vadym D; Doroshenko, Vladimir M

    2008-12-01

    Fragmentation of phosphorylated peptide ions via interaction with electronically excited metastable argon atoms was studied in a linear trap - time-of-flight mass spectrometer. Doubly charged ions of phosphorylated peptides from an Enolase digest were produced by electrospray ionization and subjected to a metastable atom beam in the linear trap. The metastable argon atoms were generated using a glow-discharge source. An intensive series of c- and z- ions were observed in all cases, with the phosphorylation group intact. The formation of molecular radical cations with reduced charge indicated that an electron transfer from a highly excited metastable state of argon to the peptide cation occurred. Additionally, singly charged Bradykinin, Substance P and Fibrinopeptide A molecular ions were fragmented via interaction with electronically excited metastable helium atoms. The fragmentation mechanism was different in this case and involved Penning ionization.

  20. 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.

  1. 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.

  2. Passive and active fragment ion mass defect labeling: distinct proteomics potential of iodine-based reagents.

    PubMed

    Shi, Yu; Bajrami, Bekim; Yao, Xudong

    2009-08-01

    The exact mass of a peptide differs characteristically from its nominal mass by a value called the mass defect. Limited by possible elemental compositions, the mass defect of peptides has a restricted range, resulting in an unoccupied mass spectral space in every mass-to-charge unit. The method of fragment ion mass defect labeling (FIMDL) places characteristic fragment ions of modified peptides as reporters into unused spectral space where no native peptide fragment ions exist. In this labeling method, peptides are chemically modified in solution and the modified peptides, upon gas-phase collision in a mass spectrometer, generate fragment ions with significantly shifted mass defects. In this work, the efficiency of iodine stable isotope-containing reagents for shifting mass defects of peptide fragment ions was systematically investigated, through derivatization of peptide N-termini with various reagents containing one or more chlorine, bromine, or iodine atoms. The observed efficiency for the iodine atom placing the labeled fragment ions into unoccupied spectral space agreed well with theoretical predictions from averagine-scaling analysis of ion masses. On the basis of the gas-phase stability of different labeling groups and their involvement in collisional dissociation of modified peptides, peptide modifications were classified into three categories: passive, type I active, and type II active. Each modification type has its unique potential in different proteome analyses. Possible proteomics applications of FIMDL are discussed and compared with proteome analyses currently being practiced in the field. Principles obtained from this survey study will provide a guideline in developing novel FIMDL reagents for advanced proteomics analysis.

  3. 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.

  4. Effects of Alkali Metal Ion Cationization on Fragmentation Pathways of Triazole-Epothilone

    NASA Astrophysics Data System (ADS)

    Duan, Xiyan; Luo, Guoan; Chen, Yue; Kong, Xianglei

    2012-06-01

    The collisionally activated dissociation mass spectra of the protonated and alkali metal cationized ions of a triazole-epothilone analogue were studied in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation pathway of the protonated ion was characterized by the loss of the unit of C3H4O3. However, another fragmentation pathway with the loss of C3H2O2 was identified for the complex ions with Na+, K+, Rb+, and Cs+. The branching ratio of the second pathway increases with the increment of the size of alkali metal ions. Theoretical calculations based on density functional theory (DFT) method show the difference in the binding position of the proton and the metal ions. With the increase of the radii of the metal ions, progressive changes in the macrocycle of the compound are induced, which cause the corresponding change in their fragmentation pathways. It has also been found that the interaction energy between the compound and the metal ion decreases with increase in the size of the latter. This is consistent with the experimental results, which show that cesiated complexes readily eject Cs+ when subject to collisions.

  5. 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

  6. 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.

  7. 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.

  8. Fragmentation of α- and β-alanine molecules by ions at Bragg-peak energies

    NASA Astrophysics Data System (ADS)

    Bari, S.; Sobocinski, P.; Postma, J.; Alvarado, F.; Hoekstra, R.; Bernigaud, V.; Manil, B.; Rangama, J.; Huber, B.; Schlathölter, T.

    2008-02-01

    The interaction of keV He+, He2+, and O5+ ions with isolated α and β isomers of the amino acid alanine was studied by means of high resolution coincidence time-of-flight mass spectrometry. We observed a strong isomer dependence of characteristic fragmentation channels which manifests in strongly altered branching ratios. Despite the ultrashort initial perturbation by the incoming ion, evidence for molecular rearrangement leading to the formation of H3+ was found. The measured kinetic energies of ionic alanine fragments can be sufficient to induce secondary damage to DNA in a biological environment.

  9. In-source fragmentation technique for the production of thermalized ions.

    PubMed

    Carl, Damon R; Moision, Robert M; Armentrout, P B

    2009-12-01

    Our electrospray ionization-ion funnel-rf hexapole (ESI-IF-6P) source is designed to produce ions for threshold collision-induced dissociation (TCID) studies in a guided ion beam mass spectrometer. This ion source forms an initial distribution of Ca2+(H2O)x ions where x is 6-9. A new in-source fragmentation technique within the hexapole ion guide of the source is described, which is easy to implement and of modest machining and electrical costs, and is able to generate smaller Ca2+(H2O)x complexes, where x = 2-5. Fragmentation is achieved by biasing an assembly of six 0.25 in. long electrodes that are inserted between the hexapole rods. The assembly is positioned in the high-pressure region of the source such that newly formed Ca2+(H2O)x ions undergo enough collisions to become thermalized, as verified by TCID studies. From the initial distribution of ions, fragmentation proceeds along the lowest energy pathway, which corresponds to sequential water loss for most complexes. However, the Ca2+(H2O) complex cannot be formed using this method because charge separation into CaOH+ and H3O+ becomes the lowest energy pathway from the Ca2+(H2O)2 complex. Therefore, this fragmentation technique can be used to identify the critical size complex for M2+(H2O)x systems, which we define as the complex size (x) at which charge separation becomes a lower energy pathway compared with simple ligand loss.

  10. Influence of fragment reaction of relativistic heavy charged particles on heavy-ion radiotherapy

    NASA Astrophysics Data System (ADS)

    Matsufuji, Naruhiro; Fukumura, Akifumi; Komori, Masataka; Kanai, Tatsuaki; Kohno, Toshiyuki

    2003-06-01

    The production of projectile fragments is one of the most important, but not yet perfectly understood, problems to be considered when planning for the utilization of high-energy heavy charged particles for radiotherapy. This paper reports our investigation of the fragments' fluence and linear energy transfer (LET) spectra produced from various incident ions using an experimental approach to reveal these physical qualities of the beams. Polymethyl methacrylate, as a substitute for the human body, was used as a target. A ΔE-E counter telescope with a plastic scintillator and a BGO scintillator made it possible to identify the species of fragments based on differences of various elements. By combining a gas-flow proportional counter with a counter telescope system, LET spectra as well as fluence spectra of the fragments were derived for each element down from the primary particles to hydrogen. Among them, the information on hydrogen and helium fragments was derived for the first time. The result revealed that the number of light fragments, such as hydrogen and helium, became larger than the number of primaries in the vicinity of the range end. However, the greater part of the dose delivered to a cell was still governed by the primaries. The calculated result of a simulation used for heavy-ion radiotherapy indicated room for improving the reaction model.

  11. 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.

  12. 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.

  13. 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}

  14. Negative ion fragmentations of deprotonated heterocycles. The isothiazole, thiazole, isoxazole, and oxazole ring systems

    NASA Astrophysics Data System (ADS)

    Adams, Gregory W.; Bowie, John H.; Hayes, Roger N.

    1992-05-01

    The major collision-induced dissociations of deprotonated isothiazole occur from the 5-anion, while deprotonated thiazole fragments almost equally through the 2- and 5-anions. Both 5-anions fragment by a simple retro cleavage yielding HC2S- and HCN. The 5-anion of isothiazole and the 2-anion of thiazole also rearrange to the common intermediate -SCH=CHCN which decomposes by losses of H2, HCN and H2S. There is no evidence for direct interconversion of isothiazole and thiazole anions. The spectra of deprotonated methylisothiazoles are complex, but the major fragmentations are of ring deprotonated ions and are generally analogous to the parent systems. The fragmentation behaviour of deprotonated isoxazole and oxazole is analogous to that of the isothiazole and thiazole systems.

  15. The abundance of N-14 at the cosmic-ray source - A study using new fragmentation cross sections

    NASA Technical Reports Server (NTRS)

    Gupta, M.; Webber, W. R.

    1989-01-01

    The abundance of N-14 at the Galactic cosmic ray source was examined using new fragmentation cross sections measured by the University of New Hampshire group for 12 different source nuclei (ranging from C-12 to Ni-58) which cover about 70 percent of all cosmic-ray nuclei arriving at earth. A new cross-section program was used to estimate unmeasured cross sections. These cross sections were then incorporated into a Galactic propagation program to calculate the interstellar production of B and N. Results indicate that atomic selection effects alone cannot explain adequately the observed depletion of N-14 relative to O-16 in the cosmic-ray source with respect to the solar corona, indicating that some part of this depletion must have a nuclear/nucleosynthetic origin.

  16. Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra.

    PubMed

    Zhang, Jingfen; Gao, Wen; Cai, Jinjin; He, Simin; Zeng, Rong; Chen, Runsheng

    2005-01-01

    A number of different approaches have been proposed to predict elemental component formulas (or molecular formulas) of molecular ions in low and medium resolution mass spectra. Most of them rely on isotope patterns, enumerate all possible formulas for an ion, and exclude certain formulas violating chemical constraints. However, these methods cannot be well generalized to the component prediction of fragment ions in tandem mass spectra. In this paper, a new method, FFP (Fragment ion Formula Prediction), is presented to predict elemental component formulas of fragment ions. In the FFP method, the prediction of the best formulas is converted into the minimization of the distance between theoretical and observed isotope patterns. And, then, a novel local search model is proposed to generate a set of candidate formulas efficiently. After the search, FFP applies a new multiconstraint filtering to exclude as many invalid and improbable formulas as possible. FFP is experimentally compared with the previous enumeration methods, and shown to outperform them significantly. The results of this paper can help to improve the reliability of de novo in the identification of peptide sequences.

  17. Domestic dogs in a fragmented landscape in the Brazilian Atlantic Forest: abundance, habitat use and caring by owners.

    PubMed

    Torres, P C; Prado, P I

    2010-11-01

    This study aimed at estimating the population size and attitudes of residents towards caring for domestic dogs, through questionnaire surveys, as well as the frequency of these animals in different habitats (anthropic and forest patch), using scent stations. The study was conducted in a severely fragmented area of the Brazilian Atlantic Forest. A large number of unrestricted dogs was recorded, averaging 6.2 ind/km². These dogs have owners and are regularly fed. Dog records decreased from the anthropogenic matrix to the forest patch edge, which suggests that dogs act as an edge effect on forest patches. Encounters between domestic dog and wild animals can still be frequent in severely fragmented landscapes, mainly at the forest edges. However the fact that most dogs have an owner and are more frequent in the anthropic habitat suggests that their putative effects are less severe than expected for a carnivore of such abundance, but the reinforcement of responsible ownership is needed to further ameliorate such effects.

  18. Kinetic and equilibrium metal-ion-binding behaviour reflected in a metal-ion-dependent antigenic determinant in bovine prothrombin. Comparison with bovine prothrombin fragment 1.

    PubMed Central

    Madar, D A; Hall, T J; Hiskey, R G; Koehler, K A

    1981-01-01

    Rabbit anti-(bovine prothrombin fragment 1) antibodies were fractionated by using fragment-1 affinity chromatography in the absence of metal ions, and showed an absolute requirement for the presence of metal ions in their interactions with bovine fragment 1 or prothrombin. These antibodies were employed to evaluate both the rate constants for a protein conformation change and the equilibrium metal-ion binding to isolated bovine fragment 1 and intact prothrombin. The close similarity of the rates obtained for the conformation change in fragment 1 and those observed in prothrombin indicated that the same process is involved in both proteins and that the non-fragment-1 region of the prothrombin has essentially no effect on this process in the fragment-1 region. Equilibrium metal-ion-binding studies indicate that the details of the metal-ion-binding process in fragment 1 and prothrombin are essentially the same. We conclude that the metal-ion-binding behaviour of the fragment-1 domain of intact prothrombin is identical with that of isolated fragment 1. PMID:6171251

  19. Time slicing in 3D momentum imaging of the hydrogen molecular ion photo-fragmentation

    NASA Astrophysics Data System (ADS)

    Kaya, N.; Kaya, G.; Pham, F. V.; Strohaber, J.; Kolomenskii, A. A.; Schuessler, H. A.

    2017-02-01

    Photo-fragmentation of the hydrogen molecular ion was investigated with 800 nm, 50 fs laser pulses by employing a time slicing 3D imaging technique that enables the simultaneous measurement of all three momentum components which are linearly related with the pixel position and slicing time. This is done for each individual product particle arriving at the detector. This mode of detection allows us to directly measure the three-dimensional fragment momentum vector distribution without having to rely on mathematical reconstruction methods, which additionally require the investigated system to be cylindrically symmetric. We experimentally reconstruct the laser-induced photo-fragmentation of the hydrogen molecular ion. In previous experiments, neutral molecules were used as a target, but in this work, performed with molecular ions, the initial vibrational level populations are well-defined after electron bombardment, which facilitates the interpretation. We show that the employed time-slicing technique allows us to register the fragment momentum distribution that reflects the initial molecular states with greater detail, revealing features that were concealed in the full time-integrated distribution on the detector.

  20. 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.

  1. 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.

  2. 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.

  3. Collision-induced dissociation of fatty acid [M - 2H + Na]- ions: charge-directed fragmentation and assignment of double bond position.

    PubMed

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

    2014-11-01

    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: ∆(9,12,15)18:3, ∆(6,9,12)18:3, and ∆(5,8,11)18:3. 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.

  4. Temperature parameters in the fragmentation of carbon ions at the energy of 0.6 GeV/nucleon

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

    Momentum distributions of nuclear fragments at an angle of 3.5° in the interaction of 0.6-GeV/nucleon carbon ions with a beryllium target are measured in the FRAGM experiment on the ITEP-TWAC facility. The measured spectra are used for testing predictions of four ion-ion interaction models: BC, QMD, INCL, and LAQGSM03.03, and for comparison with the analytical parameterization within the thermodynamic concept of fragmentation.

  5. 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.

  6. Nuclear fragmentation of high-energy heavy-ion beams in water

    NASA Astrophysics Data System (ADS)

    Schardt, D.; Schall, I.; Geissel, H.; Irnich, H.; Kraft, G.; Magel, A.; Mohar, M. F.; Münzenberg, G.; Nickel, F.; Scheidenberger, C.; Schwab, W.; Sihver, L.

    As a part of the physical-technical program of the heavy-ion therapy project at GSI we have investigated the nuclear fragmentation of high-energy ion beams delivered by the heavy-ion synchrotron SIS, using water as a tissue-equivalent target. For a direct comparison of fragmentation properties, beams of ^10B, ^12C, ^14N, and ^16O were produced simultaneously as secondary beams from a primary ^18O beam and separated in flight by magnetic beam analysis. The Z-distributions of beam fragments produced in the water target were measured via energy loss in a large ionisation chamber and a scintillator telescope. From these data we obtained both total and partial charge-changing cross sections. In addition we have performed Bragg measurements using two parallel-plate ionization chambers and a water target of variable length. The detailed shape of the measured Bragg curves and the measured cross sections are in good agreement with model calculations based on semi-empirical formulae.

  7. 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.

  8. Parasitic production of slow RI-beam from a projectile fragment separator by ion guide Laser Ion Source (PALIS)

    NASA Astrophysics Data System (ADS)

    Sonoda, Tetsu

    2009-10-01

    The projectile fragment separator BigRIPS of RIBF at RIKEN provides a wide variety of short-lived radioactive isotope (RI) ions without restrictions on their lifetime or chemical properties. A universal slow RI-beam facility (SLOWRI) to decelerate the beams from BigRIPS using an RF-carpet ion guide has been proposed as a principal facility of RIBF. However, beam time at such a modern accelerator facility is always limited and operational costs are high. We therefore propose an additional scheme as a complementary option to SLOWRI to drastically enhance the usability of such an expensive facility. In BigRIPS, a single primary beam produces thousands of isotopes but only one isotope is used for an experiment while the other >99.99% of isotopes are simply dumped in the slits or elsewhere in the fragment separator. We plan to locate a compact gas cell with 1 bar Ar at the slits. The thermalized ions in the cell will be quickly neutralized and transported to the exit by gas flow and resonantly re-ionized by lasers. Such low energy RI-beams will always be provided without any restriction to the main experiment. It will allow us to run parasitic experiments for precision atomic or decay spectroscopy, mass measurements. Furthermore, the resonance ionization in the cell itself can be used for high-sensitive laser spectroscopy, which will expand our knowledge of the ground state property of unstable nuclei.

  9. Measurement of kinetic energy release in CO fragmentation by charge-changing collisions of fast heavy ions

    SciTech Connect

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

    2010-01-15

    We study ionization and fragmentation of CO in electron loss and capture collisions of B{sup 2+}, O{sup 2+}, and Si{sup 2+} ions at an energy of 71.4 keV/u (v=1.69 a.u.). Coincidence measurements of fragment ions from CO and charge-selected ions were performed by means of a momentum three-dimensional imaging technique. Production cross sections of CO{sup r+} and branching ratios into various fragmentation channels were obtained for r=1-4. We also measured kinetic energy release (KER) in individual fragmentation channels. The KER spectra for r<=2 are found to be different for electron loss and capture collisions, while the difference becomes small for r>=3. As a measure of the degree of molecular fragmentation, the magnitude of the binding energy of the relevant electronic states seems the important parameter both in loss and capture collisions.

  10. 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.

  11. 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.

  12. 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.

  13. 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

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

    PubMed

    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.

  15. 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.

  16. DNA fragmentation pattern in human fibroblasts after irradiation with iron ions

    NASA Astrophysics Data System (ADS)

    Campa, Alessandro

    In this work we studied the fragmentation pattern produced by the double stand breaks (DSB) induced in AG1522 primary human fibroblasts by two different iron beams, one of energy 414 MeV/u, and the other of energy 115 MeV/u (with dose-average LET in water equal to 202 keV/µm and 442 keV/µm, respectively). Irradiation with several doses up to 200 Gy was performed at the HIMAC facility of the National Institute of Radiological Sciences, Chiba, Japan. Experimental data, first obtained for fragments belonging to the size ranges 23-1000 kbp and 1000-5700 kbp (Belli et al., 2006), have successively been obtained also for fragments belonging to the size ranges 1-9 kbp and 9-23 kbp; the experimental analysis was performed with pulsed and constant field electrophoresis. The RBE for DSB production was evaluated in two different fragment size ranges (i.e., 23-5700 kbp and 1-5700 kbp), and it was found larger for the wider size range, especially for the beam with the higher LET. The experimental results have been compared to those computed on the basis of the Monte Carlo PARTRAC simulation code, following the line of research started in Campa et al. (2005), and exploiting the recent update of the PARTRAC code to ions heavier than helium (Friedland et al., 2006). Because the agreement has been found satisfactory for both radiation qualities, the spectra outside the experimentally observable fragment size range were also computed in order to evaluate the overall fragmentation pattern. The marked increases of the RBEs for DSB production, obtained when also the very small fragments (< 1 kbp) are included, makes them closer to the RBE values observed for the late cellular effects. This finding is a further indication for the biological significance of the spatial correlation of DSB at short distances. This work was partially supported by ASI (Italian Space Agency, "Mo-Ma/COUNT" project). References M. Belli, A. Campa, V. Dini, G. Esposito, Y. Furusawa, G. Simone, E. Sorrentino

  17. 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.

  18. Radiation induced redox reactions and fragmentation of constituent ions in ionic liquids. 1. Anions.

    PubMed

    Shkrob, Ilya A; Marin, Timothy W; Chemerisov, Sergey D; Wishart, James F

    2011-04-14

    Room temperature ionic liquids (IL) find increasing use for the replacement of organic solvents in practical applications, including their use in solar cells and electrolytes for metal deposition, and as extraction solvents for the reprocessing of spent nuclear fuel. The radiation stability of ILs is an important concern for some of these applications, as previous studies suggested extensive fragmentation of the constituent ions upon irradiation. In the present study, electron paramagnetic resonance (EPR) spectroscopy has been used to identify fragmentation pathways for constituent anions in ammonium, phosphonium, and imidazolium ILs. Many of these detrimental reactions are initiated by radiation-induced redox processes involving these anions. Scission of the oxidized anions is the main fragmentation pathway for the majority of the practically important anions; (internal) proton transfer involving the aliphatic arms of these anions is a competing reaction. For perfluorinated anions, fluoride loss following dissociative electron attachment to the anion can be even more prominent than this oxidative fragmentation. Bond scission in the anion was also observed for NO(3)(-) and B(CN)(4)(-) anions and indirectly implicated for BF(4)(-) and PF(6)(-) anions. Among small anions, CF(3)SO(3)(-) and N(CN)(2)(-) are the most stable. Among larger anions, the derivatives of benzoate and imide anions were found to be relatively stable. This stability is due to suppression of the oxidative fragmentation. For benzoates, this is a consequence of the extensive sharing of unpaired electron density by the π-system in the corresponding neutral radical; for the imides, this stability could be the consequence of N-N σ(2)σ(*1) bond formation involving the parent anion. While fragmentation does not occur for these "exceptional" anions, H atom addition and electron attachment are prominent. Among the typically used constituent anions, aliphatic carboxylates were found to be the least

  19. Radiation induced redox reactions and fragmentation of constituent ions in ionic liquids. I. Anions.

    SciTech Connect

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

    2011-04-14

    Room temperature ionic liquids (IL) find increasing use for the replacement of organic solvents in practical applications, including their use in solar cells and electrolytes for metal deposition, and as extraction solvents for the reprocessing of spent nuclear fuel. The radiation stability of ILs is an important concern for some of these applications, as previous studies suggested extensive fragmentation of the constituent ions upon irradiation. In the present study, electron paramagnetic resonance (EPR) spectroscopy has been used to identify fragmentation pathways for constituent anions in ammonium, phosphonium, and imidazolium ILs. Many of these detrimental reactions are initiated by radiation-induced redox processes involving these anions. Scission of the oxidized anions is the main fragmentation pathway for the majority of the practically important anions; (internal) proton transfer involving the aliphatic arms of these anions is a competing reaction. For perfluorinated anions, fluoride loss following dissociative electron attachment to the anion can be even more prominent than this oxidative fragmentation. Bond scission in the anion was also observed for NO{sub 3}{sup -} and B(CN){sub 4}{sup -} anions and indirectly implicated for BF{sub 4}{sup -} and PF{sub 6}{sup -} anions. Among small anions, CF{sub 3}SO{sub 3}{sup -} and N(CN){sub 2}{sup -} are the most stable. Among larger anions, the derivatives of benzoate and imide anions were found to be relatively stable. This stability is due to suppression of the oxidative fragmentation. For benzoates, this is a consequence of the extensive sharing of unpaired electron density by the {pi}-system in the corresponding neutral radical; for the imides, this stability could be the consequence of N-N {sigma}{sup 2}{sigma}*{sup 1} bond formation involving the parent anion. While fragmentation does not occur for these 'exceptional' anions, H atom addition and electron attachment are prominent. Among the typically used

  20. Studies of peptide a- and b-type fragment ions using stable isotope labeling and integrated ion mobility/tandem mass spectrometry.

    PubMed

    Riba Garcia, Isabel; Giles, Kevin; Bateman, Robert H; Gaskell, Simon J

    2008-12-01

    The structures of peptide a- and b-type fragment ions were studied using synthetic peptides including a set of isomeric peptides, differing in the sequence location of an alanine residue labeled with (15)N and uniformly with (13)C. The pattern of isotope labeling of second-generation fragment ions derived via a(n) and b(n) ions (where n = 4 or 5) suggested that these intermediates existed in part as macrocyclic structures, where alternative sites of ring opening gave rise to different linear forms whose simple cleavage might give rise to the observed final products. Similar conclusions were derived from combined ion mobility/tandem MS analyses where different fragmentation patterns were observed for isomeric a- or b-type ions that display different ion mobilities. These analyses were facilitated by a new approach to the processing of ion mobility/tandem MS data, from which distinct and separate product ion spectra are derived from ions that are incompletely separated by ion mobility. Finally, an example is provided of evidence for a macrocyclic structure for b(n) ions where n = 8 or 9.

  1. Core-level positive-ion and negative-ion fragmentation of gaseous and condensed HCCl3 using synchrotron radiation

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

    We investigated the dissociation dynamics of positive-ion and negative-ion fragments of gaseous and condensed HCCl3 following photoexcitation of Cl 2p electrons to various resonances. Based on ab initio calculations at levels HF/cc-pVTZ and QCISD/6-311G*, the first doublet structures in Cl L-edge x-ray absorption spectrum of HCCl3 are assigned to transitions from the Cl (2P3/2,1/2) initial states to the 10a1* orbitals. The Cl 2p → 10a1* excitation of HCCl3 induces a significant enhancement of the Cl+ desorption yield in the condensed phase and a small increase in the HCCl+ yield in the gaseous phase. Based on the resonant photoemission of condensed HCCl3, excitations of Cl 2p electrons to valence orbitals decay predominantly via spectator Auger transitions. The kinetic energy distributions of Cl+ ion via the Cl 2p → 10a1* excitation are shifted to higher energy ˜0.2 eV and ˜0.1 eV relative to those via the Cl 2p → 10e* excitation and Cl 2p → shape resonance excitation, respectively. The enhancement of the yields of ionic fragments at specific core-excited resonance states is assisted by a strongly repulsive surface that is directly related to the spectator electrons localized in the antibonding orbitals. The Cl- anion is significantly reinforced in the vicinity of Cl 2p ionization threshold of gaseous HCCl3, mediated by photoelectron recapture through post-collision interaction.

  2. Ionization and fragmentation of polycyclic aromatic hydrocarbon clusters in collisions with keV ions

    SciTech Connect

    Johansson, H. A. B.; Zettergren, H.; Holm, A. I. S.; Seitz, F.; Schmidt, H. T.; Cederquist, H.; Rousseau, P.; Lawicki, A.; Capron, M.; Domaracka, A.; Lattouf, E.; Maclot, S.; Maisonny, R.; Chesnel, J.-Y.; Adoui, L.; Huber, B. A.

    2011-10-15

    We report on an experimental study of the ionization and fragmentation of clusters of k polycyclic aromatic hydrocarbon (PAH) molecules using anthracene, C{sub 14}H{sub 10}, or coronene, C{sub 24}H{sub 12}. These PAH clusters are moderately charged and strongly heated in small impact parameter collisions with 22.5-keV He{sup 2+} ions, after which they mostly decay in long monomer evaporation sequences with singly charged and comparatively cold monomers as dominating end products. We describe a simple cluster evaporation model and estimate the number of PAH molecules in the clusters that have to be hit by He{sup 2+} projectiles for such complete cluster evaporations to occur. Highly charged and initially cold clusters are efficiently formed in collisions with 360-keV Xe{sup 20+} ions, leading to cluster Coulomb explosions and several hot charged fragments, which again predominantly yield singly charged, but much hotter, monomer ions than the He{sup 2+} collisions. We present a simple formula, based on density-functional-theory calculations, for the ionization energy sequences as functions of coronene cluster size, rationalized in terms of the classic electrostatic expression for the ionization of a charged conducting object. Our analysis indicates that multiple electron removal by highly charged ions from a cluster of PAH molecules rapidly may become more important than single ionization as the cluster size k increases and that this is the main reason for the unexpectedly strong heating in these types of collisions.

  3. Three-body fragmentation of triatomic molecular ions in a strong laser field

    NASA Astrophysics Data System (ADS)

    Ablikim, U.; Zohrabi, M.; Jochim, Bethany; Berry, Ben; Carnes, K. D.; Ben-Itzhak, I.

    2014-05-01

    Coincidence three-dimensional momentum imaging measurements of three-body fragmentation of transient triply-charged CO2 molecules reveal competing fragmentation paths involving bending, symmetric and asymmetric stretching, as well as the more complex sequential breakup (i.e. one bond at a time). We have extended these studies using a CO2+molecular-ion-beam target, providing similar results for the breakup of the transient CO23+ --> O+ + C+ + O+. The detection of neutral fragments also enables kinematically complete measurements of the three-body breakup of the transient CO22+ . Our results, for CO2+in ultrashort (~26 fs) intense (1015 to 1016 W/cm2) laser pulses at 790 nm, suggest significant bending in the C+ + O+ + O+ channel as well as sequential breakup. In contrast, sequential breakup is suppressed in the O+ + C+ + O and O+ + C +O+ channels. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Entropy effects in the fragmentation of 1,1-dimethylhydrazine ions.

    PubMed

    Boulanger, Anne-Marie; Rennie, Emma E; Holland, David M P; Shaw, David A; Mayer, Paul M

    2007-06-28

    The 1,1-dimethylhydrazine ion ((CH3)2NNH2+*) has two low-energy dissociation channels, the loss of a hydrogen atom to form the fragment ion m/z 59, (CH3)(CH2)NNH2+, and the loss of a methyl radical to form the fragment ion m/z 45, the methylhydrazyl cation, CH3NNH2+. The dissociation of the 1,1-dimethylhydrazine ion has been investigated using threshold photoelectron-photoion coincidence (TPEPICO) spectroscopy, in the photon energy range 8.25-31 eV, and tandem mass spectrometry. Theoretical breakdown curves have been obtained from a variational transition state theory (VTST) modeling of the two reaction channels and compared to those obtained from experiment. Seven transition states have been found at the B3-LYP/6-31+G(d) level of theory for the methyl radical loss channel in the internal energy range of 2.32-3.56 eV. The methyl loss channel transition states are found at R(N-C) = 4.265, 4.065, 3.965, 3.165, 2.765, 2.665, and 2.565 A over this internal energy range. Three transition states have been found for the hydrogen atom loss channel: R(H-C) = 2.298, 2.198, and 2.098 A. The DeltaS++(45) value, at an internal energy of 2.32 eV and a bond distance of R(N-C) = 4.265 A, is 65 J K-1 mol-1. As the internal energy increases to 3.56 eV the variational transition state moves to lower R value so that at R(N-C) = 2.565 A, the DeltaS++ decreases to 29 J K-1 mol-1. For the hydrogen atom loss channel the variation in DeltaS++ is less than that for the methyl loss channel. To obtain agreement with the experimental breakdown curves, DeltaS++(59) = 26-16 J K-1 mol-1 over the studied internal energy range. The 0 K enthalpies of formation (DeltafH0) for the two fragment ions m/z 45 and m/z 59 have been calculated from the 0 K activation energies (E0) obtained from the fitting procedure: DeltafH0[CH3NNH2+] = 906 +/- 6 kJ mol-1 and DeltafH0[(CH3)(CH2)NNH2+] = 822 +/- 7 kJ mol-1. The calculated G3 values are DeltafH0[CH3NNH2+] = 911 kJ mol-1 and DeltafH0[(CH3)(CH2)NNH2+] = 825 k

  6. Multiple ionization and fragmentation of isolated pyrene and coronene molecules in collision with ions

    SciTech Connect

    Lawicki, A.; Rousseau, P.; Capron, M.; Maisonny, R.; Maclot, S.; Adoui, L.; Huber, B. A.; Holm, A. I. S.; Seitz, F.; Johansson, H. A. B.; Rosen, S.; Schmidt, H. T.; Zettergren, H.; Cederquist, H.; Manil, B.

    2011-02-15

    The interaction of multiply charged ions (He{sup 2+}, O{sup 3+}, and Xe{sup 20+}) with gas-phase pericondensed polycyclic aromatic hydrocarbon (PAH) molecules of coronene (C{sub 24}H{sub 12}) and pyrene (C{sub 16}H{sub 10}) is studied for low-velocity collisions (v{<=}0.6 a.u.). The mass spectrometric analysis shows that singly and up to quadruply charged intact molecules are important reaction products. The relative experimental yields are compared with the results of a simple classical over-the-barrier model. For higher molecular charge states, the experimental yields decrease much more strongly than the model predictions due to the instabilities of the multiply charged PAH molecules. Even-odd oscillations with the number of carbon atoms, n, in the intensity distributions of the C{sub n}H{sub x}{sup +} fragments indicate a linear chain structure of the fragments similar to those observed for ion-C{sub 60} collisions. The latter oscillations are known to be due to dissociation energy differences between even- and odd-n C{sub n}-chain molecules. For PAH molecules, the average numbers of H atoms attached to the C{sub n}H{sub x} chains are larger for even-n reflecting acetylenic bond systems.

  7. Fragmentation of peptide radical cations containing a tyrosine or tryptophan residue: structural features that favor formation of [x(n-1) + H]˙⁺ and [z(n-1) + H]˙⁺ ions.

    PubMed

    Mädler, Stefanie; Lau, Justin Kai-Chi; Williams, Declan; Wang, Yating; Saminathan, Irine S; Zhao, Junfang; Siu, K W Michael; Hopkinson, Alan C

    2014-06-12

    Peptide radical cations A(n)Y(•+) (where n = 3, 4, or 5) and A5W(•+) have been generated by collision-induced dissociation (CID) of [Cu(II)(tpy)(peptide)](•2+) complexes. Apart from the charge-driven fragmentation at the N-Cα bond of the hetero residue producing either [c + 2H](+) or [z - H](•+) ions and radical-driven fragmentation at the Cα-C bond to give a(+) ions, unusual product ions [x + H](•+) and [z + H](•+) are abundant in the CID spectra of the peptides with the hetero residue in the second or third position of the chain. The formation of these ions requires that both the charge and radical be located on the peptide backbone. Energy-resolved spectra established that the [z + H](•+) ion can be produced either directly from the peptide radical cation or via the fragment ion [x + H](•+). Additionally, backbone dissociation by loss of the C-terminal amino acid giving [b(n-1) - H](•+) increases in abundance with the length of the peptides. Mechanisms by which peptide radical cations dissociate have been modeled using density functional theory (B3LYP/6-31++G** level) on tetrapeptides AYAG(•+), AAYG(•+), and AWAG(•+).

  8. 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

    2016-04-05

    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.

  9. Stability and abundance of the trisulfur radical ion S3- in hydrothermal fluids

    NASA Astrophysics Data System (ADS)

    Pokrovski, Gleb S.; Dubessy, Jean

    2015-02-01

    The interpretation of sulfur behavior in geological fluids and melts is based on a long-standing paradigm that sulfate, sulfide, and sulfur dioxide are the major sulfur compounds. This paradigm was recently challenged by the discovery of the trisulfur ion S3- in aqueous S-bearing fluids from laboratory experiments at elevated temperatures. However, the stability and abundance of this potentially important sulfur species remain insufficiently quantified at hydrothermal conditions. Here we used in situ Raman spectroscopy on model thiosulfate, sulfide, and sulfate aqueous solutions across a wide range of sulfur concentration (0.5-10.0 wt%), acidity (pH 3-8), temperature (200-500 °C), and pressure (15-1500 bar) to identify the different sulfur species and determine their concentrations. Results show that in the low-density (< 0.2 g /cm3) vapor phase, H2S is the only detectable sulfur form. By contrast, in the denser liquid and supercritical fluid phase, together with sulfide and sulfate, the trisulfur radical ion S3- is a ubiquitous and thermodynamically stable species from 200 °C to at least 500 °C. In addition, the disulfur radical ion S2- is detected at 450-500 °C in most solutions, and polymeric molecular sulfur with a maximum abundance around 300 °C in S-rich solutions. These results, combined with revised literature data, allow the thermodynamic properties of S3- to be constrained, enabling quantitative predictions of its abundance over a wide temperature and pressure range of crustal fluids. These predictions suggest that S3- may account for up to 10% of total dissolved sulfur (Stot) at 300-500 °C in fluids from arc-related magmatic-hydrothermal systems, and more than 50% Stot at 600-700 °C in S-rich fluids produced via prograde metamorphism of pyrite-bearing rocks. The trisulfur ion may favor the mobility of sulfur itself and associated metals (Au, Cu, Pt, Mo) in geological fluids over a large range of depth and provide the source of these elements for

  10. Charge state dependent fragmentation of gaseous [alpha]-synuclein cations via ion trap and beam-type collisional activation

    NASA Astrophysics Data System (ADS)

    Chanthamontri, Chamnongsak; Liu, Jian; McLuckey, Scott A.

    2009-06-01

    Ions derived from nano-electrospray ionization (nano-ESI) of [alpha]-synuclein, a 14.5 kDa, 140 amino acid residue protein that is a major component of the Lewy bodies associated with Parkinson's disease, have been subjected to ion trap and beam-type collisional activation. The former samples products from fragmentation at rates generally lower than 100 s-1 whereas the latter samples products from fragmentation at rates generally greater than 103 s-1. A wide range of protein charge states spanning from as high as [M+17H]17+ to as low as [M+4H]4+ have been formed either directly from nano-ESI or via ion/ion proton transfer reactions involving the initially formed protein cations and have been subjected to both forms of collision-induced dissociation (CID). The extent of sequence information (i.e., number of distinct amide bond cleavages) available from either CID method was found to be highly sensitive to protein precursor ion charge state. Furthermore, the relative contributions of the various competing dissociation channels were also dependent upon precursor ion charge state. The qualitative trends in the changes in extent of amide bond cleavages and identities of bonds cleaved with precursor ion charge state were similar for two forms of CID. However, for every charge state examined, roughly twice the primary sequence information resulted from beam-type CID relative to ion trap CID. For example, evidence for cleavage of 86% of the protein amide bonds was observed for the [M+9H]9+ precursor ion using beam-type CID whereas 41% of the bonds were cleaved for the same precursor ion using ion trap CID. The higher energies required to drive fragmentation reactions at rates necessary to observe products in the beam experiment access more of the structurally informative fragmentation channels, which has important implications for whole protein tandem mass spectrometry.

  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. 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

  13. 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.

  14. Hydride transfer reactions via ion-neutral complex: fragmentation of protonated N-benzylpiperidines and protonated N-benzylpiperazines in mass spectrometry.

    PubMed

    Chai, Yunfeng; Jiang, Kezhi; Pan, Yuanjiang

    2010-05-01

    An ion-neutral complex (INC)-mediated hydride transfer reaction was observed in the fragmentation of protonated N-benzylpiperidines and protonated N-benzylpiperazines in electrospray ionization mass spectrometry. Upon protonation at the nitrogen atom, these compounds initially dissociated to an INC consisting of [RC(6)H(4)CH(2)](+) (R = substituent) and piperidine or piperazine. Although this INC was unstable, it did exist and was supported by both experiments and density functional theory (DFT) calculations. In the subsequent fragmentation, hydride transfer from the neutral partner to the cation species competed with the direct separation. The distribution of the two corresponding product ions was found to depend on the stabilization energy of this INC, and it was also approved by the study of substituent effects. For monosubstituted N-benzylpiperidines, strong electron-donating substituents favored the formation of [RC(6)H(4)CH(2)](+), whereas strong electron-withdrawing substituents favored the competing hydride transfer reaction leading to a loss of toluene. The logarithmic values of the abundance ratios of the two ions were well correlated with the nature of the substituents, or rather, the stabilization energy of this INC.

  15. Isospin effect of Coulomb interaction on the dissipation and fragmentation in intermediate energy heavy ion collisions

    SciTech Connect

    Liu Jianye; Guo Wenjun; Gao Yuanyi; Xing Yongzhong; Li Xiguo

    2004-09-01

    We investigate separately the isospin effects of Coulomb interaction and symmetry potential on the dissipation and fragmentation in the intermediate energy heavy ion collisions by using isospin-dependent quantum molecular dynamics model. The calculated results show that the Coulomb interaction induces the reductions of both isospin fractionation ratio and nuclear stopping (momentum dissipation). However, the Coulomb interaction not only does not change obviously the strong isospin effect of the symmetry potential on the isospin fractionation ratio but also does not change obviously that of in-medium two-body collision on the nuclear stopping. On the contrary, the symmetry potential induces the enhancement of the isospin fractionation ratio but it is insensitive to the nuclear stopping. Finally, the competition between the Coulomb interaction and symmetry potential induces the reductions of both isospin fractionation ratio and nuclear stopping for two forms of symmetry potentials in this paper.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. Calculations for ion-impact induced ionization and fragmentation of water molecules

    NASA Astrophysics Data System (ADS)

    Kirchner, Tom; Murakami, Mitsuko; Horbatsch, Marko; Jürgen Lüdde, Hans

    2012-10-01

    Charge-state correlated cross sections for single- and multiple-electron removal processes in proton-water-molecule collisions are calculated by using the non-perturbative basis generator method adapted for ion-molecule collisions [1,2]. A fragmentation model is then applied to calculate the yields of H2O^+, OH^+, H^+, and O^+ ions emerging after H2O^q+ formation [3]. A detailed comparison is made with experimental data from three groups covering the energy range from 20--5000 keV. It is found that multiple electron processes with q<=3 play an important role at the lower end of this range and are calculated accurately within an independent particle model. We are currently completing the analogous analysis for He^+-H2O collisions for which the presence of the projectile electron poses some additional challenges. [4pt] [1] H.J. L"udde et al, Phys. Rev. A 80, 060702(R) (2009)[0pt] [2] M. Murakami et al, Phys. Rev. A 85, 052704 (2012)[0pt] [3] M. Murakami et al, Phys. Rev. A 85, 052713 (2012)

  3. 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

  4. 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

  5. Fragmentation of 120 and 200 MeV u(-1)(4)He ions in water and PMMA targets.

    PubMed

    Rovituso, M; Schuy, C; Weber, U; Brons, S; Cortés-Giraldo, M A; La Tessa, C; Piasetzky, E; Izraeli, D; Schardt, D; Toppi, M; Scifoni, E; Krämer, M; Durante, M

    2017-02-21

    Recently, the use of (4)He particles in cancer radiotherapy has been reconsidered as they potentially represent a good compromise between protons and (12)C ions. The first step to achieve this goal is the development of a dedicated treatment planning system, for which basic physics information such as the characterization of the beam lateral scattering and fragmentation cross sections are required. In the present work, the attenuation of (4)He primary particles and the build-up of secondary charged fragments at various depths in water and polymethyl methacrylate were investigated experimentally for 120 and 200 MeV u(-1) beams delivered by the synchrotron at the Heidelberg Ion-Beam Therapy Center, Heidelberg. Species and isotope identification was accomplished combining energy loss and time-of-flight measurements. Differential yields and energy spectra of all fragments types were recorded between 0° and 20° with respect to the primary beam direction.

  6. Fragmentation of 120 and 200 MeV u‑1 4He ions in water and PMMA targets

    NASA Astrophysics Data System (ADS)

    Rovituso, M.; Schuy, C.; Weber, U.; Brons, S.; Cortés-Giraldo, M. A.; La Tessa, C.; Piasetzky, E.; Izraeli, D.; Schardt, D.; Toppi, M.; Scifoni, E.; Krämer, M.; Durante, M.

    2017-02-01

    Recently, the use of 4He particles in cancer radiotherapy has been reconsidered as they potentially represent a good compromise between protons and 12C ions. The first step to achieve this goal is the development of a dedicated treatment planning system, for which basic physics information such as the characterization of the beam lateral scattering and fragmentation cross sections are required. In the present work, the attenuation of 4He primary particles and the build-up of secondary charged fragments at various depths in water and polymethyl methacrylate were investigated experimentally for 120 and 200 MeV u‑1 beams delivered by the synchrotron at the Heidelberg Ion-Beam Therapy Center, Heidelberg. Species and isotope identification was accomplished combining energy loss and time-of-flight measurements. Differential yields and energy spectra of all fragments types were recorded between 0° and 20° with respect to the primary beam direction.

  7. 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

  8. 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 Central

    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.

    2015-01-01

    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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Earth Abundant Fe/Mn-Based Layered Oxide Interconnected Nanowires for Advanced K-Ion Full Batteries.

    PubMed

    Wang, Xuanpeng; Xu, Xiaoming; Niu, Chaojiang; Meng, Jiashen; Huang, Meng; Liu, Xiong; Liu, Ziang; Mai, Liqiang

    2017-01-11

    K-ion battery (KIB) is a new-type energy storage device that possesses potential advantages of low-cost and abundant resource of K precursor materials. However, the main challenge lies on the lack of stable materials to accommodate the intercalation of large-size K-ions. Here we designed and constructed a novel earth abundant Fe/Mn-based layered oxide interconnected nanowires as a cathode in KIBs for the first time, which exhibits both high capacity and good cycling stability. On the basis of advanced in situ X-ray diffraction analysis and electrochemical characterization, we confirm that interconnected K0.7Fe0.5Mn0.5O2 nanowires can provide stable framework structure, fast K-ion diffusion channels, and three-dimensional electron transport network during the depotassiation/potassiation processes. As a result, a considerable initial discharge capacity of 178 mAh g(-1) is achieved when measured for KIBs. Besides, K-ion full batteries based on interconnected K0.7Fe0.5Mn0.5O2 nanowires/soft carbon are assembled, manifesting over 250 cycles with a capacity retention of ∼76%. This work may open up the investigation of high-performance K-ion intercalated earth abundant layered cathodes and will push the development of energy storage systems.

  16. 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.

  17. 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.}

  18. Improved atmospheric trace gas measurements with an aircraft-based tandem mass spectrometer: Ion identification by mass-selected fragmentation studies

    NASA Astrophysics Data System (ADS)

    Reiner, Thomas; MöHler, Ottmar; Arnold, Frank

    1998-12-01

    We have built and employed an aircraft-borne triple quadrupole mass spectrometer (TQMS) for fragmentation studies of mass-selected ions in the upper troposphere and lower stratosphere. The fragmentation studies included both ambient and artificially produced ions relevant for the measurement of atmospheric trace gases by ion molecule reaction mass spectrometry (IMRMS) and led to an unambiguous identification of the chemical composition of important ions used for IMRMS measurements. Among these are the product ions of ion molecule reactions of CO3-(H2O)n and H3O+(H2O)n ions with HNO3, SO2, acetone, HCN, and methyl cyanide. These reactions have been studied in the laboratory, and ions having the same masses as the expected product ions have been previously observed in atmospheric IMRMS spectra. The present fragmentation studies are the first to actually identify the chemical composition of these ions during aircraft measurements in the upper troposphere and lower stratosphere and demonstrate that these ions can reliably be used for atmospheric trace gas measurements. Furthermore, the fragmentation studies gave indications for the existence and the possible identification of previously unknown ions. Among these the tentative identification of CO3-H2O2 offers the possibility for sensitive measurements of H2O2 by IMRMS. The fragmentation studies were accompanied by IMRMS measurements of atmospheric trace gases using the TQMS. Altitude profiles of HNO3, SO2, and lower limits for H2O2 are shown.

  19. 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.

  20. Monte Carlo simulation for calculation of fragments produced by 400 MeV/u carbon ion beam in water

    NASA Astrophysics Data System (ADS)

    Ou, Hai-Feng; Zhang, Bin; Zhao, Shu-Jun

    2017-04-01

    Monte Carlo simulation was an important approach to obtain accurate characteristics of radiotherapy. In this work, a 400 MeV/u carbon ion beam incident on water phantom was simulated with Gate/Geant4 tools. The authors obtained the dose distributions of H, He, Li, Be, B, C and their isotopes in water phantom, and drew a conclusion that the dose of 11C was the main reason of causing the embossment of total dose curve around 252 mm depth. The authors also studied detailedly the dose contribution distributions, yield distributions and average energy distributions of all kinds of fragments. The information of four distributions was very meaningful for understanding the effect of fragments in carbon ion beam radiotherapy. The method of this simulation was easy to extend. For example, for obtaining a special result, we may change the particle energy, particle type, target material, target geometry, physics process, detector, etc.

  1. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides.

    PubMed

    Tabb, David L; Huang, Yingying; Wysocki, Vicki H; Yates, John R

    2004-03-01

    The primary utility of trypsin digestion in proteomics is that it cleaves proteins at predictable locations, but it is also notable for yielding peptides that terminate in basic arginine and lysine residues. Tryptic peptides fragment in ion trap tandem mass spectrometry to produce prominent C-terminal y series ions. Alternative proteolytic digests may produce peptides that do not follow these rules. In this study, we examine 2568 peptides generated through proteinase K digestion, a technique that produces a greater diversity of basic residue content in peptides. We show that the position of basic residues within peptides influences the peak intensities of b and y series ions; a basic residue near the N-terminus of a peptide can lead to prominent b series peaks rather than the intense y series peaks associated with tryptic peptides. The effects of presence and position for arginine, lysine, and histidine are explored separately and in combination. Arg shows the most dominant effects followed by His and then by Lys. Fragment ions containing basic residues produce more intense peaks than those without basic residues. Doubly charged precursor ions have generally been modeled as producing only singly charged fragment ions, but fragment ions that contain two basic residues may accept both protons during fragmentation. By characterizing the influence of basic residues on gas-phase fragmentation of peptides, this research makes possible more accurate fragmentation models for peptide identification algorithms.

  2. Elemental abundance and spectral variations of the suprathermal heavy ion populations in interplanetary space

    NASA Astrophysics Data System (ADS)

    Al Dayeh, Maher Abdul Hamid

    Solar energetic particles (SEPs) associated with coronal mass ejections (CMEs) are usually accompanied by large particle intensities and magnetic clouds that often cause terrestrial geomagnetic storms. These storms present a danger to many aspects on earth, from satellites and communications, to power and pipelines, in addition to forming a danger to astronauts in space. The scientific objectives for studying SEPs in this dissertation are twofold. First is to improve our understanding of SEP sources, acceleration, and propagation in interplanetary (IP) space. The second is to improve our capabilities in space weather prediction. This dissertation investigates the source material of SEPs through detailed analysis of the temporal, compositional, and spectral variations of heavy ion species (mass > 4 nucleons) at the energy range ~0.045 MeV/nuc -10 MeV/nuc from December 1995 to December 2006, thus covering all of solar cycle 23. Data used in this dissertation are mainly from ULEIS and STEP time-of-flight mass spectrometers onboard the ACE (launched 08/1997) and Wind (launched 11/1994) spacecraft respectively. Observations reported in this work show that daily variations of low-energy heavy ions (~0.12 MeV/nucleon) in IP space are correlated with the solar cycle. Such dependence is not seen in a set of gradual SEP events. However, these events show large event-to-event fluctuations. This suggests that there exist multiple scenarios by which the seed material is injected into accelerating IP shocks, these are: (i) remnant material from previous flares that remain in IP space or get continuously replenished by frequent flare activity; (ii) direct contributions from accompanying flares, i.e., particles that escape from the flare through open field lines could encounter the CME shock, get re- accelerated and cause an enhancement in the heavy-ion abundances; (iii) the same or nearby active regions on the Sun produce suprathermal particles with flare-like composition that

  3. 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

    2015-11-06

    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.

  4. 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.

  5. Secondary radiation measurements for particle therapy applications: nuclear fragmentation produced by (4)He ion beams in a PMMA target.

    PubMed

    Marafini, M; Paramatti, R; Pinci, D; Battistoni, G; Collamati, F; De Lucia, E; Faccini, R; Frallicciardi, P M; Mancini-Terracciano, C; Mattei, I; Muraro, S; Piersanti, L; Rovituso, M; Rucinski, A; Russomando, A; Sarti, A; Sciubba, A; Solfaroli Camillocci, E; Toppi, M; Traini, G; Voena, C; Patera, V

    2017-02-21

    Nowadays there is a growing interest in particle therapy treatments exploiting light ion beams against tumors due to their enhanced relative biological effectiveness and high space selectivity. In particular promising results are obtained by the use of (4)He projectiles. Unlike the treatments performed using protons, the beam ions can undergo a fragmentation process when interacting with the atomic nuclei in the patient body. In this paper the results of measurements performed at the Heidelberg Ion-Beam Therapy center are reported. For the first time the absolute fluxes and the energy spectra of the fragments-protons, deuterons, and tritons-produced by (4)He ion beams of 102, 125 and 145 MeV u(-1) energies on a poly-methyl methacrylate target were evaluated at different angles. The obtained results are particularly relevant in view of the necessary optimization and review of the treatment planning software being developed for clinical use of (4)He beams in clinical routine and the relative bench-marking of Monte Carlo algorithm predictions.

  6. 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.

  7. Characteristic fragmentation of polysiloxane monolayer films by bombardment with monatomic and polyatomic primary ions in TOF-SIMS.

    PubMed

    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 (M(n)) 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.

  8. 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.

  9. 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.

  10. Fragment profiling of low molecular weight heparins using reversed phase ion pair liquid chromatography-electrospray mass spectrometry.

    PubMed

    Xu, Xiaohui; Li, Daoyuan; Chi, Lequan; Du, Xuzhao; Bai, Xue; Chi, Lianli

    2015-04-30

    Low molecular weight heparins (LMWHs) are linear and highly charged carbohydrate polymers prepared by chemical or enzymatic depolymerization of heparin. Compared to unfractionated heparin (UFH), LMWHs are prevalently used as clinical anticoagulant drugs due to their lower side effects and better bioavailability. The work presented herein provides a rapid and powerful fragment mapping method for structural characterization of LMWHs. The chain fragments of two types of LMWHs, enoxaparin and nadroparin, were generated by controlled enzymatic digestion with each of heparinase I (Hep I, Enzyme Commission (EC) # 4.2.2.7), heparinase II (Hep II, no EC # assigned) and heparinase III (Hep III, EC # 4.2.2.8). Reversed phase ion pair high performance liquid chromatography (RPIP-HPLC) coupled with electrospray ion trap time-of-flight mass spectrometry (ESI-IT-TOF-MS) was used to profile the oligosaccharide chains ranging from disaccharides to decasaccharides. A database containing all theoretical structural compositions was established to assist the mass spectra interpretation. The six digests derived by three enzymes from two types of LMWHs exhibited distinguishable fingerprinting patterns. And a total of 94 enoxaparin fragments and 109 nadroparin fragments were detected and identified. Besides the common LMWH oligosaccharides, many components containing characteristic LMWH structures such as saturated L-idopyranosuronic acid, 2,5-anhydro-D-mannitol, 1,6-anhydro-D-aminopyranose, as well as odd number oligosaccharides were also revealed. Quantitative comparison of major components derived from innovator and generic nadroparin products was presented. This approach to profile LMWHs' fragments offers a highly reproducible, high resolution and information-rich tool for evaluating the quality of this category of anticoagulant drugs or comparing structural similarities among samples from various sources.

  11. 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

  12. Radiation induced redox reactions and fragmentation of constituent ions in ionic liquids. 2. Imidazolium cations.

    PubMed

    Shkrob, Ilya A; Marin, Timothy W; Chemerisov, Sergey D; Hatcher, Jasmine L; Wishart, James F

    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 (1)H and (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) σσ*-bound dimer radical cation. In addition to these reactions, when methoxy or C(α)-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 trifluorosulfonate). Gradual

  13. 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.

  14. Search for projectile fragments with fractional charge in relativistic heavy ion collisions

    NASA Technical Reports Server (NTRS)

    Hoffmann, A.; Brechtmann, C.; Heinrich, W.; Benton, E. V.

    1988-01-01

    We measured the charge of about 35000 projectile fragments with Z > or = 5e produced by 14.5 GeV/nucleon and 200 GeV/nucleon 16O beams in a Pb target using CR39 plastic nuclear track detectors. A minimum track length of 3 mm in the detector without nuclear interaction was required. No evidence for fragments carrying a fractional charge was found.

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

    PubMed

    Somogyi, Arpád

    2008-12-01

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

  16. 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.

  17. 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

  18. 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.

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

    PubMed

    Fattahi, Alireza; Zekavat, Behrooz; Solouki, Touradj

    2010-03-01

    Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with H/D exchange reactions was utilized to explore the existence of different b(5)(+) and b(4)(+) fragment ion conformers/isomers of hexapeptide WHWLQL in the gas phase. Distinct H/D exchange trends for protonated WHWLQL ([M + H](+)) and its b(5)(+) and b(4)(+) fragment ions (with ND(3)) were observed. Isolated (12)C(all) isotopomers of both b(5)(+) and b(4)(+) fragment ions yielded bimodal distributions of H/D exchanged product ions. The H/D exchange reaction kinetics also confirmed that b(5)(+) and b(4)(+) fragment ions exist as combination of slow-exchanging ("s") and fast-exchanging ("f") species. The calculated rate constant for the first labile hydrogen exchange of [M + H](+) (k([M + H](+)) = 3.80 +/- 0.7 x 10(-10) cm(3) mol(-1) s(-1)) was approximately 30 and approximately 5 times greater than those for the "s" and "f" species of b(5)(+), respectively. Data from H/D exchange of isolated "s" species at longer ND(3) reaction times confirmed the existence of different conformers or isomers for b(5)(+) fragment ions. The sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) of WHWLQL combined with the H/D exchange reactions indicate that "s" and "f" species of b(5)(+) and b(4)(+) fragment ions can be produced in the ICR cell as well as the ESI source. The significance of these observations for detailed understanding of protein sequencing and ion fragmentation pathways is discussed.

  20. 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).

  1. Hydropathic influences on the quantification of equine heart cytochrome c using relative ion abundance measurements by electrospray ionization fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Gordon, E F; Mansoori, B A; Carroll, C F; Muddiman, D C

    1999-10-01

    The number of publications documenting the utility of electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) for the analysis of biological molecules has increased in geometric proportion spanning diverse areas of research. Currently, we are investigating the capabilities of ESI-FTICR to quantify relative molecular ion abundances of biopolymers, an area which has not been explored rigorously. We present here the results of an investigation of a two-component system utilizing equine heart cytochrome c (EH) as the analyte and bovine heart cytochrome c (BH) as a constant concentration internal standard. As these compounds are relatively large ( approximately 12 kDa), they will become multiply charged during the electrospray process. Using appropriate solution and instrument conditions, the 7(+) and 8(+) charge states were enhanced for both cytochrome c species. We report that using the average of the ion abundances for the two charge states observed for each species, the linear curve (intensity ratio vs concentration ratio) had a dynamic range of 0.045-2.348 microM (1.7 orders of magnitude). Linear least-squares regression analysis (LLSRA) of these averaged ion abundances (i.e. [(EH + 7H(+))(7+)/(BH + 7H(+))(7+) + (EH + 8H(+))(8+)/(BH + 8H(+))(8+)]/2) yielded the equation y = 1.005x + 0.027. The slope of the line with its calculated precision, reported as one standard deviation, is 1.005 +/- 0.0150, which is statistically ideal (i.e. equal to unity). However, LLSRA of the ion abundances of the two individual charge states were significantly different (i.e. the slope of the (EH + 7H(+))(7+)/(BH + 7H(+))(7+) peak intensity ratio vs molar ratio data was 0.885 +/- 0.0183 and the slope of the (EH + 8H(+))(8+)/(BH + 8H(+))(8+) data was 1.125 +/- 0.0308). We attribute this difference to the variation in primary amino acid sequence for the two cytochrome c species. Both have 104 amino acids, but there are three residue

  2. Influence of metal ion complexation on the metastable fragmentation of DNA hexamers

    NASA Astrophysics Data System (ADS)

    Piekarczyk, Andreas; Bald, Ilko; Flosadóttir, Helga D.; Ómarsson, Benedikt; Lafosse, Anne; Ingólfsson, Oddur

    2014-06-01

    Here, we study the metastable decay of 5'-d(TTGCTT) in the presence of 0-6 alkaline metal ions (Li+, Na+, K+, Rb+) and 0-3 alkaline earth metal ions (Mg2+ and Ca2 +), which replace the corresponding number of protons in the oligonucleotide. We find that all ions studied here stabilize the oligonucleotide with respect to simple 3'-C-O backbone cleavage, but at the same time these metal ions promote a central oligonucleotide deletion accompanied by a concomitant recombination of the terminal d(TT) groups. We find that the quenching of the 3'-C-O backbone cleavage is not ion specific, since it is due to the removal of the phosphate protons upon replacement with the respective metal ions. The central nucleotide deletion competes with the 3'-C-O backbone cleavage channels and is thus promoted through the replacement of the exchangeable protons against metal ions. However, with increasing positive charge density of the metal ions the yield of the central nucleotide deletion further increases. We attribute this effect to the necessity of sufficient proximity of the terminal d(TT) group to allow for their recombination on this reaction path. Hence, the formation of a reactive conformer is mediated by the metal ions.

  3. Ion-molecule calculation of the abundance ratio of CCD to CCH in dense interstellar clouds

    NASA Technical Reports Server (NTRS)

    Herbst, Eric; Adams, Nigel G.; Smith, David; Defrees, D. J.

    1987-01-01

    Laboratory measurements and calculations have been performed to determine the abundance ratio of the deuterated ethynyl radical (CCD) to the normal radical (CCH) which can be achieved in dense interstellar clouds via isotopic fractionation in the C2H2(+) (HD)=C2HD(+)(H2) system of reactions. According to this limited treatment, the CCD/CCH abundance ratio which can be attained is in the range 0.02-0.03 for the Orion molecular cloud and 0.0l-0.02 for TMC-1. These ranges of numbers are in reasonable agreement with the observed values in Orion and TMC-1. However, the analysis of the CCD/CCH abundance ratio is complicated via the presence of competing fractionation mechanisms, especially in the low-temperature source TMC-1.

  4. Intermediate mass fragment production in central collisions of intermediate energy heavy ions

    SciTech Connect

    Li, T.; Bauer, W.; Craig, D.; Cronqvist, M.; Gualtieri, E.; Hannuschke, S.; Lacey, R.; Llope, W.J.; Reposeur, T.; Vander Molen, A.M.; Westfall, G.D.; Wilson, W.K.; Winfield, J.S.; Yee, J.; Yennello, S.J. ); Nadasen, A. ); Tickle, R.S. ); Norbeck, E. )

    1993-03-29

    We present [ital Z] distributions for fragments with 1[le][ital Z][le]12 from central collisions of [sup 40] Ar+[sup 45]Sc at incident energies ranging from 35 to 115 MeV/nucleon. We find that the [ital Z] distributions can be described by a power law or an exponential and steepen with increasing incident energy. Over the range of incident energies studied, the average number of intermediate mass fragments decreases while the average number of particles increases. When combined with previous results for the charge distributions, a minimum is observed in the extracted power-law parameter.

  5. 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.

    1991-01-01

    The densities of the hot component in the ion population observed in the P/Halley coma by the ion mass spectrometer aboard the Giotto spacecraft has been recomputed, and the results are reported. Except for protons and H2(+), all densities are found to be at least an order of magnitude higher than predicted by the physicochemical model of Schmidt et al. (1988). These densities require ionization mechanisms in addition to, or stronger than, plasma compression. The change in the density of solar wind ions across a magnetic discontinuity located 135,000 km from the comet is 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 is due to a discontinuity in the solar wind.

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

    SciTech Connect

    Neugebauer, M.; Goldstein, R.; Goldstein, B.E.; Fuselier, S.A.; Balsiger, H. Lockheed Research Laboratories, Palo Alto, CA Bern, Universitaet )

    1991-05-01

    The densities of the hot component in the ion population observed in the P/Halley coma by the ion mass spectrometer aboard the Giotto spacecraft has been recomputed, and the results are reported. Except for protons and H2(+), all densities are found to be at least an order of magnitude higher than predicted by the physicochemical model of Schmidt et al. (1988). These densities require ionization mechanisms in addition to, or stronger than, plasma compression. The change in the density of solar wind ions across a magnetic discontinuity located 135,000 km from the comet is 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 is due to a discontinuity in the solar wind. 41 refs.

  7. 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.

  8. Relative abundance of water-group ions in Saturn's inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Perry, Mark E.; Cravens, Thomas; Tokar, Robert; Smith, Howard T.; Perryman, Rebecca; Waite, J. Hunter; McNutt, Ralph L.

    2016-10-01

    At nineteen different times over seven years, the Cassini Ion Neutral Mass Spectrometer (INMS) measured the relative fractions of water-group ions in the inner magnetosphere of Saturn near the equatorial plane between 3.8 and 6.5 Saturn radii (RS). INMS samples only a small portion of velocity space in any one measurement, but the measurements span a broad range of velocity space. The data show that H2O+ comprises the bulk of the ions near 4.0 RS, and that its fraction decreases with increasing distance from 4.0 RS, the source of neutral water at Enceladus. At 4.0 RS, the fraction of H2O+ ranges from 60% to 100%, with an average of 80%. At 6.5 RS, the three main water-group constituents, H2O+, OH+, and O+, are nearly equal. H3O+, which dominates the water-group ion fractions in the Enceladus plume, is 10% or less in Saturn's magnetosphere outside the plume. The relative ion fractions show other variations that are not clearly linked to any of the studied parameters including velocity, density, and the orbit-phase-dependent activity of Enceladus.

  9. 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)

  10. Secondary radiation measurements for particle therapy applications: nuclear fragmentation produced by 4He ion beams in a PMMA target

    NASA Astrophysics Data System (ADS)

    Marafini, M.; Paramatti, R.; Pinci, D.; Battistoni, G.; Collamati, F.; De Lucia, E.; Faccini, R.; Frallicciardi, P. M.; Mancini-Terracciano, C.; Mattei, I.; Muraro, S.; Piersanti, L.; Rovituso, M.; Rucinski, A.; Russomando, A.; Sarti, A.; Sciubba, A.; Solfaroli Camillocci, E.; Toppi, M.; Traini, G.; Voena, C.; Patera, V.

    2017-02-01

    Nowadays there is a growing interest in particle therapy treatments exploiting light ion beams against tumors due to their enhanced relative biological effectiveness and high space selectivity. In particular promising results are obtained by the use of 4He projectiles. Unlike the treatments performed using protons, the beam ions can undergo a fragmentation process when interacting with the atomic nuclei in the patient body. In this paper the results of measurements performed at the Heidelberg Ion-Beam Therapy center are reported. For the first time the absolute fluxes and the energy spectra of the fragments—protons, deuterons, and tritons—produced by 4He ion beams of 102, 125 and 145 MeV u‑1 energies on a poly-methyl methacrylate target were evaluated at different angles. The obtained results are particularly relevant in view of the necessary optimization and review of the treatment planning software being developed for clinical use of 4He beams in clinical routine and the relative bench-marking of Monte Carlo algorithm predictions.

  11. The fragmentation dynamics of small Cs(CsI)n+ cluster ions under low-energy multiple collision conditions

    NASA Astrophysics Data System (ADS)

    Herzschuh, Rainer; Drewello, Thomas

    2004-04-01

    The collision-induced dissociations of small caesium iodide cluster ions of the type Cs(CsI)n+ where n=3-7, have been investigated under low-energy multiple collision conditions. The collisions were performed in the rf-only quadrupole of a BEqQ hybrid mass spectrometer. Breakdown graphs of selected parent ions were obtained by varying the laboratory collision energy in the range of 0-400 eV. The fragmentation dynamic established under these conditions provides a link between the well-known decay behaviour occurring unimolecularly and the dissociations following high energy (keV) collisional activation. Of particular interest is the observation that the energy-dependent dissociation pattern supplies support for the occurrence of one-step fission reactions, featuring the evaporation of presumably intact (CsI)n neutrals as opposed to a sequential decay via nCsI losses. The breakdown graphs thus provide a valuable tool to enhance insight into the fragmentation mechanism of these clusters.

  12. 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.

  13. Theoretical Study of Projectile Fragmentations in Relativistic Heavy-Ion Reactions

    NASA Astrophysics Data System (ADS)

    Ogul, R.; Imal, H.; Ergun, A.; Buyukcizmeci, N.; Botvina, A. S.; Trautmann, W.

    2015-05-01

    We have investigated and interpreted the production cross sections and isotopic distributions of projectile-like residues in the reactions 124Sn + 124Sn and 112Sn + 112Sn at an incident beam energy of 1 GeV/nucleon measured with the FRS fragment separator at the GSI laboratory. For the interpretation of the data, calculations within the statistical multifragmentation model (SMM) for an ensemble of excited sources were performed with ensemble parameters. The possible modification of symmetry energy parameter, in the multifragmentation region at the low density and hot freeze-out environment, is studied. It is reconfirmed that a significant reduction of the symmetry energy term is found necessary to reproduce experimental results at these conditions. We have also found a decreasing trend of the symmetry energy for large neutron-rich fragments of low excitation energy which is interpreted as a nuclear-structure effect.

  14. R-matrix electron-impact excitation data for astrophysically abundant sulphur ions

    NASA Astrophysics Data System (ADS)

    Liang, G. Y.; Badnell, N. R.; Zhao, G.; Zhong, J. Y.; Wang, F. L.

    2011-09-01

    We present results for the electron-impact excitation of highly-charged sulphur ions (S8+-S11+) obtained using the intermediate-coupling frame transformation R-matrix approach. A detailed comparison of the target structure has been made for the four ions to assess the uncertainty on collision strengths from the target structure. Effective collision strengths (Υs) are presented at temperatures ranging from 2 × 102(z + 1)2 K to 2 × 106(z + 1)2 K (where z is the residual charge of ions). Detailed comparisons for the Υs are made with the results of previous calculations for these ions, which will pose insight on the uncertainty in their usage by astrophysical and fusion modelling codes. Data are available in the archives of APAP via http://www.apap-network.org, and OPEN-ADAS via http://open.adas.ac.uk. Data and full Tables 5 and 6 are available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/533/A87

  15. Experimental particle formation rates spanning tropospheric sulfuric acid and ammonia abundances, ion production rates, and temperatures

    NASA Astrophysics Data System (ADS)

    Kürten, Andreas; Bianchi, Federico; Almeida, Joao; Kupiainen-Määttä, Oona; Dunne, Eimear M.; Duplissy, Jonathan; Williamson, Christina; Barmet, Peter; Breitenlechner, Martin; Dommen, Josef; Donahue, Neil M.; Flagan, Richard C.; Franchin, Alessandro; Gordon, Hamish; Hakala, Jani; Hansel, Armin; Heinritzi, Martin; Ickes, Luisa; Jokinen, Tuija; Kangasluoma, Juha; Kim, Jaeseok; Kirkby, Jasper; Kupc, Agnieszka; Lehtipalo, Katrianne; Leiminger, Markus; Makhmutov, Vladimir; Onnela, Antti; Ortega, Ismael K.; Petäjä, Tuukka; Praplan, Arnaud P.; Riccobono, Francesco; Rissanen, Matti P.; Rondo, Linda; Schnitzhofer, Ralf; Schobesberger, Siegfried; Smith, James N.; Steiner, Gerhard; Stozhkov, Yuri; Tomé, António; Tröstl, Jasmin; Tsagkogeorgas, Georgios; Wagner, Paul E.; Wimmer, Daniela; Ye, Penglin; Baltensperger, Urs; Carslaw, Ken; Kulmala, Markku; Curtius, Joachim

    2016-10-01

    Binary nucleation of sulfuric acid and water as well as ternary nucleation involving ammonia are thought to be the dominant processes responsible for new particle formation (NPF) in the cold temperatures of the middle and upper troposphere. Ions are also thought to be important for particle nucleation in these regions. However, global models presently lack experimentally measured NPF rates under controlled laboratory conditions and so at present must rely on theoretical or empirical parameterizations. Here with data obtained in the European Organization for Nuclear Research CLOUD (Cosmics Leaving OUtdoor Droplets) chamber, we present the first experimental survey of NPF rates spanning free tropospheric conditions. The conditions during nucleation cover a temperature range from 208 to 298 K, sulfuric acid concentrations between 5 × 105 and 1 × 109 cm-3, and ammonia mixing ratios from zero added ammonia, i.e., nominally pure binary, to a maximum of 1400 parts per trillion by volume (pptv). We performed nucleation studies under pure neutral conditions with zero ions being present in the chamber and at ionization rates of up to 75 ion pairs cm-3 s-1 to study neutral and ion-induced nucleation. We found that the contribution from ion-induced nucleation is small at temperatures between 208 and 248 K when ammonia is present at several pptv or higher. However, the presence of charges significantly enhances the nucleation rates, especially at 248 K with zero added ammonia, and for higher temperatures independent of NH3 levels. We compare these experimental data with calculated cluster formation rates from the Atmospheric Cluster Dynamics Code with cluster evaporation rates obtained from quantum chemistry.

  16. 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

  17. ANALYTICAL FORMULAE OF MOLECULAR ION ABUNDANCES AND THE N{sub 2}H{sup +} RING IN PROTOPLANETARY DISKS

    SciTech Connect

    Aikawa, Yuri; Furuya, Kenji; Nomura, Hideko; Qi, Chunhua

    2015-07-10

    We investigate the chemistry of ion molecules in protoplanetary disks, motivated by the detection of the N{sub 2}H{sup +} ring around TW Hya. While the ring inner radius coincides with the CO snow line, it is not apparent why N{sub 2}H{sup +} is abundant outside the CO snow line in spite of the similar sublimation temperatures of CO and N{sub 2}. Using the full gas-grain network model, we reproduced the N{sub 2}H{sup +} ring in a disk model with millimeter grains. The chemical conversion of CO and N{sub 2} to less volatile species (sink effect hereinafter) is found to affect the N{sub 2}H{sup +} distribution. Since the efficiency of the sink depends on various parameters such as activation barriers of grain-surface reactions, which are not well constrained, we also constructed the no-sink model; the total (gas and ice) CO and N{sub 2} abundances are set constant, and their gaseous abundances are given by the balance between adsorption and desorption. Abundances of molecular ions in the no-sink model are calculated by analytical formulae, which are derived by analyzing the full-network model. The N{sub 2}H{sup +} ring is reproduced by the no-sink model, as well. The 2D (R-Z) distribution of N{sub 2}H{sup +}, however, is different among the full-network model and no-sink model. The column density of N{sub 2}H{sup +} in the no-sink model depends sensitively on the desorption rate of CO and N{sub 2} and the cosmic-ray flux. We also found that N{sub 2}H{sup +} abundance can peak at the temperature slightly below the CO sublimation, even if the desorption energies of CO and N{sub 2} are the same.

  18. 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.

  19. Top-down protein fragmentation by infrared multiphoton dissociation in a dual pressure linear ion trap.

    PubMed

    Madsen, James A; Gardner, Myles W; Smith, Suncerae I; Ledvina, Aaron R; Coon, Joshua J; Schwartz, Jae C; Stafford, George C; Brodbelt, Jennifer S

    2009-11-01

    Infrared multiphoton dissociation (IRMPD) was implemented in a novel dual pressure linear ion trap for rapid top-down proteomics. The high pressure cell provided improved trapping and isolation efficiencies while the isotopic profiles of 10+ charged ions could be resolved by mass analysis in the low pressure cell that enabled effective top down protein identification. Striking differences between IRMPD in the low pressure cell and CID in the high pressure cell were observed for proteins ranging from 8.6 to 29 kDa. Because of secondary dissociation, IRMPD yielded product ions in significantly lower charge states as compared to CID, thus facilitating more accurate mass identification and streamlining product ion assignment. This outcome was especially useful for database searching of larger proteins (approximately 29 kDa) as IRMPD substantially improved protein identification and scoring confidence. Also, IRMPD showed an increased selectivity toward backbone cleavages N-terminal to proline and C-terminal to acidic residues (especially for the lowest charge states), which could be useful for a priori spectral predictions and enhanced database searching for protein identification.

  20. High resolution Coulomb explosion spectra and angular distributions of fragment ions of N 2 in a femtosecond laser field

    NASA Astrophysics Data System (ADS)

    Shi, Mingyuan; Huang, Shaochuan; Xi, Wei; Liu, Zuoye; Du, Hongchuan; Ding, Baowei; Hu, Bitao

    2017-03-01

    Femtosecond laser field-induced ionization and Coulomb explosion are systematically investigated using high-resolution time-of-flight mass spectroscopy. Meanwhile a good alignment of the N2 is achieved geometrically. Based on the energy and momentum conservation laws, the events from different Coulomb explosion channels are identified accurately and further used to obtain the Kinetic Energy Release (KER) by the created molecular ion pairs and the angular distributions of the fragment ions. The KERs measured at laser intensities varying from 4 × 10^{14} W/cm2 to 2 × 10^{15} W/cm2 are found to stay constant. The angular distributions are measured at laser intensity of 9 × 10^{14} W/cm2. The atomic ions N+, N^{2+} and N^{3+} exhibit highly anisotropic distributions and for higher charge state, the angular distributions become narrower. With good exclusion of channel N(1,0), the non-zeroes normal to the laser polarization vector in channel N(1,1) still exist, which indicates the presence of geometric alignments (GA). The elusive shrink structure at θ=0° for channels N(1,1), N(1,2) and N(2,3) is observed, which implies that the non-sequential process exists, and the electron rescattering plays role in the ionization process.

  1. Fragmentation of oxime and silyl oxime ether odd-electron positive ions by the McLafferty rearrangement: new insights on structural factors that promote α,β fragmentation

    PubMed Central

    Laulhé, Sébastien; Bogdanov, Bogdan; Johannes, Leah M.; Gutierrez, Osvaldo; Harrison, Jason G.; Tantillo, Dean J.; Zhang, Xiang; Nantz, Michael H.

    2012-01-01

    The McLafferty rearrangement is an extensively studied fragmentation reaction for the odd-electron positive ions from a diverse range of functional groups and molecules. Here, we present experimental and theoretical results of 12 model compounds that were synthesized and investigated by GC-TOF MS and density functional theory calculations. These compounds consisted of three main groups: carbonyls, oximes and silyl oxime ethers. In all electron ionization mass spectra, the fragment ions that could be attributed to the occurrence of a McLafferty rearrangement were observed. For t-butyldimethylsilyl oxime ethers with oxygen in a β-position, the McLafferty rearrangement was accompanied by loss of the t-butyl radical. The various mass spectra showed that the McLafferty rearrangement is relatively enhanced compared with other primary fragmentation reactions by the following factors: oxime versus carbonyl, oxygen versus methylene at the β-position and ketone versus aldehyde. Calculations predict that the stepwise mechanism is favored over the concerted mechanism for all but one compound. For carbonyl compounds, C–C bond breaking was the rate-determining step. However, for both the oximes and t-butyldimethylsilyl oxime ethers with oxygen at the β-position, the hydrogen transfer step was rate limiting, whereas with a CH2 group at the β-position, the C–C bond breaking was again rate determining. n-Propoxy-acetaldehyde, bearing an oxygen atom at the β-position, is the only case that was predicted to proceed through a concerted mechanism. The synthesized oximes exist as both the (E)- and (Z)-isomers, and these were separable by GC. In the mass spectra of the two isomers, fragment ions that were generated by the McLafferty rearrangement were observed. Finally, fragment ions corresponding to the McLafferty reverse charge rearrangement were observed for all compounds at varying relative ion intensities compared with the conventional McLafferty rearrangement. PMID

  2. 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 ...

  3. 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.

  4. Automated LC-HRMS(/MS) approach for the annotation of fragment ions derived from stable isotope labeling-assisted untargeted metabolomics.

    PubMed

    Neumann, Nora K N; Lehner, Sylvia M; Kluger, Bernhard; Bueschl, Christoph; Sedelmaier, Karoline; Lemmens, Marc; Krska, Rudolf; Schuhmacher, Rainer

    2014-08-05

    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 (12)C- and uniformly (13)C (U-(13)C)-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-(13)C-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.

  5. Quantum molecular dynamics approach to heavy ion collisions: Description of the model, comparison with fragmentation data, and the mechanism of fragment formation

    NASA Astrophysics Data System (ADS)

    Aichelin, J.; Peilert, G.; Bohnet, A.; Rosenhauer, A.; Stöcker, H.; Greiner, W.

    1988-06-01

    We present a detailed microscopic quantum molecular dynamic analysis of fragment formation in the reaction Ne(1.05 GeV/nucleon) + Au. The theoretical predictions of the total mass yield, the multiplicity distribution of clusters, their average momentum, and their angular distribution agree well with the available data. We find a rather localized hot participant zone, which predominantly emits protons and neutrons. The multiplicity of light clusters depends strongly on the impact parameter whereas the heavier fragments A>=40 result from the decay of spectator residues. Their yield can provide a good measure for the impact parameter. The hypothesis of a compound system of AP and AT nucleons which is globally heated and equilibrated is not supported by our results. Light and massive fragments occupy different regions in phase space. Semiperipheral reactions do not lead to a stopping of the projectile. We observe a power law behavior of the inclusive mass yield distribution. Its form, however, is caused by averaging over different impact parameters. This rules out inclusive mass yield distributions as candidates for revealing a possible liquid gas phase transition. Light and intermediate mass fragments are formed during the early compressional stage of the reaction. We find that the projectile causes a high density wave to travel through the target. It causes the target to fragment and transfers transverse momentum to the intermediate mass fragments. Lighter fragments receive additional momentum transfer due to n-n collisions.

  6. Studies of complex fragment emission in heavy ion reactions. Progress report, January 1, 1993--September 15, 1993

    SciTech Connect

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

    1993-09-12

    The study of intermediate-energy heavy-ion nuclear reactions is reported. This work has two foci: the properties of nuclear matter under abnormal conditions, in this energy domain, predominately low densities and the study of the relevant reaction mechanisms. Nuclear matter properties, such as phase transitions, are reflected in the dynamics of the reactions. 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. The program has the following objectives: to study energy, mass, and angular momentum deposition by studying incomplete fusion reactions; to gain confidence in the understanding of 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 (where intermediate mass fragment emission is not improbable) with excitation function studies; and to learn about the dynamics of the decays using particle-particle correlations. The last effort focuses on simple systems, where definitive statements are possible. These avenues of research share a common theme, large complex fragment production. It is this feature, more than any other, which distinguishes the intermediate energy domain.

  7. 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.

  8. 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

  9. Fragmentation of protonated 2-(2-phenylethyl)chromones from agarwood: the diagnostic role of ion/neutral complexes as reactive intermediates.

    PubMed

    Yang, Delan; Xia, Bing; Jiang, Yan; Mei, Wenli; Kuck, Dietmar

    2015-01-01

    A positive-ion electrospray ionisation collision-induced dissociation mass spectrometric study on the fragmentation of the [M + H](+) ions of 2-(2-phenylethyl)chromone and a set of nine hydroxyl- and/or methoxy-substituted derivatives has revealed a highly prominent fragmentation channel, the loss of benzoquinomethanes or a benzaldehyde, respectively, as a diagnostic feature for 2-(2-phenylethyl)chromones that bear a hydroxyl group at the para- (4'-), ortho- (2'-) and/or benzylic (α-) position of the phenylethyl residue. Derivatives that bear only a meta- (3'-) hydroxyl group do not undergo this elimination. The intermediacy of ion/neutral complexes (INCs) is invoked to explain this fragmentation, which involves the remarkable intra-complex proton or hydrogen atom transfer from the remote 4'-OH (or the 2'- or α-OH) functionalities. Density functional theory (B3LYP/6-31G(d)) calculations confirm the energetic preference for these elimination channels and agree with the limited thermochemical data known for para- and ortho- benzoquinomethanes. The INC-mediated losses of the benzaldehydes from the [M + H](+) ions of the α-hydroxy-substituted 2-(2-phenylethyl)chromones correspond to a particularly facile (vinylogous) Grob fragmentation. The study may be viewed as a telling example of the diagnostic role of ion/neutral complexes as intermediates for the structural assignment of constitutional isomers by mass spectrometry.

  10. Beam optical design of in-flight fragment separator for high-power heavy ion beam

    NASA Astrophysics Data System (ADS)

    Yun, C. C.; Kim, Mi-Jung; Kim, D. G.; Song, J. S.; Kim, Myeong-Jin; Kim, J. W.; Kim, J. R.; Wan, W.

    2013-12-01

    An in-flight fragment separator has been designed for the rare isotope science project (RISP) in Korea. A beam used for the design is 238U in the energy of 200 MeV/u with the maximum beam power of 400 kW. The use of high-power beam requires careful removal of the primary beam by pre-separator, for which its configuration was revised to employ four dipole magnets instead of two. Different configurations of the separator have been tested in search of optimal design in non-linear optics, which was complicated by the space needed for the target, beam dump and radiation shielding. Non-linear optical calculations have been carried out using GICOSY and COSY Infinity including the fringe fields of large-aperture quadrupole magnets. Correction of non-linear terms is made with multipole coils located inside the superconducting quadrupole magnets and by external multipole magnets. Beam simulations using LISE++ and MOCADI have been performed to consider the effects of multiple charge states of the primary and isotope beams produced at the target. Layout of the separator is being finalized, and detailed optics simulation will continue to refine its design.

  11. 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

  12. Complementary b/y fragment ion pairs from post-source decay of metastable YahO for calibration of MALDI-TOF-TOF-MS/MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complementary b/y fragment ion pairs from post-source decay (PSD) of metastable YahO protein ion were evaluated for use in the calibration of MALDI-TOF-TOF for tandem mass spectrometry (MS/MS). The yahO gene from pathogenic Escherichia coli O157:H7 strain EDL933 was cloned into a pBAD18 plasmid vect...

  13. One-electron Initiated Two-electron Oxidation of Water by Aluminum Porphyrins with Earth's Most Abundant Metal Ion.

    PubMed

    Kuttassery, Fazalurahman; Mathew, Siby; Sagawa, Shogo; Remello, Sebastian Nybin; Thomas, Arun; Yamamoto, Daisuke; Onuki, Satomi; Nabetani, Yu; Tachibana, Hiroshi; Inoue, Haruo

    2017-03-20

    We report here a new molecular catalyst for efficient water splitting, aluminum porphyrins (tetra-methylpyridiniumylporphyrinatealuminum: AlTMPyP), containing the Earth's most abundant metal as the central ion. One-electron oxidation of the aluminum porphyrin initiates the two-electron oxidation of water to form hydrogen peroxide as the primary reaction product with the lowest known overpotential (97 mV). The aluminum-peroxo complex was clearly detected by a cold-spray ionization mass-spectrometry in HRMS mode and the structure of the intermediate was further confirmed using laser-Raman spectroscopy, indicating the hydroperoxy complex of AlTMPyP to be the key intermediate in the reaction. The two-electron oxidation of water to form hydrogen peroxide was essentially quantitative, with a Faradaic efficiency of 99%. The catalytic reaction was found to be highly efficient, with a turnover frequency up to ~ 2 × 10⁴ s¯¹. A reaction mechanism is proposed involving oxygen-oxygen bond formation by the attack of a hydroxide ion on the oxyl-radical-like axial ligand oxygen atom in the one-electron-oxidized form of AlTMPyP(O¯)₂, followed by a second electron transfer to the electrode.

  14. Precursor Ion Scan Mode-Based Strategy for Fast Screening of Polyether Ionophores by Copper-Induced Gas-Phase Radical Fragmentation Reactions.

    PubMed

    Crevelin, Eduardo J; Possato, Bruna; Lopes, João L C; Lopes, Norberto P; Crotti, Antônio E M

    2017-04-04

    The potential of copper(II) to induce gas-phase fragmentation reactions in macrotetrolides, a class of polyether ionophores produced by Streptomyces species, was investigated by accurate-mass electrospray tandem mass spectrometry (ESI-MS/MS). Copper(II)/copper(I) transition directly induced production of diagnostic acylium ions with m/z 199, 185, 181, and 167 from α-cleavages of [macrotetrolides + Cu](2+). A UPLC-ESI-MS/MS methodology based on the precursor ion scan of these acylium ions was developed and successfully used to identify isodinactin (1), trinactin (2), and tetranactin (3) in a crude extract of Streptomyces sp. AMC 23 in the precursor ion scan mode. In addition, copper(II) was also used to induce radical fragmentation reactions in the carboxylic acid polyether ionophore nigericin. The resulting product ions with m/z 755 and 585 helped to identify nigericin in a crude extract of Streptomyces sp. Eucal-26 by means of precursor ion scan experiments, demonstrating that copper-induced fragmentation reactions can potentially identify different classes of polyether ionophores rapidly and selectively.

  15. ToF-SIMS Analysis of Adsorbed Proteins: Principal Component Analysis of the Primary Ion Species Effect on the Protein Fragmentation Patterns.

    PubMed

    Muramoto, Shin; Graham, Daniel J; Wagner, Matthew S; Lee, Tae Geol; Moon, Dae Won; Castner, David G

    2011-12-15

    In time-of-flight secondary ion mass spectrometry (ToF-SIMS), the choice of primary ion used for analysis can influence the resulting mass spectrum. This is because different primary ion types can produce different fragmentation pathways. In this study, analysis of single-component protein monolayers were performed using monatomic, tri-atomic, and polyatomic primary ion sources. Eight primary ions (Cs(+), Au(+), Au(3) (+), Bi(+), Bi(3) (+), Bi(3) (++), C(60) (+)) were used to examine to the low mass (m/z < 200) fragmentation patterns from five different proteins (bovine serum albumin, bovine serum fibrinogen, bovine immunoglobulin G and chicken egg white lysozyme) adsorbed onto mica surfaces. Principal component analysis (PCA) processing of the ToF-SIMS data showed that variation in peak intensity caused by the primary ions was greater than differences in protein composition. The spectra generated by Cs(+), Au(+) and Bi(+) primary ions were similar, but the spectra generated by monatomic, tri-atomic and polyatomic primary ion ions varied significantly. C(60) primary ions increased fragmentation of the adsorbed proteins in the m/z < 200 region, resulting in more intense low m/z peaks. Thus, comparison of data obtained by one primary ion species with that obtained by another primary ion species should be done with caution. However, for the spectra generated using a given primary ion beam, discrimination between the spectra of different proteins followed similar trends. Therefore, a PCA model of proteins created with a given ion source should only be applied to datasets obtained using the same ion source. The type of information obtained from PCA depended on the peak set used. When only amino acid peaks were used, PCA was able to identify the relationship between proteins by their amino acid composition. When all peaks from m/z 12-200 were used, PCA separated proteins based on a ratio of C(4)H(8)N(+) to K(+) peak intensities. This ratio correlated with the thickness

  16. Ortho-hydroxyl effect and proton transfer via ion-neutral complex: the fragmentation study of protonated imine resveratrol analogues in mass spectrometry.

    PubMed

    Yue, Lei; Li, Jing; Xie, Xiaodong; Guo, Cheng; Yin, Xinchi; Yin, Qi; Chen, Yinjuan; Pan, Yuanjiang; Ding, Chuanfan

    2016-07-01

    The fragmentation pathways of protonated imine resveratrol analogues in the gas-phase were investigated by electrospray ionization-tandem mass spectrometry. Benzyl cations were formed in the imine resveratrol analogues that had an ortho-hydroxyl group on the benzene ring A. The specific elimination of the quinomethane neutral, CH2  = C6 H4  = O, from the two isomeric ions [M1 + H](+) and [M3 + H](+) via the corresponding ion-neutral complexes was observed. The fragmentation pathway for the related meta-isomer, ion [M2 + H](+) and the other congeners was not observed. Accurate mass measurements and additional experiments carried out with a chlorinated analogue and the trideuterated isotopolog of M1 supported the overall interpretation of the fragmentation phenomena observed. It is very helpful for understanding the intriguing roles of ortho-hydroxyl effect and ion-neutral complexes in fragmentation reactions and enriching the knowledge of the gas-phase chemistry of the benzyl cation. Copyright © 2016 John Wiley & Sons, Ltd.

  17. Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase.

    PubMed

    Poully, Jean-Christophe; Vizcaino, Violaine; Schwob, Lucas; Delaunay, Rudy; Kocisek, Jaroslav; Eden, Samuel; Chesnel, Jean-Yves; Méry, Alain; Rangama, Jimmy; Adoui, Lamri; Huber, Bernd

    2015-08-03

    Collisions between O(3+) ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum-chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non-negligible amount of the radical cation monomer is observed. New fragment-ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.

  18. 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

    2015-01-06

    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.

  19. Heavy-ion peripheral collisions in the Fermi energy domain : Fragmentation processes or dissipative collisions ?

    NASA Astrophysics Data System (ADS)

    Borderie, B.; Rivet, M. F.; Tassan-Got, L.

    For several years a new field in nuclear physics has been opened by the opportunity to accelerate heavy ions through an energy domain including the Fermi energy of nucleons. The new domain has to be seen as a link between dissipative processes observed at low energies, dominated by mean field considerations, and high energy collisions for which nucleon-nucleon collisions play an important role. This paper reviews our present knowledge on peripheral collisions. A reminder of contiguous energy domains is done as well as their extension in the new field. Specific calculations are also presented. Finally a wide comparison between experiments and calculations is performed. A fast dissipative stage proves to be responsible for the dominant mechanisms involved, at least when the incident energy is lower than 50 MeV/nucleon. Un nouveau champ d'études de la physique nucléaire s'est ouvert depuis quelques années avec la possibilité de réaliser des collisions noyau-noyau dans un domaine en énergie franchissant l'énergie de Fermi des nucléons. Ce nouveau domaine constitue le lien entre les processus dissipatifs observés à basse énergie, dominés par le concept de champ moyen, et les réactions à grande énergie pour lesquelles les collisions nucléon-nucléon jouent un rôle important. Cet article sur les collisions périphériques fait le point sur l'état actuel de nos connaissances. Après un rappel des domaines en énergie connexes, de leurs eventuelles extensions dans le domaine considéré, des calculs spécifiques au domaine sont décrits. Enfin une importante comparaison calculs théoriques-expériences est présentée. Une dissipation en énergie très rapide est responsable des processus dominants observés jusqu'à des énergies incidentes d'environ 50 MeV/nucléon.

  20. First fragmentation function measurements from full jet reconstruction in heavy-ion collisions at sqrt{s_{NN}}=200 GeV by STAR

    NASA Astrophysics Data System (ADS)

    Putschke, Jörn

    2009-06-01

    Measurements of inclusive hadron suppression and di-hadron azimuthal correlations in ultra-relativistic nuclear collisions at RHIC have provided important insights into jet quenching in hot QCD matter, but are limited in their sensitivity due to well-known biases. Full jet reconstruction in heavy-ion collisions would conceptually provide a direct measurement of the energy of the scattered parton before energy loss, alleviating such biases and allowing a measurement of the energy loss probability distribution in a model-independent way from hard probes. In these proceedings we utilize recent progress in the reconstruction of jets in the heavy ion environment and present the first measurement of the fragmentation function from fully reconstructed jets in heavy ion collisions. The fragmentation function measured in central Au + Au collisions at sqrt{s_{NN}}=200 GeV will be presented and discussed with respect to p + p reference measurements.

  1. 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 +}.

  2. 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

  3. 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

  4. Fragmentation Characteristics of Deprotonated N-linked Glycopeptides: Influences of Amino Acid Composition and Sequence

    NASA Astrophysics Data System (ADS)

    Nishikaze, Takashi; Kawabata, Shin-ichirou; Tanaka, Koichi

    2014-06-01

    Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., 2,4AR, 2,4AR-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + 0,2X0-H]- and [peptide-NH3-H]-). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36]-, was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides.

  5. 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.

  6. Determination of triclosan metabolites by using in-source fragmentation from high-performance liquid chromatography/negative atmospheric pressure chemical ionization ion trap mass spectrometry.

    PubMed

    Wu, Jian-lin; Liu, Jie; Cai, Zongwei

    2010-07-15

    Triclosan is a widely used broad-spectrum antibacterial agent that acts by specifically inhibiting enoyl-acyl carrier protein reductase. An in vitro metabolic study of triclosan was performed by using Sprague-Dawley (SD) rat liver S9 and microsome, while the in vivo metabolism was investigated on SD rats. Twelve metabolites were identified by using in-source fragmentation from high-performance liquid chromatography/negative atmospheric pressure chemical ionization ion trap mass spectrometry (HPLC/APCI-ITMS) analysis. Compared to electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS) that gave little fragmentation for triclosan and its metabolites, the in-source fragmentation under APCI provided intensive fragmentations for the structural identifications. The in vitro metabolic rate of triclosan was quantitatively determined by using HPLC/ESI-ITMS with the monitoring of the selected triclosan molecular ion. The metabolism results indicated that glucuronidation and sulfonation were the major pathways of phase II metabolism and the hydroxylated products were the major phase I metabolites. Moreover, glucose, mercapturic acid and cysteine conjugates of triclosan were also observed in the urine samples of rats orally administrated with triclosan.

  7. Fragmentation Processes

    NASA Astrophysics Data System (ADS)

    Whelan, Colm T.

    2012-12-01

    Preface; 1. Direct and resonant double-photoionization: from atoms to solids L. Avaldi and G. Stefani; 2. The application of propagation exterior complex scaling to atomic collisions P. L. Bartlett and A. T. Stelbovics; 3. Fragmentation of molecular-ion beams in intense ultra-short laser pulses I. Ben-Itzhak; 4. Atoms with one and two active electrons in strong laser fields I. A. Ivanov and A. S. Kheifets; 5. Experimental aspects of ionization studies by positron and positronium impact G. Laricchia, D. A. Cooke, Á. Kövér and S. J. Brawley; 6. (e,2e) spectroscopy using fragmentation processes J. Lower, M. Yamazaki and M. Takahashi; 7. A coupled pseudostate approach to the calculation of ion-atom fragmentation processes M. McGovern, H. R. J. Walters and C. T. Whelan; 8. Electron Impact Ionization using (e,2e) coincidence techniques from threshold to intermediate energies A. J. Murray; 9. (e,2e) processes on atomic inner shells C. T. Whelan; 10. Spin resolved atomic (e,2e) processes J. Lower and C. T. Whelan; Index.

  8. 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.

  9. 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.

  10. Retrospective screening of relevant pesticide metabolites in food using liquid chromatography high resolution mass spectrometry and accurate-mass databases of parent molecules and diagnostic fragment ions.

    PubMed

    Polgár, László; García-Reyes, Juan F; Fodor, Péter; Gyepes, Attila; Dernovics, Mihály; Abrankó, László; Gilbert-López, Bienvenida; Molina-Díaz, Antonio

    2012-08-03

    In recent years, the detection and characterization of relevant pesticide metabolites in food is an important task in order to evaluate their formation, kinetics, stability, and toxicity. In this article, a methodology for the systematic screening of pesticides and their main metabolites in fruit and vegetable samples is described, using LC-HRMS and accurate-mass database search of parent compounds and their diagnostic fragment ions. The approach is based on (i) search for parent pesticide molecules; (ii) search for their metabolites in the positive samples, assuming common fragmentation pathways between the metabolites and parent pesticide molecules; and (iii) search for pesticide conjugates using the data from both parent species and diagnostic fragment ions. An accurate-mass database was constructed consisting of 1396 compounds (850 parent compounds, 447 fragment ions and 99 metabolites). The screening process was performed by the software in an automated fashion. The proposed methodology was evaluated with 29 incurred samples and the output obtained was compared to standard pesticide testing methods (targeted LC-MS/MS). Examples on the application of the proposed approach are shown, including the detection of several pesticide glycosides derivatives, which were found with significantly relevant intensities. Glucose-conjugated forms of parent compounds (e.g., fenhexamid-O-glucoside) and those of metabolites (e.g., despropyl-iprodione-N-glycoside) were detected. Facing the lack of standards for glycosylated pesticides, the study was completed with the synthesis of fenhexamid-O-glucoside for quantification purposes. In some cases the pesticide derivatives were found in a relatively high ratio, drawing the attention to these kinds of metabolites and showing that they should not be neglected in multi-residue methods. The global coverage obtained on the 29 analyzed samples showed the usefulness and benefits of the proposed approach and highlights the practical

  11. Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H₄ and the ion channel serotonin 5-HT₃A.

    PubMed

    Verheij, Mark H P; de Graaf, Chris; de Kloe, Gerdien E; Nijmeijer, Saskia; Vischer, Henry F; Smits, Rogier A; Zuiderveld, Obbe P; Hulscher, Saskia; Silvestri, Linda; Thompson, Andrew J; van Muijlwijk-Koezen, Jacqueline E; Lummis, Sarah C R; Leurs, Rob; de Esch, Iwan J P

    2011-09-15

    A fragment library was screened against the G protein-coupled histamine H(4) receptor (H(4)R) and the ligand-gated ion channel serotonin 5-HT(3A) (5-HT(3A)R). Interestingly, significant overlap was found between H(4)R and 5-HT(3A)R hit sets. The data indicates that dual active H(4)R and 5 HT(3A)R fragments have a higher complexity than the selective compounds which has important implications for chemical genomics approaches. The results of our fragment-based library screening study illustrate similarities in ligand recognition between H(4)R and 5-HT(3A)R and have important consequences for selectivity profiling in ongoing drug discovery efforts on H(4)R and 5-HT(3A)R. The affinity profiles of our fragment screening studies furthermore match the chemical properties of the H(4)R and 5-HT(3A)R binding sites and can be used to define molecular interaction fingerprints to guide the in silico prediction of protein-ligand interactions and structure.

  12. 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.

  13. 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.

  14. Multistage fragmentation of ion trap mass spectrometry system and pseudo-MS3 of triple quadrupole mass spectrometry characterize certain (E)-3-(dimethylamino)-1-arylprop-2-en-1-ones: a comparative study.

    PubMed

    Abdelhameed, Ali S; Kadi, Adnan A; Abdel-Aziz, Hatem A; Angawi, Rihab F; Attwa, Mohamed W; Al-Rashood, Khalid A

    2014-01-01

    A new approach was recently introduced to improve the structure elucidation power of tandem mass spectrometry simulating the MS(3) of ion trap mass spectrometry system overcoming the different drawbacks of the latter. The fact that collision induced dissociation in the triple quadrupole mass spectrometer system provides richer fragment ions compared to those achieved in the ion trap mass spectrometer system utilizing resonance excitation. Moreover, extracting comprehensive spectra in the ion trap needs multistage fragmentation, whereas similar fragment ions may be acquired from one stage product ion scan using the triple quadrupole mass spectrometer. The new strategy was proven to enhance the qualitative performance of tandem mass spectrometry for structural elucidation of different chemical entities. In the current study we are endeavoring to prove our hypothesis of the efficiency of the new pseudo-MS(3) technique via its comparison with the MS(3) mode of ion trap mass spectrometry system. Ten pharmacologically and synthetically important (E)-3-(dimethylamino)-1-arylprop-2-en-1-ones (enaminones 4a-j) were chosen as model compounds for this study. This strategy permitted rigorous identification of all fragment ions using triple quadrupole mass spectrometer with sufficient specificity. It can be used to elucidate structures of different unknown components. The data presented in this paper provide clear evidence that our new pseudo-MS(3) may simulate the MS(3) of ion trap spectrometry system.

  15. 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

  16. 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.

  17. Enhanced analyte detection using in-source fragmentation of field asymmetric waveform ion mobility spectrometry-selected ions in combination with time-of-flight mass spectrometry.

    PubMed

    Brown, Lauren J; Smith, Robert W; Toutoungi, Danielle E; Reynolds, James C; Bristow, Anthony W T; Ray, Andrew; Sage, Ashley; Wilson, Ian D; Weston, Daniel J; Boyle, Billy; Creaser, Colin S

    2012-05-01

    Miniaturized ultra high field asymmetric waveform ion mobility spectrometry (FAIMS) is used for the selective transmission of differential mobility-selected ions prior to in-source collision-induced dissociation (CID) and time-of-flight mass spectrometry (TOFMS) analysis. The FAIMS-in-source collision induced dissociation-TOFMS (FISCID-MS) method requires only minor modification of the ion source region of the mass spectrometer and is shown to significantly enhance analyte detection in complex mixtures. Improved mass measurement accuracy and simplified product ion mass spectra were observed following FAIMS preselection and subsequent in-source CID of ions derived from pharmaceutical excipients, sufficiently close in m/z (17.7 ppm mass difference) that they could not be resolved by TOFMS alone. The FISCID-MS approach is also demonstrated for the qualitative and quantitative analysis of mixtures of peptides with FAIMS used to filter out unrelated precursor ions thereby simplifying the resulting product ion mass spectra. Liquid chromatography combined with FISCID-MS was applied to the analysis of coeluting model peptides and tryptic peptides derived from human plasma proteins, allowing precursor ion selection and CID to yield product ion data suitable for peptide identification via database searching. The potential of FISCID-MS for the quantitative determination of a model peptide spiked into human plasma in the range of 0.45-9.0 μg/mL is demonstrated, showing good reproducibility (%RSD < 14.6%) and linearity (R(2) > 0.99).

  18. 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.

  19. 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.

  20. [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.

  1. 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.

  2. 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

  3. Hadrons from coalescence plus fragmentation in A A collisions at energies available at the BNL Relativistic Heavy Ion Collider to the CERN Large Hadron Collider

    NASA Astrophysics Data System (ADS)

    Minissale, Vincenzo; Scardina, Francesco; Greco, Vincenzo

    2015-11-01

    In a coalescence plus independent fragmentation approach we calculate the pT spectra of the main hadrons: π ,K ,p ,p ¯,Λ ,ϕ in a wide range of transverse momentum from low pT up to about 10 GeV. The approach in its main features was developed several years ago at Relativistic Heavy Ion Collider (RHIC) energy. Augmenting the model with the inclusion of some more main resonance decays, we show that the approach correctly predicts the evolution of the pT spectra from RHIC to LHC (Large Hadron Collider) energy and in particular the baryon-to-meson ratios p /π ,p ¯/π ,Λ /K that reach a value of the order of unit at pT˜3 GeV . This is achieved without any change of the coalescence parameters. The more recent availability of experimental data up to pT˜10 GeV for Λ spectrum as well as for p /π and Λ /K shows some lack of yield in a limited pT range around 6 GeV. This indicates that the baryons pT spectra from Albino-Kniehl-Kramer fragmentation functions are too flat at pT≲8 GeV . We also show that in a coalescence plus fragmentation approach one predicts a nearly pT independent p /ϕ ratio up to pT˜4 GeV followed by a significant decrease at higher pT. Such a behavior is driven by a similar radial flow effect at pT<2 GeV and the dominance of fragmentation for ϕ at larger pT.

  4. Initial yields of DNA double-strand breaks and DNA Fragmentation patterns depend on linear energy transfer in tobacco BY-2 protoplasts irradiated with helium, carbon and neon ions.

    PubMed

    Yokota, Yuichiro; Yamada, Shinya; Hase, Yoshihiro; Shikazono, Naoya; Narumi, Issay; Tanaka, Atsushi; Inoue, Masayoshi

    2007-01-01

    The ability of ion beams to kill or mutate plant cells is known to depend on the linear energy transfer (LET) of the ions, although the mechanism of damage is poorly understood. In this study, DNA double-strand breaks (DSBs) were quantified by a DNA fragment-size analysis in tobacco protoplasts irradiated with high-LET ions. Tobacco BY-2 protoplasts, as a model of single plant cells, were irradiated with helium, carbon and neon ions having different LETs and with gamma rays. After irradiation, DNA fragments were separated into sizes between 1600 and 6.6 kbp by pulsed-field gel electrophoresis. Information on DNA fragmentation was obtained by staining the gels with SYBR Green I. Initial DSB yields were found to depend on LET, and the highest relative biological effectiveness (about 1.6) was obtained at 124 and 241 keV/microm carbon ions. High-LET carbon and neon ions induced short DNA fragments more efficiently than gamma rays. These results partially explain the large biological effects caused by high-LET ions in plants.

  5. Determination of N-linked Glycosylation in Viral Glycoproteins by Negative Ion Mass Spectrometry and Ion Mobility.

    PubMed

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

    2015-01-01

    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.

  6. 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

  7. Comparison of in-gel and on-membrane digestion methods at low to sub-pmol level for subsequent peptide and fragment-ion mass analysis using matrix-assisted laser-desorption/ionization mass spectrometry.

    PubMed

    Courchesne, P L; Luethy, R; Patterson, S D

    1997-01-01

    The success of the mass spectrometric-based approaches for the identification of gel-separated proteins relies upon recovery of peptides, without high levels of ionization-suppressing contaminants, in solvents compatible with the mass spectrometer being employed. We sought to determine whether in-gel or on-membrane digestion provided a significant advantage when low to sub-pmol quantities of gel-separated proteins were analyzed by matrix-assisted laser-desorption/ionization mass spectrometry (MALDI-MS) with respect to the number and size of released peptides. Serial dilutions of five standard proteins of M(r) 17,000 to 97,000 (from 16 pmol to 125 fmol) were electrophoresed and subjected to in-gel digestion (using a microcolumn clean-up protocol, Courchesne, P.L. and Patterson, S. D., BioTechniques, 1997, in press) or on-membrane digestion following blotting to the PVDF-based membranes, Immobilon-P and Immobilon-CD. Peptide maps were able to be obtained for all proteins at the detection limit of each method (Immobilon-P and Immobilon-CD, 0.5 pmol; and in-gel, 125 fmol), and searches of Swiss-Prot or a non-redundant database (> 193000 entries) successfully identified all of the proteins, except beta-casein. Fragment-ion spectra using a curved-field reflector MALDI-MS were obtained from more than one peptide per protein at loads down to 250 fmol (except beta-casein). Using the uninterpreted data, a search of the nonredundant database and a six-way translation of GenBank dbEST (> 2,208,000 entries total) was able to identify myoglobin, carbonic anhydrase II, and phosphorylase b.

  8. Improving fragmentation of poorly fragmenting peptides and phosphopeptides during collision-induced dissociation by malondialdehyde modification of arginine residues.

    PubMed

    Leitner, Alexander; Foettinger, Alexandra; Lindner, Wolfgang

    2007-07-01

    Despite significant technological and methodological advancements in peptide sequencing by mass spectrometry, analyzing peptides that exhibit only poor fragmentation upon collision-induced dissociation (CID) remains a challenge. A major cause for unfavorable fragmentation is insufficient proton 'mobility' due to charge localization at strongly basic sites, in particular, the guanidine group of arginine. We have recently demonstrated that the conversion of the guanidine group of the arginine side chain by malondialdehyde (MDA) is a convenient tool to reduce the basicity of arginine residues and can have beneficial effects for peptide fragmentation. In the present work, we have focused on peptides that typically yield incomplete sequence information in CID-MS/MS experiments. Energy-resolved tandem MS experiments were carried out on angiotensins and arginine-containing phosphopeptides to study in detail the influence of the modification step on the fragmentation process. MDA modification dramatically improved the fragmentation behavior of peptides that exhibited only one or two dominant cleavages in their unmodified form. Neutral loss of phosphoric acid from phosphopeptides carrying phosphoserine and threonine residues was significantly reduced in favor of a higher abundance of fragment ions. Complementary experiments were carried out on three different instrumental platforms (triple-quadrupole, 3D ion trap, quadrupole-linear ion trap hybrid) to ascertain that the observation is a general effect.

  9. 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

    2014-12-02

    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.

  10. 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…

  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.

  12. Characterization of the herb-derived components in rats following oral administration of Carthamus tinctorius extract by extracting diagnostic fragment ions (DFIs) in the MS(n) chromatograms.

    PubMed

    Chen, Jin-Feng; Song, Yue-Lin; Guo, Xiao-Yu; Tu, Peng-Fei; Jiang, Yong

    2014-12-21

    In this study, a new strategy named extracting diagnostic fragment ions (DFIs) in the MS(n) chromatograms [E(DFI)MS(n)Cs] was proposed to rapidly detect and identify the in vivo components derived from the extract of Carthamus tinctorius (ECT), using high performance liquid chromatography coupled with hybrid ion trap-time of flight mass spectrometry. In order to comprehensively summarize the DFIs for the global identification of in vivo constituents of ECT, chemical profiling was carried out, and then the typical metabolic pathways of the primary components were proposed according to their chemical categories, by orally administering representative reference compounds. Based on the proposed metabolic pathways and the fragmentation rules, a list of DFIs was constructed and adopted to differentiate and identify the metabolites from the endogenous substances in the MS(n) chromatograms of ECT-treated biological samples, in combination with the neutral loss scan mode as a supplement. As a result, a total of 156 compounds were tentatively assigned in vivo, including 63, 73, 50, and 17 components from rat plasma, urine, bile, and feces, respectively, following oral administration of ECT. Deglycosylation, oxidation, methylation, sulfonation, and glucuronidation were observed as the major metabolic pathways for the chemical constituents of ECT, and dehydroxylation was detected at the A-ring of flavones for the first time. The findings suggested that the E(DFI)MS(n)Cs-based strategy which integrated ideas from single compounds to herbal extracts and from extract chemical profiling to in vivo metabolite profiling, could be used as a reliable tool for rapidly discovering and identifying herb-related constituents in vivo.

  13. Ultra-high performance liquid chromatography with linear ion trap-Orbitrap hybrid mass spectrometry combined with a systematic strategy based on fragment ions for the rapid separation and characterization of components in Stellera chamaejasme extracts.

    PubMed

    Wang, Zhixin; Qu, Yang; Wang, Li; Zhang, Xiaozhe; Xiao, Hongbin

    2016-04-01

    Stellera chamaejasme, a famous toxic herb, has been used in traditional Chinese medicine to treat various diseases. For decades, increasing attention in modern pharmacological studies has been drawn to S. chamaejasme because of its potential anti-tumor, anti-virus, and anti-fungus activities. However, due to the intrinsic complexity of chemical constitutes, hardly any investigations formed an overall recognition for the chemical profiles of this herb. In this study, a rapid and sensitive ultra-high performance liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry method was developed to characterize the chemical components of S. chamaejasme extracts. Based on optimized ultra-high performance liquid chromatography and mass spectrometry conditions and systematic fragment ions-based strategy, a total of 47 components including flavones, diterpenes, coumarins, and lignans were simultaneously detected and identified or tentatively identified for the first time. The MS(n) fragmentation patterns of all the characterized compounds in positive or negative electrospray ionization modes were also explored and summarized. These results provided essential data for further pharmacological research on S. chamaejasme. Moreover, the method was demonstrated to be an efficient tool for rapid qualitative analysis of secondary metabolites from natural resources.

  14. 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)

  15. 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

  16. Effects of ion/ion proton transfer reactions on conformation of gas-phase cytochrome c ions.

    PubMed

    Zhao, Qin; Schieffer, Gregg M; Soyk, Matthew W; Anderson, Timothy J; Houk, R S; Badman, Ethan R

    2010-07-01

    Positive ions from cytochrome c are studied in a 3-D ion trap/ion mobility (IM)/quadrupole-time-of-flight (TOF) instrument with three independent ion sources. The IM separation allows measurement of the cross section of the ions. Ion/ion reactions in the 3-D ion trap that remove protons cause the cytochrome c ions to refold gently without other degradation of protein structure, i.e., fragmentation or loss of heme group or metal ion. The conformation(s) of the product ions generated by ion/ion reactions in a given charge state are similar regardless of whether the cytochrome c ions are originally in +8 or +9 charge states. In the lower charge states (+1 to +5) cytochrome c ions made by the ion/ion reaction yield a single IM peak with cross section of approximately 1110 to 1180 A(2), even if the original +8 ion started with multiple conformations. The conformation expands slightly when the charge state is reduced from +5 to +1. For product ions in the +6 to +8 charge states, ions created from higher charge states (+9 to +16) by ion/ion reaction produce more compact conformation(s) in somewhat higher abundances compared with those produced directly by the electrospray ionization (ESI) source. For ions in intermediate charge states that have a variety of resolvable conformers, the voltage used to inject the ions into the drift tube, and the voltage and duration of the pulse that extracts ions from the ion trap, can affect the observed abundances of various conformers.

  17. 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.

  18. 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.

  19. Chemometric exploration of the abundance of trace metals and ions in desalinated and bottled drinking water in Kuwait.

    PubMed

    Al-Mudhaf, Humood F; Astel, Aleksander M; Al-Hayan, Mohammad N; Abu-Shady, Abdel-Sattar I

    2014-01-01

    Chemometric exploration of desalinated and bottled water in Kuwait was employed to interpret the spatial variation in the physicochemical parameters. The data set consisted of the concentrations of principal macronutrient elements, ions, trace elements, temperature, pH, electrolytic conductivity, and total dissolved solids measured in indoor, outdoor, and bottled water samples. Quantitative assessment of the Cd, Hg, and Sb contents revealed rare cases of elevated concentrations; however, these concentrations were always below international health agency standards. Two general clusters of similar parameters were discovered in the variables mode and were associated with "natural" water characteristics or "conditions" of the pipeline system. We found that an increase in temperature facilitates the leaching of metals from the metallic equipment in the system. Spatial variation in the water quality was discovered, which indicates that residential areas fed from the Az-Zoor plant are supplied with water that contains lower concentrations of Ca, Cr, Mg, Mo, Ni, Na, TDS, and SO4 (2-) than the desalinated water produced and fed from the Doha plant. However, on the basis of the aluminum concentration in the water, cement mortar lining is assumed to be prevalent in the pipeline systems of the Mubarak Al-Kabeer, Ahmadi, Umm Al-Haiman, and Sorra areas.

  20. Determination of the abundance of delta15N in nitrate ion in contaminated groundwater samples using an elemental analyzer coupled to a mass spectrometer.

    PubMed

    Ogawa, Y; Nishikawa, M; Nakasugi, O; Ii, H; Hirata, T

    2001-07-01

    A rapid method for measuring the delta15N of nitrate ion in water samples using an isotope ratio mass spectrometer coupled to an elemental analyzer system (EA-MS) was investigated. The water should be removed from the analytical sample before measurement with this system. We investigated the application of a super-absorbent polymer resin powder to various water samples. Each 1 mg of polymer resin powder can absorb about 50-100 mg of solution depending on the concentrations of major ions. Only samples which contain more than 100 mg l(-1) of nitrate-nitrogen are suitable to be absorbed by the polymer resin for the determination of delta15N of nitrate. Preconcentration by rotary evaporation was necessary for dilute samples but the temperature should be kept below 60 degrees C. The polymer resin (about 8 mg) containing the nitrate was directly analyzed using an EA-MS after being oven-dried at 80 degrees C. Good accuracy (precision +/- 0.3%) for delta15N measurements of nitrate-nitrogen in a sample without any isotope fractionation effects during pre-treatment was observed. Results for delta15N of nitrate in contaminated groundwater samples collected in the spring at a tea plantation area in Shizuoka, Japan, were from 9.8 to 10.6%, which were close to the delta15N abundance in organic fertilizers.

  1. 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.

  2. Collision-induced dissociation products of the protonated dipeptide carnosine: structural elucidation, fragmentation pathways and potential energy surface analysis.

    PubMed

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

    2015-05-21

    Collision-induced dissociation (CID) experiments on protonated carnosine, [carnosine + H](+), with several collision energies were shown to yield eleven different fragment ions with the generation of product ions [carnosine-H2O + H](+) and [carnosine-NH3 + H](+) being the lowest energy processes. Energy-resolved CID showed that at slightly higher collision energies the ions [histidine + H](+) and [histidine-H2O-CO + H](+) are formed. At even higher energies four other product ions were observed, however, attained relatively lower abundances. Quantum chemistry calculations, carried out at different levels of theory, were employed to probe fragmentation mechanisms that account for all the experimental data. All the adopted computational protocols give similar energetic trends, and the range of the calculated free energy barrier values for the generation of all the observed product ions is in agreement with the fragmentation mechanisms offered here.

  3. Low-energy SiC2H6+ and SiC3H9+ ion beam productions by the mass-selection of fragments produced from hexamethyldisilane for SiC film formations

    NASA Astrophysics Data System (ADS)

    Yoshimura, Satoru; Sugimoto, Satoshi; Murai, Kensuke; Kiuchi, Masato

    2016-12-01

    We have been attempting to produce low-energy ion beams from fragments produced through the decomposition of hexamethyldisilane (HMD) for silicon carbide (SiC) film formations. We mass-selected SiC2H6+ and SiC3H9+ ions from fragments produced from HMD, and finally produced low-energy SiC2H6+ and SiC3H9+ ion beams. The ion energy was approximately 100 eV. Then, the ion beams were irradiated to Si(100) substrates. The temperature of the Si substrate was 800°C during the ion irradiation. The X-ray diffraction and Raman spectroscopy of the substrates obtained following SiC2H6+ ion irradiation demonstrated the occurrence of 3C-SiC deposition. On the other hand, the film deposited by the irradiation of SiC3H9+ ions included diamond-like carbon in addition to 3C-SiC.

  4. Receptor-mediated toxicity of human amylin fragment aggregated by short- and long-term incubations with copper ions.

    PubMed

    Caruso, Giuseppe; Distefano, Donatella A; Parlascino, Paolo; Fresta, Claudia G; Lazzarino, Giuseppe; Lunte, Susan M; Nicoletti, Vincenzo G

    2017-01-01

    Human amylin (hA1-37) is a polypeptide hormone secreted in conjunction with insulin from the pancreatic β-cells involved in the pathogenesis of type 2 diabetes mellitus (T2DM). The shorter fragment hA17-29 than full-length peptide is capable to form amyloids "in vitro". Here, we monitored the time course of hA17-29 β-amyloid fibril and oligomer formation [without and with copper(II)], cellular toxicity of different amyloid aggregates, and involvement of specific receptors (receptor for advanced glycation end-products, RAGE; low-affinity nerve growth factor receptor, p75-NGFR) in aggregate toxicity. Fibril and oligomer formation of hA17-29 incubated at 37 °C for 0, 48, and 120 h, without or with copper(II), were measured by the thioflavin T fluorescence assay and ELISA, respectively. Toxicity of hA17-29 aggregates and effects of anti-RAGE and anti-p75-NGFR antibodies were evaluated on neuroblastoma SH-SY5Y viability. Fluorescence assay of hA17-29 indicates an initial slow rate of soluble fibril formation (48 h), followed by a slower rate of insoluble aggregate formation (120 h). The highest quantity of oligomers was recorded when hA17-29 was pre-aggregated for 48 h in the presence of copper(II) showing also the maximal cell toxicity (-44% of cell viability, p < 0.01 compared to controls). Anti-RAGE or anti-p75-NGFR antibodies almost abolished cell toxicity of hA17-29 aggregates. These results indicate that copper(II) influences the aggregation process and hA17-29 toxicities are especially attributable to oligomeric aggregates. hA17-29 aggregate toxicity seems to be mediated by RAGE and p75-NGFR receptors which might be potential targets for new drugs in T2DM treatment.

  5. Characteristic fragmentation of thromboxane B2 in thermospray high-performance liquid chromatography-mass spectrometry.

    PubMed

    Abián, J; Gelpí, E

    1991-01-02

    Cyclo- and lipo-oxygenase metabolites of arachidonic acid have been reported to have very simple thermospray mass spectra. However, thromboxane B2 (TXB) in ammonium acetate-methanol and at interface temperatures below the point of total vaporization shows a mass spectral pattern characterized by abundant ions at low masses. The more abundant TXB fragment ions have been characterized as adducts from four principal fragments with molecular masses of 156, 170, 196 and 326. Positive- and negative-ion mass spectra, and mass spectra obtained with an alternative thermospray buffer (butylammonium acetate) support the molecular masses of these fragments. A tentative assignment of the fragments can be made by comparison of the thermospray mass spectra of TXB, 2,3-dinor-TXB and some of their methyl ester and methyl oxime derivatives. Interface temperature and solvent composition effects on the fragmentation, as well as in the electron-capture processes observed when working in the filament-on mode, are discussed. Fragmentation mechanisms can be related to those observed for monosaccharides, and imply retro-Diels-Alder as well as retroaldolic condensation-type rearrangements.

  6. Potential curves and nonadiabatic matrix elements for collisions involving fragments of the HeN + molecular ion

    NASA Astrophysics Data System (ADS)

    Gu, Jian-ping; Buenker, Robert J.; Hirsch, Gerhard; Kimura, Mineo

    1995-05-01

    Ab initio multireference CI calculations have been carried out for the HeN+ molecular ion in order to describe collision processes between its constituent neutral and ionized atoms. The accuracy of these calculations is evaluated by means of a comparison of results obtained at large internuclear separations with the corresponding asymptotic energies deduced from atomic spectral data. Energy values are computed for the eleven lowest He++N and He+N+ atomic limits and average discrepancies relative to the experimental excitation energies up to 110 000 cm-1 are found to lie in the 1000-3000 cm-1 range, of which only 200 cm-1 appears to be the fault of the configuration interaction (CI) technique itself, with the main portion of the error stemming from the choice of atomic orbital (AO) basis instead. The HeN+ X 3Σ- ground state is calculated to have a De value of only 1414 cm-1, but the excited 2 3Π state has a much larger value of 22 133 cm-1 by virtue of an avoided crossing with the lower state of this symmetry. The corresponding radial nonadiabatic coupling is responsible for a large cross section for an excitation process between the N+(3Pg)+He and N+(3Du)+He channels which indirectly provides an efficient electron-capture mechanism leading to the N(4Su)+He+ exit channel. Additional nonadiabatic matrix elements for rotational and spin-orbit coupling have also been obtained and analyzed, as well as transition moments between the various HeN+ molecular states calculated.

  7. 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.

  8. 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.

  9. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap.

    PubMed

    Lin, Shanhua; Shaler, Thomas A; Becker, Christopher H

    2006-08-15

    A method is presented to quantify intermediate-abundance proteins in human serum using a single-quadrupole linear ion trap mass spectrometer-in contrast, for example, to a triple-quadrupole mass spectrometer. Stable-isotope-labeled (tryptic) peptides are spiked into digested protein samples as internal standards, aligned with the traditional isotope dilution approach. As a proof-of-concept experiment, four proteins of intermediate abundance were selected, coagulation factor V, adiponectin, C-reactive protein (CRP), and thyroxine binding globulin. Stable-isotope-labeled peptides were synthesized with one tryptic sequence from each of these proteins. The normal human serum concentration ranges of these proteins are from 1 to 30 microg/mL (or 20 to 650 pmol/mL). These labeled peptides and their endogenous counterparts were analyzed by LC-MS/MS using multiple reaction monitoring, a multiplexed form of the selected reaction monitoring technique. For these experiments, only one chromatographic dimension (on-line reversed-phase capillary column) was used. Improved limits of detection will result with multidimensional chromatographic methods utilizing more material per sample. Standard curves of the spiked calibrants were generated with concentrations ranging from 3 to 700 pmol/mL using both neat solutions and peptides spiked into the complex matrix of digested serum protein solution where ion suppression effects and interferences are common. Endogenous protein concentrations were determined by comparing MS/MS peak areas of the endogenous peptides to the isotopically labeled internal calibrants. The derived concentrations from a normal human serum pool (neglecting loss of material during sample processing) were 9.2, 110, 120, and 246 pmol/mL for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively. These concentrations generally agree with the reported normal ranges for these proteins. As a measure of analytical reproducibility of this

  10. Coordination of copper(II) ions by the fragments of neuropeptide gamma containing D1, H9, H12 residues and products of copper-catalyzed oxidation.

    PubMed

    Jankowska, Elżbieta; Pietruszka, Marta; Kowalik-Jankowska, Teresa

    2012-02-14

    conditions the (1-2,7-21)NPG and Ac-(1-2,7-21)NPG undergo fragmentations by cleavage of the S(8)-H(9), H(9)-K(10), R(11)-H(12) and H(12)-K(13) peptide bonds supporting the participation of the H(9) and H(12) residues in the coordination of copper(II) ions. For the (1-2,7-21)NPG peptide chain the involvement of the D(1) residue in the coordination of metal ions is supported by the alkoxyl radical modification of this amino acid residue.

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

    PubMed

    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 N2). Singly as well as multiply charged clusters were formed in both positive and negative ion modes with the general formulae, (HCOOLi)nLi(+), (HCOOLi)nLim (m+), (HCOOLi)nHCOO(-), and (HCOOLi)n(HCOO)m (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)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.

  12. 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.

  13. 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. 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.

  14. 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.

  15. Peptide Fragmentation Induced by Radicals at Atmospheric Pressure

    PubMed Central

    Vilkov, Andrey N.; Laiko, Victor V.; Doroshenko, Vladimir M.

    2009-01-01

    A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essentially atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to ECD/ETD, along with the y-/b- fragments that are specific to CAD. In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source. PMID:19034885

  16. Chameleon fragmentation

    SciTech Connect

    Brax, Philippe

    2014-02-01

    A scalar field dark energy candidate could couple to ordinary matter and photons, enabling its detection in laboratory experiments. Here we study the quantum properties of the chameleon field, one such dark energy candidate, in an ''afterglow'' experiment designed to produce, trap, and detect chameleon particles. In particular, we investigate the possible fragmentation of a beam of chameleon particles into multiple particle states due to the highly non-linear interaction terms in the chameleon Lagrangian. Fragmentation could weaken the constraints of an afterglow experiment by reducing the energy of the regenerated photons, but this energy reduction also provides a unique signature which could be detected by a properly-designed experiment. We show that constraints from the CHASE experiment are essentially unaffected by fragmentation for φ{sup 4} and 1/φ potentials, but are weakened for steeper potentials, and we discuss possible future afterglow experiments.

  17. 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.

  18. 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.

  19. Versatile lipid profiling by liquid chromatography-high resolution mass spectrometry using all ion fragmentation and polarity switching. Preliminary application for serum samples phenotyping related to canine mammary cancer.

    PubMed

    Gallart-Ayala, H; Courant, F; Severe, S; Antignac, J-P; Morio, F; Abadie, J; Le Bizec, B

    2013-09-24

    Lipids represent an extended class of substances characterized by such high variety and complexity that makes their unified analyses by liquid chromatography coupled to either high resolution or tandem mass spectrometry (LC-HRMS or LC-MS/MS) a real challenge. In the present study, a new versatile methodology associating ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-HRMS/MS) have been developed for a comprehensive analysis of lipids. The use of polarity switching and "all ion fragmentation" (AIF) have been two action levels particularly exploited to finally permit the detection and identification of a multi-class and multi-analyte extended range of lipids in a single run. For identification purposes, both higher energy collision dissociation (HCD) and in-source CID (collision induced dissociation) fragmentation were evaluated in order to obtain information about the precursor and product ions in the same spectra. This approach provides both class-specific and lipid-specific fragments, enhancing lipid identification. Finally, the developed method was applied for differential phenotyping of serum samples collected from pet dogs developing spontaneous malignant mammary tumors and health controls. A biological signature associated with the presence of cancer was then successfully revealed from this lipidome analysis, which required to be further investigated and confirmed at larger scale.

  20. A semiempirical nuclear fragmentation model

    NASA Technical Reports Server (NTRS)

    Wilson, John W.; Townsend, Lawrence W.; Badavi, F. F.

    1987-01-01

    An abrasion/ablation model of heavy ion fragmentation is derived which includes a second order correction for the surface energy term and provides a reasonable representation of the present elemental fragmentation cross sections. The full development of the model must await the resolution of disagreement among different experiments and an expansion of the experimental data base to a broader set of projectile-target combinations.

  1. QGP and Modified Jet Fragmentation

    SciTech Connect

    Wang, Xin-Nian

    2005-04-18

    Recent progresses in the study of jet modification in hotmedium and their consequences in high-energy heavy-ion collisions are reviewed. In particular, I will discuss energy loss for propagating heavy quarks and the resulting modified fragmentation function. Medium modification of the parton fragmentation function due to quark recombination are formulated within finite temperature field theory and their implication on the search for deconfined quark-gluon plasma is also discussed.

  2. Influence of the density of states on the odd-even staggering in the charge distribution of the emitted fragments in nuclear heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Calleya, N. L.; Souza, S. R.; Carlson, B. V.; Donangelo, R.; Lynch, W. G.; Tsang, M. B.; Winkelbauer, J. R.

    2014-11-01

    The fragmentation of thermalized sources is studied using a version of the Statistical Multifragmentation Model which employs state densities that take the pairing gap in the nuclear levels into account. Attention is focused on the properties of the charge distributions observed in the breakup of the source. Since the microcanonical version of the model used in this study provides the primary fragment excitation energy distribution, one may correlate the reduction of the odd-even staggering in the charge distribution with the increasing occupation of high-energy states. Thus, in the framework of this model, such staggering tends to disappear as a function of the total excitation energy of the source, although the energy per particle may be small for large systems. We also find that, although the deexcitation of the primary fragments should, in principle, blur these odd-even effects as the fragments follow their decay chains, the consistent treatment of pairing may significantly enhance these staggering effects on the final yields. In the framework of this model, we find that odd-even effects in the charge distributions should be observed in the fragmentation of relatively light systems at very low excitation energies. Our results also suggest that the odd-even staggering may provide useful information on the nuclear state density.

  3. 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

  4. 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.

  5. New example of proline-induced fragmentation in electrospray ionization mass spectrometry of peptides.

    PubMed

    Maux, Delphine; Enjalbal, Christine; Martinez, Jean; Aubagnac, Jean-Louis

    2002-01-01

    The positive ion electrospray ionization (ESI+) mass spectra of peptides usually display only protonated molecules provided that soft ionization conditions are applied (low cone voltage to prevent in-source dissociations). Such ions can be multiply charged depending on the molecular weight of the studied compounds. We have experienced an unexpected behavior during the ESI analysis of a modified peptide of relatively high mass (3079 Da). A specific fragmentation occurred even under soft energetic conditions, leading to a mass spectrum containing multiply charged molecular and fragment ions. The selective rupture involved the amide bond between the glutamic acid and proline residues (E-P sequence). The successive replacement of each amino acid by an alanine residue (positional scanning study) was undertaken to assess which part of the sequence induced such selective and abundant fragmentation on multiply charged species. The succession P-P was evidenced as the minimum unit giving rise to the first peptide bond rupture in the sequence X-P-P. Any acidic amino acid at the X position (X = D, E) favored the fragmentation by an intramolecular interaction. Such proline-induced fragmentation occurring readily in the source differed from the literature data on the specific behavior of proline-containing peptides where bond ruptures occur solely in dissociation conditions.

  6. Comparing Fragmentation Functions in Pb-Pb Collisions using JEWEL

    NASA Astrophysics Data System (ADS)

    Davis, Harrison

    2016-09-01

    Collisions between lead nuclei at relativistic speeds create a hot, dense state of deconfined quark matter called the quark gluon plasma (QGP). Due to its extreme density, temperature, and abundance of color charge, the QGP gives us a unique opportunity to study strong interactions and test the limits of QCD. Collisions between nuclei produce jets, clusters of particles hadronized from an energetic parton. Jets produced in heavy ion collisions must travel through the energetic and dense QGP, which changes the structure and momenta of the jets, a phenomenon known as jet quenching. By analyzing the changes in hadron fragmentation and momenta, we probe the properties and structure of the QGP. To analyze the jet fragmentation, we simulated lead-lead collisions with JEWEL, a modification to the Monte-Carlo (MC) generator PYTHIA6, and compared the results with ATLAS data at 2.76 TeV and 5 TeV. These comparisons between the ATLAS data and the MC simulation are important for understanding jet quenching in heavy ion collisions. This poster gives an overview of the results of the simulation and how they compare with ATLAS data on fragmentation.

  7. 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

  8. 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.

  9. 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.

  10. Unusual fragmentation pathways in collagen glycopeptides

    PubMed Central

    Perdivara, Irina; Perera, Lalith; Sricholpech, Marnisa; Terajima, Masahiko; Pleshko, Nancy; Yamauchi, Mitsuo; Tomer, Kenneth B.

    2013-01-01

    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. PMID:23633013

  11. 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

  12. 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.

  13. 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

  14. IN SITU PLASMA MEASUREMENTS OF FRAGMENTED COMET 73P SCHWASSMANN–WACHMANN 3

    SciTech Connect

    Gilbert, J. A.; Lepri, S. T.; Combi, M.; Zurbuchen, T. H.; Rubin, M.

    2015-12-10

    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{sup −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{sup +}/O{sup +}, and water-group ions.

  15. Angular and energy distributions of fragment ions in dissociative double photoionization of acetylene molecules in the 31.9-50.0 eV photon energy range

    NASA Astrophysics Data System (ADS)

    Falcinelli, Stefano; Alagia, Michele; Farrar, James M.; Kalogerakis, Konstantinos S.; Pirani, Fernando; Richter, Robert; Schio, Luca; Stranges, Stefano; Rosi, Marzio; Vecchiocattivi, Franco

    2016-09-01

    The two-body dissociation reactions of the dication C2H2+2, initiated via double ionization of acetylene molecules by photons in the energy range 31.9-50.0 eV, have been studied by coupling photoelectron-photoion-photoion coincidence and ion imaging techniques. The angular distributions and kinetic energy of product ions, measured in the 31.9-50.0 eV energy range, exhibit significant differences for the three leading dissociation reactions with respect to a previous investigation carried out at a fixed energy of 39.0 eV, providing thus new information on the dynamical evolution of the system. The analysis of the results indicates that such dissociation reactions occur with a different mechanism. In particular, the symmetric dissociation in two CH+ ions is characterized by different dynamics, and the anisotropy of the angular distribution of ionic products increases with photon energy in a more pronounced way than the other two reactions. Moreover, the kinetic energy distribution of the symmetric dissociation reaction exhibits several components that change with photon energy. The new experimental findings cast light on the microscopic evolution of the system and can provide a laboratory reference for new theoretical calculations on specific features of the multidimensional potential energy surface, namely, the structure, energy and symmetry of dication states, the electronic state of dissociation products, energy barriers and their dependence on the geometry of the intermediate state.

  16. Implications of Saito's coronal density model on the polar solar wind flow and heavy ion abundances. [mathematical models of proton flux density and solar activity

    NASA Technical Reports Server (NTRS)

    Feldman, W. C.

    1976-01-01

    A comparison of polar solar wind proton flux upper limits derived using a coronal density model, with Lyman alpha measurements of the length of the neutral H tail of comet Bennet at high latitudes, shows that either extended heating beyond 2 solar radii is necessary some of the time or that the model's polar densities are too low. Whichever possibility is the case, the fact that the solar wind particle flux does not appear to decrease with increasing latitude indicates that the heavy element content of the high latitude wind may be similar to that observed in the ecliptic. It was then shown that solar wind heavy ion observations at high latitudes allow a determination of the electron temperature at heights which bracket the nominal location of the coronal temperature maximum thus providing information concerning the magnitude and extent of mechanical dissipation in the intermediate corona.

  17. 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.

  18. Fragmentation of intra-peptide and inter-peptide disulfide bonds of proteolytic peptides by nanoESI collision-induced dissociation.

    PubMed

    Mormann, Michael; Eble, Johannes; Schwöppe, Christian; Mesters, Rolf M; Berdel, Wolfgang E; Peter-Katalinić, Jasna; Pohlentz, Gottfried

    2008-11-01

    Characterisation and identification of disulfide bridges is an important aspect of structural elucidation of proteins. Covalent cysteine-cysteine contacts within the protein give rise to stabilisation of the native tertiary structure of the molecules. Bottom-up identification and sequencing of proteins by mass spectrometry most frequently involves reductive cleavage and alkylation of disulfide links followed by enzymatic digestion. However, when using this approach, information on cysteine-cysteine contacts within the protein is lost. Mass spectrometric characterisation of peptides containing intra-chain disulfides is a challenging analytical task, because peptide bonds within the disulfide loop are believed to be resistant to fragmentation. In this contribution we show recent results on the fragmentation of intra and inter-peptide disulfide bonds of proteolytic peptides by nano electrospray ionisation collision-induced dissociation (nanoESI CID). Disulfide bridge-containing peptides obtained from proteolytic digests were submitted to low-energy nanoESI CID using a quadrupole time-of-flight (Q-TOF) instrument as a mass analyser. Fragmentation of the gaseous peptide ions gave rise to a set of b and y-type fragment ions which enabled derivation of the sequence of the amino acids located outside the disulfide loop. Surprisingly, careful examination of the fragment-ion spectra of peptide ions comprising an intramolecular disulfide bridge revealed the presence of low-abundance fragment ions formed by the cleavage of peptide bonds within the disulfide loop. These fragmentations are preceded by proton-induced asymmetric cleavage of the disulfide bridge giving rise to a modified cysteine containing a disulfohydryl substituent and a dehydroalanine residue on the C-S cleavage site.

  19. Performance Evaluation of a Dual Linear Ion Trap-Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Proteomics Research

    PubMed Central

    Weisbrod, Chad R.; Hoopmann, Michael R.; Senko, Michael W.; Bruce, James E.

    2014-01-01

    A novel dual cell linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) and its performance characteristics are reported. A linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer has been modified to incorporate a LTQ-Velos mass spectrometer. This modified instrument features efficient ion accumulation and fast MS/MS acquisition capabilities of dual cell linear RF ion trap instruments coupled to the high mass accuracy, resolution, and dynamic range of a FT-ICR for improved proteomic coverage. The ion accumulation efficiency is demonstrated to be an order of magnitude greater than that observed with LTQ-FT Ultra instrumentation. The proteome coverage with yeast was shown to increase over the previous instrument generation by 50% (100% increase on the peptide level). In addition, many lower abundance level yeast proteins were only detected with this modified instrument. This novel configuration also enables beam type CID fragmentation using a dual cell RF ion trap mass spectrometer. This technique involves accelerating ions between traps while applying an elevated DC offset to one of the traps to accelerate ions and induce fragmentation. This instrument design may serve as a useful option for labs currently considering purchasing new instrumentation or upgrading existing instruments. PMID:23590889

  20. 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.

  1. 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

    2016-08-02

    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.

  2. 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

  3. New features of site-specific horseradish peroxidase (HRP) glycosylation uncovered by nano-LC-MS with repeated ion-isolation/fragmentation cycles.

    PubMed

    Wuhrer, Manfred; Balog, Crina I A; Koeleman, Carolien A M; Deelder, André M; Hokke, Cornelis H

    2005-05-25

    Horseradish peroxidase (HRP) is widely used in biomedical research as a reporter enzyme in diagnostic assays. In addition, it is of considerable interest as a model glycoprotein with core-xylosylated and -(alpha1-3)-fucosylated N-glycans that form antigenic elements of plant allergens and parasitic helminths. Using a combination of techniques comprising (1) nano-liquid chromatography (LC)-mass spectrometry (MS)/MS with multiple selection/fragmentation cycles of HRP tryptic (glyco-)peptides, (2) nano-electrospray MS of intact HRP, and (3) carbohydrate linkage analysis, it was revealed that most of the HRP N-glycosylation sites can be occupied with an alternative Fuc(1-3)GlcNAc-disaccharide. Two main variants of HRP occur: The major population (approximately 60%) has eight glycosylation sites carrying core(1-3)fucosylated, xylosylated, trimannosyl N-glycans, with the ninth potential N-glycosylation site Asn316 not occupied. Another group of HRP carries seven of the above-mentioned N-glycans, with an eighth N-glycosylation site carrying the alternative Fuc(1-3)GlcNAc-unit (approximately 35%). In addition, minor subsets of HRP were found to contain a xylosylated, trimannosyl N-glycan lacking core-fucosylation as a ninth N-glycan attached to Asn316, which has hitherto been assumed to be unoccupied. The finding of these new features of glycosylation of an already exceptionally well-studied glycoprotein underscores the potential of the nano-LC-MS(n) based analytical approach followed.

  4. Imidazole and imidazolium porphyrins: gas-phase chemistry of multicharged ions.

    PubMed

    Ramos, Catarina I V; Pereira, Patrícia M R; Santana-Marques, M Graça; De Paula, Rodrigo; Simões, Mário M Q; Neves, M Graça P M S; Cavaleiro, José A S

    2014-05-01

    Electrospray ionization mass spectrometry/mass spectrometry in the positive ion mode was used to investigate the gas-phase chemistry of multicharged ions from solutions of porphyrins with 1,3-dimethylimidazolium-2-yl (DMIM) and 1-methylimidazol-2-yl (MIm) meso-substituents. The studied compounds include two free bases and 12 complexes with transition metals (Cu(II), Zn(II), Mn(III), and Fe(III)). The observed multicharged ions are either preformed or formed during the electrospraying process by reduction or protonation and comprise closed-shell and hypervalent mono-radical and bi-radical ions. The observed extensive and abundant fragmentation of the DMIM and MIm meso-substituents is a characteristic feature of these porphyrins. Fragments with the same mass values can be lost from the meso-substituents either as charged or neutral species and from closed-shell and hypervalent radical ions. Reduction processes are observed for both the free bases and the metallated DMIM porphyrins and occur predominantly by formation of hypervalent radicals that fragment, at low energy collisions, by loss of methyl radicals with formation of the corresponding MIm functionalities. These findings confirm that, when using electrospray ionization, reduction is an important characteristic of cationic meso-substituted tetrapyrrolic macrocycles, always occurring when delocalization of the formed hypervalent radicals is possible. For the Fe(III) and Mn(III) complexes, reduction of the metal centers is also observed as the predominant fragmentation of the corresponding reduced ions through losses of charged fragments testifies. The fragmentation of the closed-shell ions formed by protonation of the MIm porphyrins mirrors the fragmentation of the closed-shell ions of their DMIM counterparts.

  5. Comparison of abundances, compositions and sources of elements, inorganic ions and organic compounds in atmospheric aerosols from Xi'an and New Delhi, two megacities in China and India.

    PubMed

    Li, Jianjun; Wang, Gehui; Aggarwal, Shankar G; Huang, Yao; Ren, Yanqin; Zhou, Bianhong; Singh, Khem; Gupta, Prabhat K; Cao, Junji; Zhang, Rong

    2014-04-01

    Wintertime TSP samples collected in the two megacities of Xi'an, China and New Delhi, India were analyzed for elements, inorganic ions, carbonaceous species and organic compounds to investigate the differences in chemical compositions and sources of organic aerosols. The current work is the first time comparing the composition of urban organic aerosols from China and India and discussing their sources in a single study. Our results showed that the concentrations of Ca, Fe, Ti, inorganic ions, EC, PAHs and hopanes in Xi'an are 1.3-2.9 times of those in New Delhi, which is ascribed to the higher emissions of dust and coal burning in Xi'an. In contrast, Cl(-), levoglucosan, n-alkanes, fatty alcohols, fatty acids, phthalates and bisphenol A are 0.4-3.0 times higher in New Delhi than in Xi'an, which is attributed to strong emissions from biomass burning and solid waste incineration. PAHs are carcinogenic while phthalates and bisphenol A are endocrine disrupting. Thus, the significant difference in chemical compositions of the above TSP samples may suggest that residents in Xi'an and New Delhi are exposed to environmental hazards that pose different health risks. Lower mass ratios of octadecenoic acid/octadecanoic acid (C18:1/C18:0) and benzo(a)pyrene/benzo(e)pyrene (BaP/BeP) demonstrate that aerosol particles in New Delhi are photochemically more aged. Mass closure reconstructions of the wintertime TSP indicate that crustal material is the most abundant component of ambient particles in Xi'an and New Delhi, accounting for 52% and 48% of the particle masses, respectively, followed by organic matter (24% and 23% in Xi'an and New Delhi, respectively) and secondary inorganic ions (sulfate, nitrate plus ammonium, 16% and 12% in Xi'an and New Delhi, respectively).

  6. Fragmentation dynamics of argon clusters (Arn, n =2 to 11) following electron-impact ionization: Modeling and comparison with experiment

    NASA Astrophysics Data System (ADS)

    Bonhommeau, David; Halberstadt, Nadine; Viel, Alexandra

    2006-05-01

    The fragmentation dynamics of argon clusters ionized by electron impact is investigated for initial cluster sizes up to n =11 atoms. The dynamics of the argon atoms is modeled using a mixed quantum-classical method in which the nuclei are treated classically and the transitions between electronic states quantum mechanically. The potential-energy surfaces are derived from a diatomics-in-molecules model with the addition of the induced dipole-induced dipole and spin-orbit interactions. The results show extensive and fast fragmentation. The dimer is the most abundant ionic fragment, with a proportion increasing from 66% for n =2 to a maximum of 95% for n =6 and then decreasing down to 67% for n =11. The next abundant fragment is the monomer for n <7 and the trimer otherwise. The parent ion dissociation lifetimes are all in the range of 1ps. Long-lived trajectories appear for initial cluster sizes of seven and higher, and favor the formation of the larger fragments (trimers and tetramers). Our results show quantitative agreement with available experimental results concerning the extensive character of the fragmentation: Ar+ and Ar2+ are the only ionic fragments for sizes up to five atoms; their overall proportion is in quantitative agreement for all the studied sizes; Ar2+ is the main fragment for all sizes; stable Ar3+ fragments only appear for n ⩾5, and their proportion increases smoothly with cluster size from there. However, the individual ionic monomer and dimer fragment proportions differ. The experimental ones exhibit oscillations with initial cluster size, with a slight tendency to decrease on average for the monomer. In contrast our results show a monotonic, systematic evolution, similar to what was found in our earlier studies on neon and krypton clusters. Several hypotheses are discussed in order to find the origin of this discrepancy. Finally, the metastable II(1/2)u and II(1/2)g states of Ar2+ are found to decay with a lifetime of 3.5 and 0.1ps

  7. Partial De Novo Sequencing and Unusual CID Fragmentation of a 7 kDa, Disulfide-Bridged Toxin

    NASA Astrophysics Data System (ADS)

    Medzihradszky, Katalin F.; Bohlen, Christopher J.

    2012-05-01

    A 7 kDa toxin isolated from the venom of the Texas coral snake ( Micrurus tener tener) was subjected to collision-induced dissociation (CID) and electron-transfer dissociation (ETD) analyses both before and after reduction at low pH. Manual and automated approaches to de novo sequencing are compared in detail. Manual de novo sequencing utilizing the combination of high accuracy CID and ETD data and an acid-related cleavage yielded the N-terminal half of the sequence from the reduced species. The intact polypeptide, containing 3 disulfide bridges produced a series of unusual fragments in ion trap CID experiments: abundant internal amino acid losses were detected, and also one of the disulfide-linkage positions could be determined from fragments formed by the cleavage of two bonds. In addition, internal and c-type fragments were also observed.

  8. 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.

  9. Chestnut-Like TiO2@α-Fe2O3 Core-Shell Nanostructures with Abundant Interfaces for Efficient and Ultralong Life Lithium-Ion Storage.

    PubMed

    Yang, Jingling; Wu, Qili; Yang, Xianfeng; He, Shiman; Khan, Javid; Meng, Yuying; Zhu, Xiuming; Tong, Shengfu; Wu, Mingmei

    2017-01-11

    Transition metal oxides caused much attention owing to the scientific interests and potential applications in energy storage systems. In this study, a free-standing three-dimensional (3D) chestnut-like TiO2@α-Fe2O3 core-shell nanostructure (TFN) is rationally synthesized and utilized as a carbon-free electrode for lithium-ion batteries (LIBs). Two new interfaces between anatase TiO2 and α-Fe2O3 are observed and supposed to provide synergistic effect. The TiO2 microsphere framework significantly improves the mechanical stability, while the α-Fe2O3 provides large capacity. The abundant boundary structures offer the possibility for interfacial lithium storage and electron transport. The as-prepared TFN delivers a high capacity of 820 mAh g(-1) even after 1000 continuous cycles with a Coulombic efficiency of ca. 99% at a current of 500 mA g(-1), which is better than the works reported previously. A thin gel-like SEI (solid electrolyte interphase) film and Fe(0) phase yielded during charge/discharge cycling have been confirmed which makes it possible to alleviate the volumetric change and enhance the electronic conductivity. This confirmation is helpful for understanding the mechanism of lithium-ion storage in α-Fe2O3-based materials. The as-prepared free-standing TFN with excellent stability and high capacity can be an appropriate candidate for carbon-free anode material in LIBs.

  10. ION COMPOSITION ELUCIDATION (ICE)

    EPA Science Inventory



    Ion Composition Elucidation (ICE) utilizes selected ion recording with a double focusing mass spectrometer to simultaneously determine exact masses and relative isotopic abundances from mass peak profiles. These can be determined more accurately and at higher sensitivity ...

  11. 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.

  12. Impact of energetic cosmic-ray ions on astrophysical ice grains

    NASA Astrophysics Data System (ADS)

    Mainitz, Martin; Anders, Christian; Urbassek, Herbert M.

    2017-02-01

    Using molecular-dynamics simulation with REAX potentials, we study the consequences of cosmic-ray ion impact on ice grains. The grains are composed of a mixture of H2O, CO2, NH3, and CH3OH molecules. Due to the high energy deposition of the cosmic-ray ion, 5 keV/nm, a strong pressure wave runs through the grain, while the interior of the ion track gasifies. Abundant molecular dissociations occur; reactions of the fragments form a variety of novel molecular product species.

  13. 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.

  14. Parton fragmentation functions

    NASA Astrophysics Data System (ADS)

    Metz, A.; Vossen, A.

    2016-11-01

    The field of fragmentation functions of light quarks and gluons is reviewed. In addition to integrated fragmentation functions, attention is paid to the dependence of fragmentation functions on transverse momenta and on polarization degrees of freedom. Higher-twist and di-hadron fragmentation functions are considered as well. Moreover, the review covers both theoretical and experimental developments in hadron production in electron-positron annihilation, deep-inelastic lepton-nucleon scattering, and proton-proton collisions.

  15. 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.

  16. Fragmentation Analysis - Fundamental Processes

    DTIC Science & Technology

    Wausau quartzite and anorthosite of 3.0 to 3.5 inch size were fragmented in this device. An analysis of the fragment distribution results of the drop...disc-shaped specimens of Wausau quartzite, anorthosite , and Felch marble were then fragmented with the impact pendulum device. Computer programs were

  17. Ultraviolet Photodissociation of Carboxylate-Derivatized Peptides in a Quadrupole Ion Trap

    NASA Astrophysics Data System (ADS)

    Ko, Byoung Joon; Brodbelt, Jennifer S.

    2011-01-01

    The fragmentation patterns obtained by ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) in a quadrupole ion trap mass spectrometer were compared for peptides modified at their C-termini and at acidic amino acids. Attachment of Alexa Fluor 350 or 7-amino-4-methyl-coumarin chromophores at the C-terminal and acidic residues enhances the UV absorptivity of the peptides and all fragment ions that retain the chromophore, such as the y ions that contain the chromophore-modified C-terminus. Whereas CID results in the formation of the typical array of mainly y-type and a/b-type fragment ions, UVPD produces predominantly a/b-type ions with greatly reduced abundances of y ions. Immonium ions, mostly ones from aromatic or basic amino acids, are also observed in the low m/ z range upon UVPD. UVPD of peptides containing two chromophore moieties (with one at the C-terminus and another at an acidic residue) results in even more efficient photodissociation at the expense of the annihilation of almost all diagnostic b and y ions containing the chromophore.

  18. Thermodynamical string fragmentation

    NASA Astrophysics Data System (ADS)

    Fischer, Nadine; Sjöstrand, Torbjörn

    2017-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  19. Fragmentation reactions of deprotonated peptides containing aspartic acid

    NASA Astrophysics Data System (ADS)

    Harrison, Alex G.; Young, Alex B.

    2006-09-01

    The fragmentation reactions of deprotonated peptides containing aspartic acid have been elucidated using MS2 and MS3 experiments and accurate mass measurements where necessary. The disposition of labile (N and O bonded) hydrogens in the fragmentation products has been studied by exchanging the labile hydrogens for deuterium whereby the [MD]- ion is formed on electrospray ionization. [alpha]-Aspartyl and [beta]-aspartyl dipeptides give very similar fragment ion spectra on collisional activation, involving for both species primarily formation of the y1 ion and loss of H2O from [MH]- followed by further fragmentation, thus precluding the distinction of the isomeric species by negative ion tandem mass spectrometry. Dipeptides of sequence HXxxAspOH give characteristic spectra different from the [alpha]- and [beta]-isomers. For larger peptides containing aspartic acid a common fragmentation reaction involves nominal cleavage of the NC bond N-terminal to the aspartic acid residue to form a c ion (deprotonated amino acid amide (c1) or peptide amide (cn)) and the complimentary product involving elimination of a neutral amino acid amide or peptide amide. When aspartic acid is in the C-terminal position this fragmentation reaction occurs from the [MH]- ion while when the aspartic acid is not in the C-terminal position the fragmentation reaction occurs mainly from the [MHH2O]- ion. The products of this NC bond cleavage reaction serve to identify the position of the aspartic acid residue in the peptide.

  20. 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.

  1. Phenocryst fragments in rhyolitic lavas and lava domes

    NASA Astrophysics Data System (ADS)

    Allen, S. R.; McPhie, J.

    2003-08-01

    Although rhyolitic lavas and lava domes are characterised by evenly porphyritic textures, not all the phenocrysts are whole euhedra. We undertook image analysis of 46 rhyolitic lava and lava dome samples to determine the abundance and shape of quartz and feldspar phenocryst fragments. Phenocryst fragments were identified in nearly all samples. On average, fragments amount to ˜5% of the total phenocryst population, or ˜0.5 modal%. The abundance of fragments in lavas and lava domes is not related to the groundmass texture (whether vesicular, flow banded, massive, glassy or crystalline), nor to distance from source. Fragments are, however, more abundant in samples with higher phenocryst contents. The phenocryst fragments in rhyolitic lavas and lava domes are mainly medium to large (0.5-3.5 mm), almost euhedral crystals with only a small portion removed, or chunky, equant, subhedral fragments, and occur in near-jigsaw-fit or clast-rotated pairs or groups. The fragments probably formed in response to decompression of large melt inclusions. Shear during laminar flow then dismembered the phenocrysts; continued laminar shear separated and rotated the fragments. Fractures probably formed preferentially along weaknesses in the phenocrysts, such as zones of melt inclusions, cleavage planes and twin composition planes. Rare splintery fragments are also present, especially within devitrified domains. Splinters are attributed to comminution of solid lava adjacent to fractures that were later healed. For comparison, we measured crystal abundance in a further 12 rhyolite samples that include block and ash flow deposits and ignimbrite. Phenocryst fragments within clasts in the block and ash flow samples showed similar shapes and abundances to those fragments within the lava and lava domes. Crystal fragments are much more abundant in ignimbrite (exceeding 67% of the crystal population) however, and dominated by small, equant, anhedral chunks or splinters. The larger crystals in

  2. Influence of Coronal Abundance Variations

    NASA Technical Reports Server (NTRS)

    Gurman, Joseph (Technical Monitor); DeLuca, Edward

    2005-01-01

    During the final year of this program we concentrated on understanding the how to constrain the models with the best available observations. Work on developing accurate temperature and density diagnostics fkom TRACE and CDS together with constrained fits of non-potential force free fields will be extremely useful in the guiding the next generation of coronal models. The program has produced three fully operation numerical codes that model multi-species of ions in coronal loops: Static models and constant flow models. The time dependent numerical models have not been completed. We have extended the steady flow investigations to study the effect these flows have on coronal structure as observed with TRACE. Coronal observations derive from heavy-ion emission; thus, we focus on the extent to which flow may modify coronal abundances by examining the heavy-ion abundance stratification within long-lived loops. We discuss the magnitudes of the physical effects modeled and compare simulated results with TRACE observations. These results can have a profound effect on the interpretation of TRACE observations.

  3. 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.

  4. Systematic analysis of reactivities and fragmentation of glutathione and its isomer GluCysGly.

    PubMed

    Feng, Shan; Zheng, Xiaoyan; Wang, Dong; Gong, Yiyi; Wang, Qingtao; Deng, Haiteng

    2014-09-18

    Glutathione (GSH) is the most abundant tripeptide in human cells and plays an important role in protecting cells' integrity against oxidative stress. GSH has an unusual amide linkage formed between the γ-carboxylic group of the glutamic acid in its side-chain and the amine group of cysteine residue. In the present study, we have compared reactivities of GSH to its isomer GluCysGly (ECG), which has a regular amide bond formed between the α-carboxylic group of glutamic acid and the amine group of cysteine residue. The fragmentation pattern of GSH ions in the gas phase is different from that of ECG ions, showing that the loss of H2O is the major dissociation pathway in ECG fragmentation. This is consistent with the dissociation pathway predicted by density functional calculation. Formation of GSSG from oxidation of GSH is faster than that of ECG disulfide, and the gas phase fragmentation pattern of GSSG is different from that of ECG disulfide. GSH and ECG display similar rates in nucleophilic aromatic substitution when reacting with 1-chloro-2,4-dinitrobenzene (CDNB). However, in the presence of glutathione S-transferases (GST), substitution of CDNB by GSH is 10 times faster than that by ECG. GSH and ECG also show differences in clustering patterns in the gas phase. Taken together, our results shed light on understanding effects of unique boding structure in GSH on its stability and reactivities.

  5. β-Methylphenylethylamines: common fragmentation pathways with amphetamines in electrospray ionization collision-induced dissociation.

    PubMed

    Brown, David H; Hansson, Robert; Oosthuizen, Francois; Sumner, Nathan

    2016-01-01

    β-Methylphenylethylamines are positional isomers of amphetamines and have been discovered in sporting supplements. Although the fragmentation of the β-methylphenylethylamine and N-methyl-β-methylphenylethylamine in gas chromatography-electron ionization-mass spectrometry (GC-EI-MS) systems is significantly different to their amphetamine and methylamphetamine isomers, under electrospray ionization commonly used in liquid chromatography-mass spectrometry (LC-MS) systems, the fragmentation of each of the isomeric pairs is almost identical. The similarities in fragmentation make it possible for the misidentification of the β-methylphenylethylamines as the illicit amphetamines. It is proposed that the similarities are due to a fragmentation pathway involving a common phenonium ion intermediate. By careful control of fragmentation energies in liquid chromatography-tandem mass spectrometry (LC-MS/MS) systems and/or close examination of the relative abundances of product ions formed by collision-induced dissociation (qualifier ratios), it is possible to distinguish the β-methylphenylethylamines from the amphetamines, even if significant retention time separation is not achieved. In liquid chromatography-electrospray ionization-quadrupole time of flight (LC-ESI-QTOF) systems the mass spectra of the β-methylphenylethylamines are identical to their amphetamine isomers. In such systems, retention time separation of the isomers is critical to avoid misidentification. During this study β-methylphenylethylamine and N-methyl-β-methylphenylethylamine have been identified in commercially available sporting supplements and oral fluid samples taken during the course of road-side drugs-in-drivers and workplace testing programmes. Copyright © 2015 John Wiley & Sons, Ltd.

  6. 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

  7. 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.

  8. Comet 73P Measurements of Solar Wind Interactions, Cometary Ion Pickup, and Spatial Distribution

    NASA Astrophysics Data System (ADS)

    Gilbert, J. A.; Lepri, S. T.; Rubin, M.; Combi, M. R.; Zurbuchen, T.

    2015-12-01

    Several fragments of Comet 73P/Schwassmann-Wachmann 3 passed near the Earth following a 2006 disintegration episode. Unique measurements regarding the charge state composition and the elemental abundances of both cometary and heliospheric plasma were made during this time by both the ACE/SWICS and Wind/STICS sensors. As the solar wind passed through the neutral cometary coma, it experienced charge exchange that was observed as an increase in the ratio of He+/He++. In addition, particles originating from fragments trailing the major cometary objects were ionized and picked up by the solar wind. The cometary material can be identified by the concentrations of water-group pickup ions having a mass-per-charge ratio of 16-18 amu/e, indicating that these are actively sublimating fragments. Here we present an analysis of cometary composition, spatial distribution, directionality, and heliospheric interactions with a focus on Helium, Carbon (C/O), and water-group ions.

  9. 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.

  10. Complex fragment emission at low and high excitation energy

    SciTech Connect

    Moretto, L.G.

    1986-08-01

    Complex fragment emission has been certified as a compound nucleus process at low energies. An extension of the measurements to heavy ion reactions up to 50 MeV/u shows that most complex fragments are emitted by highly excited compound nuclei formed in incomplete fusion reactions. 12 refs., 26 figs.

  11. 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…

  12. Fragment Hazard Investigation Program

    DTIC Science & Technology

    1978-10-01

    53 Ballistic Density (k) ............................................. 53 Ejection A ngle (a...54 Ejection Velocity (V) ................................................. 54 DEVELOPMENT OF EMPIRICAL RELATION...5S 54 Fragment Weight Versus Gamma for Test QD-155-08 ......................... 56 55 Fragment Range Versus Ejection Angle as a Function of

  13. Fragmentation of fullerenes

    NASA Astrophysics Data System (ADS)

    Chancey, Ryan T.; Oddershede, Lene; Harris, Frank E.; Sabin, John R.

    2003-04-01

    We have performed classical molecular-dynamics simulations of the fragmentation collisions of neutral fullerenes (C24, C60, C100, and C240) with a hard wall. The interactions between the carbon atoms are modeled by a Tersoff potential and the position of each carbon atom at each time step is calculated using a sixth-order predictor-corrector method. The statistical distribution of the fragments depends on impact energy. At low energies, the fragment distribution appears symmetric, with both the large and small fragment distributions well fitted by an exponential function of the same exponent, the value of which decreases with impact energy. At intermediate energies, the distribution of the smallest fragments can be fitted equally well by a power law or an exponential function. At high impact energies, the entire fragmentation pattern is well described by a single exponential function, the exponent increasing with energy. The observed tendencies in fragment distributions as well as the obtained exponents are in agreement with experimental observations. The fragmentation behavior of the four investigated fullerenes is very similar, and it is noted that C60 appears to be the most stable.

  14. Intermediate fragmentation per se provides stable predator-prey metapopulation dynamics.

    PubMed

    Cooper, Jennifer K; Li, Jiqiu; Montagnes, David J S

    2012-08-01

    The extent to which a landscape is fragmented affects persistence of predator-prey dynamics. Increasing fragmentation concomitantly imposes conditions that stabilise and destabilise metapopulations. For the first time, we explicitly assessed the hypothesis that intermediate levels provide optimal conditions for stability. We examine four structural changes arising from increased fragmentation: increased fragment number; decreased fragment size; increased connectedness (corridors scaled to fragment); increased fragment heterogeneity (based on connectedness). Using the model predator-prey system (Didinium-Paramecium) we support our hypothesis, by examining replicated metapopulations dynamics at five fragmentation levels. Although both species became extinct without fragmentation, prey survived at low and high levels, and both survived at intermediate levels. By examining time to extinction, maximum abundances, and population asynchrony we conclude that fragmentation produces structural heterogeneity (independent of environmental heterogeneity), which influences stability. Our analysis suggests why some theoretical, field and microcosm studies present conflicting views of fragmentation effects on population persistence.

  15. 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.

  16. Abundances in Przybylski's star

    NASA Astrophysics Data System (ADS)

    Cowley, C. R.; Ryabchikova, T.; Kupka, F.; Bord, D. J.; Mathys, G.; Bidelman, W. P.

    2000-09-01

    We have derived abundances for 54 elements in the extreme roAp star HD101065. ESO spectra with a resolution of about 80000, and S/N of 200 or more were employed. The adopted model has Teff=6600K, and log(g)=4.2. Because of the increased line opacity and consequent low gas pressure, convection plays no significant role in the temperature structure. Lighter elemental abundances through the iron group scatter about standard abundance distribution (SAD) (solar) values. Iron and nickel are about one order of magnitude deficient while cobalt is enhanced by 1.5dex. Heavier elements, including the lanthanides, generally follow the solar pattern but enhanced by 3 to 4dex. Odd-Z elements are generally less abundant than their even-Z neighbours. With a few exceptions (e.g. Yb), the abundance pattern among the heavy elements is remarkably coherent, and resembles a displaced solar distribution.

  17. Infrared multiphoton dissociation of peptide cations in a dual pressure linear ion trap mass spectrometer.

    PubMed

    Gardner, Myles W; Smith, Suncerae I; Ledvina, Aaron R; Madsen, James A; Coon, Joshua J; Schwartz, Jae C; Stafford, George C; Brodbelt, Jennifer S

    2009-10-01

    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 x 10(-3) Torr and the second a low pressure cell operated at nominally 3 x 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 y(1) fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of approximately 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.

  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. Fragmentation of monoclonal antibodies

    PubMed Central

    Vlasak, Josef

    2011-01-01

    Fragmentation is a degradation pathway ubiquitously observed in proteins despite the remarkable stability of peptide bond; proteins differ only by how much and where cleavage occurs. The goal of this review is to summarize reports regarding the non-enzymatic fragmentation of the peptide backbone of monoclonal antibodies (mAbs). The sites in the polypeptide chain susceptible to fragmentation are determined by a multitude of factors. Insights are provided on the intimate chemical mechanisms that can make some bonds prone to cleavage due to the presence of specific side-chains. In addition to primary structure, the secondary, tertiary and quaternary structures have a significant impact in modulating the distribution of cleavage sites by altering local flexibility, accessibility to solvent or bringing in close proximity side chains that are remote in sequence. This review focuses on cleavage sites observed in the constant regions of mAbs, with special emphasis on hinge fragmentation. The mechanisms responsible for backbone cleavage are strongly dependent on pH and can be catalyzed by metals or radicals. The distribution of cleavage sites are different under acidic compared to basic conditions, with fragmentation rates exhibiting a minimum in the pH range 5–6; therefore, the overall fragmentation pattern observed for a mAb is a complex result of structural and solvent conditions. A critical review of the techniques used to monitor fragmentation is also presented; usually a compromise has to be made between a highly sensitive method with good fragment separation and the capability to identify the cleavage site. The effect of fragmentation on the function of a mAb must be evaluated on a case-by-case basis depending on whether cleavage sites are observed in the variable or constant regions, and on the mechanism of action of the molecule. PMID:21487244

  20. 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.

  1. Universality in Fragmentation

    NASA Astrophysics Data System (ADS)

    Åström, J. A.; Holian, B. L.; Timonen, J.

    2000-04-01

    Fragmentation of a two-dimensional brittle solid by impact and ``explosion,'' and a fluid by ``explosion'' are all shown to become critical. The critical points appear at a nonzero impact velocity, and at infinite explosion duration, respectively. Within the critical regimes, the fragment-size distributions satisfy a scaling form qualitatively similar to that of the cluster-size distribution of percolation, but they belong to another universality class. Energy balance arguments give a correlation length exponent that is exactly one-half of its percolation value. A single crack dominates fragmentation in the slow-fracture limit, as expected.

  2. Fragmentation in Biaxial Tension

    SciTech Connect

    Campbell, G H; Archbold, G C; Hurricane, O A; Miller, P L

    2006-06-13

    We have carried out an experiment that places a ductile stainless steel in a state of biaxial tension at a high rate of strain. The loading of the ductile metal spherical cap is performed by the detonation of a high explosive layer with a conforming geometry to expand the metal radially outwards. Simulations of the loading and expansion of the metal predict strain rates that compare well with experimental observations. A high percentage of the HE loaded material was recovered through a soft capture process and characterization of the recovered fragments provided high quality data, including uniform strain prior to failure and fragment size. These data were used with a modified fragmentation model to determine a fragmentation energy.

  3. 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.

  4. Hyperthermal Energy Collisions of CF3+ Ions With Modified Surfaces: Surface-Induced Dissociation

    SciTech Connect

    Rezayat, Talayeh; Shukla, Anil K.

    2004-12-01

    The dissociative scattering of low-energy ions, especially polyatomic ions, from surfaces has become an active area of research in chemistry, physics and material sciences. The interaction between an ion and a surface is more complicated than ion and gaseous neutral collisions and needs to be explored in detail to understand the ion excitation and dissociation phenomena associated with Surface-induced dissociation (SID) of ions, a technique used for the analysis of high mass ions from biological molecules. However, dynamics studies of SID have been performed only for a few simple systems, viz., ethanol, acetone, benzene and carbon disulfide ions. We have therefore undertaken a study of the SID 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. These experiment 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 mass and scattering angle. In contrast with the previous studies of the SID of ethanol and acetone cations where the inelastically scattered primary ions dominated the collision process (up to {approx}50 eV maximum energy used in those experiments), we did not observe a measurable abundance of inelastically scattered undissociated CF3+ ions up to the lowest energy 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 SID efficiency decreased significantly as the collision energy was increased from 106 eV to 159 eV. The energy distributions of 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 the

  5. 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.

  6. Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation- Tandem Time-of-Flight Mass Spectrometry Approach

    SciTech Connect

    Ibrahim, Yehia M.; Prior, David C.; Baker, Erin Shammel; Smith, Richard D.; Belov, Mikhail E.

    2010-06-01

    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 a novel approach for collision-induced dissociation (CID) with an 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 the matching drift time profiles and by effectively utilizing high mass measurement accuracy of the TOFMS. In a single IMS separation with a tryptic digest of bovine serum albumin (BSA), we have reliably identified 20 unique peptides using 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%.

  7. 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.

  8. 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

  9. Extending the laserspray ionization concept to produce highly charged ions at high vacuum on a time-of-flight mass analyzer.

    PubMed

    Trimpin, Sarah; Ren, Yue; Wang, Beixi; Lietz, Christopher B; Richards, Alicia L; Marshall, Darrell D; Inutan, Ellen D

    2011-07-15

    A new matrix compound, 2-nitrophloroglucinol, is reported which not only produces highly charged ions similar to electrospray ionization (ESI) under atmospheric pressure (AP) and intermediate pressure (IP) laserspray ionization (LSI) conditions but also the most highly charged ions so far observed for small proteins in mass spectrometry (MS) under high vacuum (HV) conditions. This new matrix extends the compounds that can successfully be employed as matrixes with LSI, as demonstrated on an LTQ Velos (Thermo) at AP, a matrix-assisted laser desorption/ionization (MALDI)-ion mobility spectrometry (IMS) time-of-flight (TOF) SYNAPT G2 (Waters) at IP, and MALDI-TOF Ultraflex, UltrafleXtreme, and Autoflex Speed (Bruker) mass spectrometers at HV. Measurements show that stable multiple charged molecular ions of proteins are formed under all pressure conditions indicating softer ionization than MALDI, which suffers a high degree of metastable fragmentation when multiply charged ions are produced. An important analytical advantage of this new LSI matrix are the potential for high sensitivity equivalent or better than AP-LSI and vacuum MALDI and the potential for enhanced mass selected fragmentation of the abundant highly charged protein ions. A second new LSI matrix, 4,6-dinitropyrogallol, produces abundant multiply charged ions at AP but not under HV conditions. The differences in these similar compounds ability to produce multiply charged ions under HV conditions is believed to be related to their relative ability to evaporate from charged matrix/analyte clusters.

  10. 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.

  11. 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.

  12. Fragmentation of methane molecules by antiproton impact

    NASA Astrophysics Data System (ADS)

    Salehzadeh, Arash; Kirchner, Tom

    2016-09-01

    Extending previous work for proton impact, we have investigated the fragmentation of methane molecules due to collisions with antiprotons in the 25 keV to 5 MeV impact energy range. The multi-center nature of the problem is addressed by using a spectral representation of the molecular Hartree-Fock-level Hamiltonian and a single-center expansion of the initially populated molecular orbitals. The two-center basis generator method (TC-BGM) is used for orbital propagation. Electron-removal cross sections obtained from the TC-BGM solutions are complemented with a dynamical decay-route fragmentation model to calculate cross sections for the production of fragment ions. Good agreement with the available experimental data is observed for CH4+,CH3+,CH2+and CH+. Work supported by NSERC, Canada.

  13. Comparison of infrared multiphoton dissociation and collision-induced dissociation of supercharged peptides in ion traps.

    PubMed

    Madsen, James A; Brodbelt, Jennifer S

    2009-03-01

    The number and types of diagnostic ions obtained by infrared multiphoton dissociation (IRMPD) and collision-induced dissociation (CID) were evaluated for supercharged peptide ions created by electrospray ionization of solutions spiked with m-nitrobenzyl alcohol. IRMPD of supercharged peptide ions increased the sequence coverage compared with that obtained by CID for all charge states investigated. The number of diagnostic ions increased with the charge state for IRMPD; however, this trend was not consistent for CID because the supercharged ions did not always yield the greatest number of diagnostic ions. Significantly different fragmentation pathways were observed for the different charge states upon CID or IRMPD with the latter yielding far more immonium ions and often fewer uninformative ammonia, water, and phosphoric acid neutral losses. Pulsed-Q dissociation resulted in an increase in the number of internal product ions, a decrease in sequence-informative ions, and reduced overall ion abundances. The enhanced sequence coverage afforded by IRMPD of supercharged ions was demonstrated for a variety of model peptides, as well as for a tryptic digest of cytochrome c.

  14. Linkage analysis of chromophore-labeled disaccharides and linear oligosaccharides by negative ion fast atom bombardment ionization and collisional-induced dissociation with B/E scanning.

    PubMed

    Li, D T; Her, G R

    1993-06-01

    Negative ion fast atom bombardment ionization in combination with collisional-induced dissociation mass spectrometry differentiates the linkage position(s) of chromophore-labeled di- and oligosaccharides. The formation of glycosylamines rather than the more popular reductive amination has been used to label the reducing end of sugars with ultraviolet or fluorescence tags. Two types of fragment ions were detected, one with the charge carried on the chromophore end and the other with the charge carried on the nonreducing terminus. These ions are essential to the determination of interglycosidic linkage and they are produced from the ring cleavage of the reducing end monosaccharide. Additionally, the anomeric configuration of the 1-4-linked residue could be assigned according to the relative abundance of the fragment ions.

  15. 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.

  16. Aromatic organosulfates in atmospheric aerosols: synthesis, characterization, and abundance.

    PubMed

    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

    2014-09-01

    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 - 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.

  17. 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.

  18. The Argonne fragment mass analyzer

    SciTech Connect

    Davids, C.N.; Larson, J.D.

    1988-01-01

    The Fragment Mass Analyzer (FMA) is currently under construction at the ATLAS facility. The FMA is an eight-meter long recoil mass spectrometer which will be used to separate nuclear reaction products from the primary heavy-ion beam and disperse them by A/q (mass/charge) at the focal plane. The FMA will be used in many different types of experiments. Gamma rays originating from very weak fusion-evaporation channels can be observed in coincidence with the recoil nucleus identified at the FMA focal plane. Production and decay of nuclei far from stability will be studied at the focal plane by implanting exotic recoils directly into detectors or by using a fast tape transport system. The FMA will also be used for reaction mechanism studies. A radioactive beam facility behind the focal plane is planned, which will allow beta-NMR and nuclear moment measurements to be made. The FMA will utilize the wide range of beam and intensities to be provided by the new ECR-positive ion injector also under construction at ATLAS. 8 refs., 4 figs., 1 tab.

  19. Laser ion source for isobaric heavy ion collider experiment

    SciTech Connect

    Kanesue, T. Okamura, M.; Kumaki, M.; Ikeda, S.

    2016-02-15

    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 {sup 96}Ru + {sup 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.

  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.

  1. 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

  2. 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

  3. Light fragments from (C + Be) interactions at 0.6 GeV/nucleon

    DOE PAGES

    Abramov, B. M.; Alekseev, P. N.; Borodin, Yu. A.; ...

    2016-05-01

    We measured nuclear fragments emitted at 3.5° in 12C fragmentation at 0.6 GeV/nucleon. We also used the spectra obtained to test the predictions of four ion-ion interaction models: INCL++, BC, LAQGSM03.03 and QMD as well as for the comparison with the analytical parametrization in the framework of thermodynamical picture of fragmentation.

  4. Light fragments from (C + Be) interactions at 0.6 GeV/nucleon

    SciTech Connect

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

    2016-05-01

    We measured nuclear fragments emitted at 3.5° in 12C fragmentation at 0.6 GeV/nucleon. We also used the spectra obtained to test the predictions of four ion-ion interaction models: INCL++, BC, LAQGSM03.03 and QMD as well as for the comparison with the analytical parametrization in the framework of thermodynamical picture of fragmentation.

  5. Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids

    PubMed Central

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

    2012-01-01

    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 NO2− anion or neutral loss of HNO2. The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional 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 NO2− rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of 13C and 15N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples. PMID:21953257

  6. The Fragmentation of Learning.

    ERIC Educational Resources Information Center

    Downes, Stephen

    2001-01-01

    Information and communication technologies, especially the Internet, have vastly increased access to information and educational opportunities. Steadily increasing consumer demand is driving the development of online educational materials. The end result may be a "fragmentation" of learning involving multiple learning providers and delivery modes,…

  7. Linear ion trap MS(n) of enzymatically synthesized 13C-labeled fructans revealing differentiating fragmentation patterns of β (1-2) and β (1-6) fructans and providing a tool for oligosaccharide identification in complex mixtures.

    PubMed

    Harrison, Scott; Xue, Hong; Lane, Geoff; Villas-Boas, Silas; Rasmussen, Susanne

    2012-02-07

    Fructans are polymeric carbohydrates, which play important roles as plant reserve carbohydrates and stress protectants, and are beneficial for human health and animal production. Fructans are formed by the addition of β-d-fructofuranosyl units to sucrose, leading to very complex mixtures of 1-kestose based inulins, 6-kestose linked levans, and 6G-kestose derived neoseries inulins and levans in cool season grasses such as Lolium perenne. The identification of isomeric fructan oligomers in chromatographic analysis of crude plant extracts is often hampered by the lack of authentic standards, and unambiguous peak assignment usually requires time-consuming analyses of purified fructan oligomers. We have developed a LC-MS(n) method for the separation and detection of fructan isomers and present here evidence for specific MS(n) fragmentation patterns associated with β 1-2 (inulins) and β 2-6 (levans) fructans. LC-MS(n) analysis of (13)C labeled fructan oligomers produced by L. perenne fructosyltransferases expressed in yeast has enabled us to account for the observed fragmentation patterns in terms of preferential cleavage of the glycosidic bond between O- and fructose C2 in both inulins and levans and to differentiate reducing-end from nonreducing end cross ring cleavages in levans. We propose that higher order MS fragmentation patterns can be used to distinguish between the two major classes of fructan, i.e., inulins and levans, without the need for authentic standards.

  8. Study on Fragments Emission in the 64Ni + 64Ni Reaction at 40 AMeV

    NASA Astrophysics Data System (ADS)

    Yang, Kun; Cao, Xiguang; Shi, Fudong; Liu, Xingquan; Zhang, Suyalatu; Huang, Meirong; Wang, Jiansong; Chen, Zhiqiang; Wada, R.; Kowalski, S.; Keutgen, T.; Hagel, K.; Bonasera, A.; B. Natowitz, J.; Materna, T.; L., Qin; K. Sahu, P.

    2012-05-01

    The multiplicity of fragments in Fermi energy heavy-ion collisions was experimentally extracted. Compared with the results of calculation using the antisymmetrized molecular dynamics (AMD) model which accounts for the primary fragments only, the results calculated using the AMD together with a statistical decay code GEMINI to account for the deexcitation of excited primary fragments are in better agreement with those extracted from the experiment. This observation indicates that the experimental multiplicity distribution may be significantly different from those of primary fragments.

  9. On the abundance enigma in Ionized Regions

    NASA Astrophysics Data System (ADS)

    Bohigas, J.

    2009-04-01

    In ionized regions with temperature gradients and fluctuations, the ratio of the ion abundance obtained from a recombination line to that found from a collisionally excited line (CEL), or ADF, is smaller than observed (ADF ≥ 2). Larger ADFs are found when there is an additional component that is ≥ 30% colder. The temperature in the cold component must be ≈ 500, 200 and 100 K if the ADF found from an IR CEL is ≃2, 5 and 10. Most of the mass is in the hot region. The total H+ mass has been underestimated if it was found from the intensity of a Balmer line. [O IIII]5007/Hβ images can also render the relative distribution of cold and hot matter. The determination of accurate abundances is forestalled by the fact that observations cannot discriminate light from these components, the existence of distinct abundance sets and insufficient spectral information for the hot region.

  10. 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.

  11. 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.

  12. 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.

  13. Statistical models of brittle fragmentation

    NASA Astrophysics Data System (ADS)

    Åström, J. A.

    2006-06-01

    Recent developments in statistical models for fragmentation of brittle material are reviewed. The generic objective of these models is understanding the origin of the fragment size distributions (FSDs) that result from fracturing brittle material. Brittle fragmentation can be divided into two categories: (1) Instantaneous fragmentation for which breakup generations are not distinguishable and (2) continuous fragmentation for which generations of chronological fragment breakups can be identified. This categorization becomes obvious in mining industry applications where instantaneous fragmentation refers to blasting of rock and continuous fragmentation to the consequent crushing and grinding of the blasted rock fragments. A model of unstable cracks and crack-branch merging contains both of the FSDs usually related to instantaneous fragmentation: the scale invariant FSD with the power exponent (2-1/D) and the double exponential FSD which relates to Poisson process fragmentation. The FSDs commonly related to continuous fragmentation are: the lognormal FSD originating from uncorrelated breakup and the power-law FSD which can be modeled as a cascade of breakups. Various solutions to the generic rate equation of continuous fragmentation are briefly listed. Simulations of crushing experiments reveal that both cascade and uncorrelated fragmentations are possible, but that also a mechanism of maximizing packing density related to Apollonian packing may be relevant for slow compressive crushing.

  14. 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.

  15. Ammonia abundances in comets

    NASA Astrophysics Data System (ADS)

    Wyckoff, S.; Tegler, S.; Engel, L.

    The emission band strengths of the NH2 bands of Comets Halley, Hartley-Good, Thiele, and Borrelly were measured to determine the NH2 column densities for the comets. Production rates obtained using the Haser and vectorial models are in agreement within the observational errors, suggesting that a simple two-step decay model may be used to approximate the NH2 distribution in a comet's coma. Ammonia-to-water abundance ratios from 0.01 to 0.4 percent were found for the four comets. The ratio in Comet Halley is found to be Q(NH3)/Q(H2O) = 0.002 + or - 0.001. No significant difference in the ammonia abundance was found before or after perihelion in Comet Halley.

  16. Fragmentation of Fractal Random Structures

    NASA Astrophysics Data System (ADS)

    Elçi, Eren Metin; Weigel, Martin; Fytas, Nikolaos G.

    2015-03-01

    We analyze the fragmentation behavior of random clusters on the lattice under a process where bonds between neighboring sites are successively broken. Modeling such structures by configurations of a generalized Potts or random-cluster model allows us to discuss a wide range of systems with fractal properties including trees as well as dense clusters. We present exact results for the densities of fragmenting edges and the distribution of fragment sizes for critical clusters in two dimensions. Dynamical fragmentation with a size cutoff leads to broad distributions of fragment sizes. The resulting power laws are shown to encode characteristic fingerprints of the fragmented objects.

  17. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry.

    PubMed

    Bythell, Benjamin J; Abutokaikah, Maha T; Wagoner, Ashley R; Guan, Shanshan; Rabus, Jordan M

    2016-11-28

    We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the (0,2) A 2 ion from the sodiated forms. Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies. Graphical Abstract ᅟ.

  18. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry

    NASA Astrophysics Data System (ADS)

    Bythell, Benjamin J.; Abutokaikah, Maha T.; Wagoner, Ashley R.; Guan, Shanshan; Rabus, Jordan M.

    2016-11-01

    We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms. Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies.

  19. 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.

  20. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    DOE PAGES

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

    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

  1. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    PubMed Central

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; Holman, Jerry D.; Chen, Kan; Liebler, Daniel C.; Orton, Daniel J.; Purvine, Samuel O.; Monroe, Matthew E.; Chung, Chang Y.; Rose, Kristie L.; Tabb, David L.

    2013-01-01

    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. PMID:23499924

  2. Nuclear fragmentation measurements for hadrontherapy and space radiation protection

    NASA Astrophysics Data System (ADS)

    De Napoli, M.; Agodi, C.; Battistoni, G.; Blancato, A. A.; Bondı, M.; Cappuzzello, F.; Carbone, D.; Cavallaro, M.; Cirrone, G. A. P.; Cuttone, G.; Giacoppo, F.; Morone, M. C.; Nicolosi, D.; Pandola, L.; Raciti, G.; Rapisarda, E.; Romano, F.; Sardina, D.; Scuderi, V.; Sfienti, C.; Tropea, S.

    2013-04-01

    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 12C 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. 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.

  4. RELATIVE ABUNDANCE MEASUREMENTS IN PLUMES AND INTERPLUMES

    SciTech Connect

    Guennou, C.; Hahn, M.; Savin, D. W.

    2015-07-10

    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.

  5. 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.

  6. The elemental abundances in interplanetary dust particles

    NASA Astrophysics Data System (ADS)

    Arndt, Peter; Bohsung, Jörg; Maetz, Mischa; Jessberger, Elmar K.

    1996-11-01

    We compiled a table of all major, minor, and trace-element abundances in 89 interplanetary dust particles (IDPs) that includes data obtained with proton-induced x-ray emission (PIXE), synchroton x-ray fluorescence (SXRF), and secondary ion mass spectrometry (SIMS). For the first time, the reliability of the trace-element abundances in IDPs is tested by various crosschecks. We also report on the results of cluster analyses that we performed on IDP compositions. Because of the incompleteness of the data set, we included only the elements Cr, Mn, Ni, Cu, and Zn, normalized to Fe and CI chondrite abundances, that are determined in 73 IDPs. The data arrange themselves in four rather poorly defined groups that we discuss in relation to CI chondrites following the assumption that on the average CI abundances are most probable. The largest group (chondritic), with 44 members, has close to CI abundances for many refractory and moderately refractory elements (Na, Al, Si, P, K, Sc, Ti, V, Cr, Co, Ge, Sr). It is slightly depleted in Fe and more in Ca and S, while the volatile elements (Cl, Cu, Zn, Ga, Se, Rb) are enriched by =1.7 × CI and Br by 21 × CI. The low-Zn group, with 12 members, is very similar to the chondritic group except for its Zn-depletion, stronger Ca-depletion and Fe-enrichment. The low-Ni group, with 11 members, has Ni/Fe = 0.03 × CI and almost CI-like Ca, but its extraterrestrial origin is not established. The last group (6 members) contains non-systematic particles of unknown origin. We found that Fe is inhomogeneously distributed on a micron scale. Furthermore, the abundances of elements that are measured near their limits of detection are easily overestimated. These biases involved, the incomplete data set and possible contaminating processes prevent us from obtaining information on the specific origin(s) of IDPs from elemental abundances.

  7. 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.

  8. Identification of membrane proteins by tandem mass spectrometry of protein ions.

    PubMed

    Carroll, Joe; Altman, Matthew C; Fearnley, Ian M; Walker, John E

    2007-09-04

    The most common way of identifying proteins in proteomic analyses is to use short segments of sequence ("tags") determined by mass spectrometric analysis of proteolytic fragments. The approach is effective with globular proteins and with membrane proteins with significant polar segments between membrane-spanning alpha-helices, but it is ineffective with other hydrophobic proteins where protease cleavage sites are either infrequent or absent. By developing methods to purify hydrophobic proteins in organic solvents and by fragmenting ions of these proteins by collision induced dissociation with argon, we have shown that partial sequences of many membrane proteins can be deduced easily by manual inspection. The spectra from small proteolipids (1-4 transmembrane alpha-helices) are dominated usually by fragment ions arising from internal amide cleavages, from which internal sequences can be obtained, whereas the spectra from larger membrane proteins (5-18 transmembrane alpha-helices) often contain fragment ions from N- and/or C-terminal parts yielding sequences in those regions. With these techniques, we have, for example, identified an abundant protein of unknown function from inner membranes of mitochondria that to our knowledge has escaped detection in proteomic studies, and we have produced sequences from 10 of 13 proteins encoded in mitochondrial DNA. They include the ND6 subunit of complex I, the last of its 45 subunits to be analyzed. The procedures have the potential to be developed further, for example by using newly introduced methods for protein ion dissociation to induce fragmentation of internal regions of large membrane proteins, which may remain partially folded in the gas phase.

  9. 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.

  10. Rain forest fragmentation and the proliferation of successional trees.

    PubMed

    Laurance, William F; Nascimento, Henrique E M; Laurance, Susan G; Andrade, Ana C; Fearnside, Philip M; Ribeiro, José E L; Capretz, Robson L

    2006-02-01

    The effects of habitat fragmentation on diverse tropical tree communities are poorly understood. Over a 20-year period we monitored the density of 52 tree species in nine predominantly successional genera (Annona, Bellucia, Cecropia, Croton, Goupia, Jacaranda, Miconia, Pourouma, Vismia) in fragmented and continuous Amazonian forests. We also evaluated the relative importance of soil, topographic, forest dynamic, and landscape variables in explaining the abundance and species composition of successional trees. Data were collected within 66 permanent 1-ha plots within a large (approximately 1000 km2) experimental landscape, with forest fragments ranging from 1 to 100 ha in area. Prior to forest fragmentation, successional trees were uncommon, typically comprising 2-3% of all trees (> or =10 cm diameter at breast height [1.3 m above the ground surface]) in each plot. Following fragmentation, the density and basal area of successional trees increased rapidly. By 13-17 years after fragmentation, successional trees had tripled in abundance in fragment and edge plots and constituted more than a quarter of all trees in some plots. Fragment age had strong, positive effects on the density and basal area of successional trees, with no indication of a plateau in these variables, suggesting that successional species could become even more abundant in fragments over time. Nonetheless, the 52 species differed greatly in their responses to fragmentation and forest edges. Some disturbance-favoring pioneers (e.g., Cecropia sciadophylla, Vismia guianensis, V. amazonica, V. bemerguii, Miconia cf. crassinervia) increased by >1000% in density on edge plots, whereas over a third (19 of 52) of all species remained constant or declined in numbers. Species responses to fragmentation were effectively predicted by their median growth rate in nearby intact forest, suggesting that faster-growing species have a strong advantage in forest fragments. An ordination analysis revealed three main

  11. Multigenerational Broadband Collision-Induced Dissociation of Precursor Ions in a Linear Quadrupole Ion Trap

    NASA Astrophysics Data System (ADS)

    Snyder, Dalton T.; Cooks, R. Graham

    2016-12-01

    A method of fragmenting ions over a wide range of m/ z values while balancing energy deposition into the precursor ion and available product ion mass range is demonstrated. In the method, which we refer to as "multigenerational collision-induced dissociation", the radiofrequency (rf) amplitude is first increased to bring the lowest m/ z of the precursor ion of interest to just below the boundary of the Mathieu stability diagram (q = 0.908). A supplementary AC signal at a fixed Mathieu q in the range 0.2-0.35 (chosen to balance precursor ion potential well depth with available product ion mass range) is then used for ion excitation as the rf amplitude is scanned downward, thus fragmenting the precursor ion population from high to low m/ z. The method is shown to generate high intensities of product ions compared with other broadband CID methods while retaining low mass ions during the fragmentation step, resulting in extensive fragment ion coverage for various components of complex mixtures. Because ions are fragmented from high to low m/ z, space charge effects are minimized and multiple discrete generations of product ions are produced, thereby giving rise to "multigenerational" product ion mass spectra.

  12. Multigenerational Broadband Collision-Induced Dissociation of Precursor Ions in a Linear Quadrupole Ion Trap.

    PubMed

    Snyder, Dalton T; Cooks, R Graham

    2016-12-01

    A method of fragmenting ions over a wide range of m/z values while balancing energy deposition into the precursor ion and available product ion mass range is demonstrated. In the method, which we refer to as "multigenerational collision-induced dissociation", the radiofrequency (rf) amplitude is first increased to bring the lowest m/z of the precursor ion of interest to just below the boundary of the Mathieu stability diagram (q = 0.908). A supplementary AC signal at a fixed Mathieu q in the range 0.2-0.35 (chosen to balance precursor ion potential well depth with available product ion mass range) is then used for ion excitation as the rf amplitude is scanned downward, thus fragmenting the precursor ion population from high to low m/z. The method is shown to generate high intensities of product ions compared with other broadband CID methods while retaining low mass ions during the fragmentation step, resulting in extensive fragment ion coverage for various components of complex mixtures. Because ions are fragmented from high to low m/z, space charge effects are minimized and multiple discrete generations of product ions are produced, thereby giving rise to "multigenerational" product ion mass spectra. Graphical Abstract ᅟ.

  13. Fragmentation of random trees

    NASA Astrophysics Data System (ADS)

    Kalay, Z.; Ben-Naim, E.

    2015-01-01

    We study fragmentation of a random recursive tree into a forest by repeated removal of nodes. The initial tree consists of N nodes and it is generated by sequential addition of nodes with each new node attaching to a randomly-selected existing node. As nodes are removed from the tree, one at a time, the tree dissolves into an ensemble of separate trees, namely, a forest. We study statistical properties of trees and nodes in this heterogeneous forest, and find that the fraction of remaining nodes m characterizes the system in the limit N\\to ∞ . We obtain analytically the size density {{φ }s} of trees of size s. The size density has power-law tail {{φ }s}˜ {{s}-α } with exponent α =1+\\frac{1}{m}. Therefore, the tail becomes steeper as further nodes are removed, and the fragmentation process is unusual in that exponent α increases continuously with time. We also extend our analysis to the case where nodes are added as well as removed, and obtain the asymptotic size density for growing trees.

  14. Fragmentation of random trees

    NASA Astrophysics Data System (ADS)

    Kalay, Ziya; Ben-Naim, Eli

    2015-03-01

    We investigate the fragmentation of a random recursive tree by repeated removal of nodes, resulting in a forest of disjoint trees. The initial tree is generated by sequentially attaching new nodes to randomly chosen existing nodes until the tree contains N nodes. As nodes are removed, one at a time, the tree dissolves into an ensemble of separate trees, namely a forest. We study the statistical properties of trees and nodes in this heterogeneous forest. In the limit N --> ∞ , we find that the system is characterized by a single parameter: the fraction of remaining nodes m. We obtain analytically the size density ϕs of trees of size s, which has a power-law tail ϕs ~s-α , with exponent α = 1 + 1 / m . Therefore, the tail becomes steeper as further nodes are removed, producing an unusual scaling exponent that increases continuously with time. Furthermore, we investigate the fragment size distribution in a growing tree, where nodes are added as well as removed, and find that the distribution for this case is much narrower.

  15. Projectile fragmentation wall for CHICSi detector

    NASA Astrophysics Data System (ADS)

    Budzanowski, A.; Czech, B.; Siwek, A.; Skwirczyńska, I.; Staszel, P.; CHIC Collaboration

    2002-04-01

    The Forward Wall Detector (FWD) is designed to identify projectile-like fragments from heavy-ion reactions at the CELSIUS storage ring in Uppsala, Sweden. FWD covers the polar angle from 3.9° to 11.7° with geometrical efficiency of 81%. The single-detection module can be either of phoswich type (10 mm fast plastic+80 mm CsI(Tl)) or Δ E- E telescope (750 μm Si+80 mm CsI(Tl)). It is expected to have charge identification up to Z=18 and mass resolution for H and He isotopes.

  16. From cysteine to longer chain thiols: thermodynamic analysis of cadmium binding by phytochelatins and their fragments.

    PubMed

    Chekmeneva, Elena; Gusmão, Rui; Díaz-Cruz, José Manuel; Ariño, Cristina; Esteban, Miquel

    2011-08-01

    Isothermal Titration Calorimetry (ITC) was used to study the binding of Cd(2+) by phytochelatins ((γGlu-Cys)(n)-Gly, PC(n); n = 1-5) and their selected fragments (Cys, Cys-Gly and γGlu-Cys) in order to understand the influence of the chain length on the complex stabilities and the origin of the enhanced affinities in Tris buffer at pH 7.5 and 8.5 and at 25 °C. Different complexes are formed with glutathione (GSH) and its fragments, Cys, Cys-Gly and γGlu-Cys, and their stabilities depend on the corresponding pK(a) value of the thiol group in the ligands. The stability of Cd-PC(n) complexes increases moving towards higher PC(2-5), as well as the complexing capacity expressed as the number of metal ions that can be bound by one ligand molecule. The affinity of Cd(2+) for the PC(n) can be described by the following GSH < PC(2) < PC(3)≤ PC(4)≤ PC(5) sequence. On the basis of these thermodynamic data it is possible to explain the abundance of certain Cd-PC(n) complexes found in nature. The comprehension of the thermodynamic rules that govern the interactions of Cd(2+) with PC(n) and their constituents is of great service in the research with real plant samples subjected to metal stress and in the development of new strategies of bio/phytoremediation.

  17. Transient X-ray fragmentation: probing a prototypical photoinduced ring opening.

    PubMed

    Petrović, Vladimir S; Siano, Marco; White, James L; Berrah, Nora; Bostedt, Christoph; Bozek, John D; Broege, Douglas; Chalfin, Max; Coffee, Ryan N; Cryan, James; Fang, Li; Farrell, Joseph P; Frasinski, Leszek J; Glownia, James M; Gühr, Markus; Hoener, Matthias; Holland, David M P; Kim, Jaehee; Marangos, Jonathan P; Martinez, Todd; McFarland, Brian K; Minns, Russell S; Miyabe, Shungo; Schorb, Sebastian; Sension, Roseanne J; Spector, Limor S; Squibb, Richard; Tao, Hongli; Underwood, Jonathan G; Bucksbaum, Philip H

    2012-06-22

    We report the first study of UV-induced photoisomerization probed via core ionization by an x-ray laser. We investigated x-ray ionization and fragmentation of the cyclohexadiene-hexatriene system at 850 eV during the ring opening. We find that the ion-fragmentation patterns evolve over a picosecond, reflecting a change in the state of excitation and the molecular geometry: the average kinetic energy per ion fragment and H(+)-ion count increase as the ring opens and the molecule elongates. We discuss new opportunities for molecular photophysics created by optical pump x-ray probe experiments.

  18. 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.

  19. Nitrocellulose film substrate minimizes fragmentation in matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of triacylglycerols.

    PubMed

    Picariello, Gianluca; Romano, Raffaele; Addeo, Francesco

    2010-07-01

    The potential of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) for the analysis of intact triacylglycerols (TAGs) is generally limited by the extensive in-source prompt fragmentation. The sequential deposition of matrix and TAGs over the stainless steel target precoated with a thin layer of nitrocellulose (NC) drastically reduced fragmentation in the MALDI-TOF MS profiling of oils and fats. The NC MALDI-TOF MS profiles of native and thermally stressed virgin olive oil and butter are reported as case studies, along with test analyses of a standard mixture of mono-, di-, and triacylglycerols. Mass spectra were almost completely devoid of both fragment and matrix ion signals, thus disclosing relevant information, especially in the low molecular mass range. The detection of several partial acylglycerols of low abundance and minor TAGs that are barely observed with other techniques also provided evidence for an increased dynamic range of NC MALDI-TOF MS that was due to the minimization of suppressive effects. The NC film substrate also improved the shot-to-shot and sample-to-sample reproducibility of the ion production through the exhibition of a more homogeneous matrix/analyte cocrystallization, thus enabling MALDI-based measurements to a consistent quantification of TAGs.

  20. 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

  1. Characterization of monoferric fragments obtained by tryptic cleavage of bovine transferrin.

    PubMed Central

    Brock, J H; Arzabe, F R; Richardson, N E; Deverson, E V

    1978-01-01

    1. The electrophoretically fast (F) and slow (S) fragments obtained by tryptic cleavage of bovine iron-saturated transferrin differed in carbohydrate content and peptide 'maps'. 2. A fragment capable of binding one Fe3+ ion per molecule was isolated after brief tryptic digestion of bovine apotransferrin and shown closely to resemble the S fragment obtained from the iron-saturated protein. 3. Fragments F and S are probably derived from the N- and C-terminal halves of the transferrin molecule respectively. 4. Bovine transferrin could donate iron to rabbit reticulocytes, but the monoferric fragments possessed little iron-donating ability. Images PLATE 1 PMID:646825

  2. 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.

  3. Geographic variation in cowbird distribution, abundance, and parasitism

    USGS Publications Warehouse

    Morrison, M.L.; Hahn, D.C.; George, T. Luke; Dobkin, David S.

    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

  4. 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.

  5. Fragment ion diagnostic strategies for the comprehensive identification of chemical profile of Gui-Zhi-Tang by integrating high-resolution MS, multiple-stage MS and UV information.

    PubMed

    Wang, Shufang; Chen, Lulin; Leng, Jing; Chen, Pinghong; Fan, Xiaohui; Cheng, Yiyu

    2014-09-01

    Gui-Zhi-Tang was considered to be the most famous formula in Shang-Han-Lun, treating 32 symptoms of disease after adding up or cutting down crude drugs. The chemical constituents in Gui-Zhi-Tang were comprehensively studied by rapid resolution liquid chromatography quadrupole time-of-flight mass spectrometry (RRLC-Q-TOF-MS) combined with rapid resolution liquid chromatography - diode array detector - ion trap mass spectrometry (RRLC-DAD-IT-MS) in this work, and a total number of 187 compounds were detected. Systematic diagnostic ion filtering strategies were recommended for flavonoids and oleanane-type triterpenoids, respectively. On the basis of the summarized strategies, compounds in Glycyrrhizae could be easily classified into flavones, isoflavones, flavanones or chalcones with special structures, and triterpene saponins with different sugar moieties. Consequently, among 187 compounds, 144 ones were confirmed or assumed tentatively. In addition, nine potential novel compounds were reported for the first time. This approach provided a rapid method for characterizing the constituents in Gui-Zhi-Tang, and would be also helpful in other TCM formulae analysis.

  6. The Largest Fragment of a Homogeneous Fragmentation Process

    NASA Astrophysics Data System (ADS)

    Kyprianou, Andreas; Lane, Francis; Mörters, Peter

    2017-03-01

    We show that in homogeneous fragmentation processes the largest fragment at time t has size e^{-t Φ '(overline{p})}t^{-3/2 (log Φ )'(overline{p})+o(1)}, where Φ is the Lévy exponent of the fragmentation process, and overline{p} is the unique solution of the equation (log Φ )'(bar{p})=1/1+bar{p}. We argue that this result is in line with predictions arising from the classification of homogeneous fragmentation processes as logarithmically correlated random fields.

  7. 20-150-keV proton-impact-induced ionization of uracil: Fragmentation ratios and branching ratios for electron capture and direct ionization

    SciTech Connect

    Tabet, J.; Eden, S.; Feil, S.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Ouaskit, S.; Maerk, T. D.

    2010-01-15

    Fragmentation ratios and branching ratios are measured for ionization and dissociative ionization for 20-150 keV (0.9-2.4v{sub 0}) proton collisions with gas-phase uracil molecules. Through event-by-event determination of the postcollision projectile charge, it is possible for such a key biomolecule to distinguish between electron capture (EC) by the incident proton and direct ionization (DI) without projectile neutralization. While the same fragment ion groups are observed in the mass spectra for both processes, EC induces dissociation with greater efficiency than DI in the impact energy range of 35-150 keV (1.2-2.4v{sub 0}). In this range EC is also less abundant than DI with a branching ratio for EC/total ionization of <50%. Moreover, whereas fragmentation ratios do not change with energy in the case of EC, DI mass spectra show a tendency for increased fragmentation at lower impact energies.

  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. 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.

  10. Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest.

    PubMed

    Callens, Tom; Galbusera, Peter; Matthysen, Erik; Durand, Eric Y; Githiru, Mwangi; Huyghe, Jeroen R; Lens, Luc

    2011-05-01

    Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species-specific responses to fragmentation. Here, we compare levels of past population differentiation, estimated from microsatellite genotypes, with contemporary dispersal rates, estimated from multi-strata capture-recapture models, to infer changes in mobility over time in seven sympatric, forest-dependent bird species of a Kenyan cloud forest archipelago. Overall, populations of sedentary species were more strongly differentiated and clustered compared to those of vagile ones, while geographical patterning suggested an important role of landscape structure in shaping genetic variation. However, five of seven species with broadly similar levels of genetic differentiation nevertheless differed substantially in their current dispersal rates. We conclude that post-fragmentation levels of vagility, without reference to past population connectivity, may not be the best predictor of how forest fragmentation affects the life history of forest-dependent species. As effective conservation strategies often hinge on accurate prediction of shifts in ecological and genetic relationships among populations, conservation practices based solely upon current population abundances or movements may, in the long term, prove to be inadequate.

  11. 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

  12. Contrasting effects of habitat loss and fragmentation on coral-associated reef fishes.

    PubMed

    Bonin, Mary C; Almany, Glenn R; Jones, Geoffrey P

    2011-07-01

    Disturbance can result in the fragmentation and/or loss of suitable habitat, both of which can have important consequences for survival, species interactions, and resulting patterns of local diversity. However, effects of habitat loss and fragmentation are typically confounded during disturbance events, and previous attempts to determine their relative significance have proved ineffective. Here we experimentally manipulated live coral habitats to examine the potential independent and interactive effects of habitat loss and fragmentation on survival, abundance, and species richness of recruitment-stage, coral-associated reef fishes. Loss of 75% of live coral from experimental reefs resulted in low survival of a coral-associated damselfish and low abundance and richness of other recruits 16 weeks after habitat manipulations. In contrast, fragmentation had positive effects on damselfish survival and resulted in greater abundance and species richness of other recruits. We hypothesize that spacing of habitat through fragmentation weakens competition within and among species. Comparison of effect sizes over the course of the study period revealed that, in the first six weeks following habitat manipulations, the positive effects of fragmentation were at least four times stronger than the effects of habitat loss. This initial positive effect of fragmentation attenuated considerably after 16 weeks, whereas the negative effects of habitat loss increased in strength over time. There was little indication that the amount of habitat influenced the magnitude of the habitat fragmentation effect. Numerous studies have reported dramatic declines in coral reef fish abundance and diversity in response to disturbances that cause the loss and fragmentation of coral habitats. Our results suggest that these declines occur as a result of habitat loss, not habitat fragmentation. Positive fragmentation effects may actually buffer against the negative effects of habitat loss and contribute

  13. 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.

  14. Molecular secondary ion mass spectrometry: New dimensions in chemical characterization

    NASA Astrophysics Data System (ADS)

    Colton, Richard J.; Campana, Joseph E.; Kidwell, David A.; Ross, Mark M.; Wyatt, Jeffrey R.

    1985-04-01

    Secondary ion mass spectrometry (SIMS) has become a diverse tool for the study of many substances other than metals and semiconductors. This paper discusses the emission of polyatomic and molecular ions from surfaces that contain various inorganic and organic compounds including polymers and biomolecules. The mass and abundance distribution of cluster ions emitted from various solids — Van der Waals, metallic, ionic and covalent — are compared. Trends in the emission patterns are discussed in terms of a recombination or direct emission mechanism. The emission of molecular ions is also discussed with respect to the method of ionization and the various sample preparation and matrix-assisted procedures used. The matrices include various solid-state and liquid matrices such as ammonium chloride, charcoal, glycerol and gallium. Various chemical derivatization procedures have been developed to enhance the sensitivity of molecular SIMS and to detect selectively components in mixtures. The procedures are demonstrated for the low-level detection of airborne contaminants from paints, for the analysis of drugs in biological fluids, and for the sequencing of biomolecules such as peptides and sugars. The emission of characteristic fragment ions from the surfaces of polymers is also described for thick, insulating films.

  15. 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.

  16. Binary stars - Formation by fragmentation

    NASA Technical Reports Server (NTRS)

    Boss, Alan P.

    1988-01-01

    Theories of binary star formation by capture, separate nuclei, fission and fragmentation are compared, assessing the success of theoretical attempts to explain the observed properties of main-sequence binary stars. The theory of formation by fragmentation is examined, discussing the prospects for checking the theory against observations of binary premain-sequence stars. It is concluded that formation by fragmentation is successful at explaining many of the key properties of main-sequence binary stars.

  17. 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.

  18. Carbon Fragmentation Cross Sections for Hadrontherapy and Space Radiation Protection

    NASA Astrophysics Data System (ADS)

    De Napoli, M.; Agodi, C.; Cirrone, G. A. P.; Cuttone, G.; Nicolosi, D.; Pandola, L.; Raciti, G.; Romano, F.; Sardina, D.; Scuderi, V.; Tropea, S.; Bondì, M.; Cappuzzello, F.; Carbone, D.; Cavallaro, M.

    2014-05-01

    Fragmentation reactions represent a serious complication in hadrontherapy and space radiation protection. In order to predict their effects, both reliable Monte Carlo codes and experimental data are needed. The shortage of precise measurements, especially of double differential cross sections, has triggered many dedicated experiments at relativistic energies. Aiming to explore the Fermi energy regime, as well, where different reaction mechanisms are involved, we measured the 12C fragmentation at 62 AMeV on a 12C and a 197Au target. A high granularity Si-CsI hodoscope allowed to identify the charge and the mass of detected fragments and measure their energy and emission angle. In this work we report the double differential cross sections for the production of different fragments as a function of the emission angle. Experimental results are compared with the GEANT-4 Monte Carlo predictions performed using two reaction models, the Quantum Molecular Dynamic and the Binary Light Ion Cascade.

  19. Sensitivity and fragmentation calibration of the time-of-flight mass spectrometer RTOF on board ESA's Rosetta mission

    NASA Astrophysics Data System (ADS)

    Gasc, Sébastien; Altwegg, Kathrin; Fiethe, Björn; Jäckel, Annette; Korth, Axel; Le Roy, Léna; Mall, Urs; Rème, Henri; Rubin, Martin; Hunter Waite, J.; Wurz, Peter

    2017-01-01

    The European Space Agency's Rosetta spacecraft, with the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) onboard, has been following and observing comet 67P/Churyumov-Gerasimenko since summer 2014. Prior to this period, and due to a technical failure also during this period, optimization and calibration campaigns have been conducted on ground with the Reflectron-type Time Of Flight (RTOF) mass spectrometer as a preparatory work for the analysis of data recorded during the science phase of the mission. In this work, we show the evolution of the performance of RTOF, and demonstrate and quantify the sensitivity and functionality of RTOF onboard Rosetta. We also present a fragmentation and sensitivity database for the most abundant molecules observed around the comet such as H2O, CO, CO2, as well as the noble gases.

  20. Species–fragmented area relationship

    PubMed Central

    Hanski, Ilkka; Zurita, Gustavo A.; Bellocq, M. Isabel; Rybicki, Joel

    2013-01-01

    The species–area relationship (SAR) gives a quantitative description of the increasing number of species in a community with increasing area of habitat. In conservation, SARs have been used to predict the number of extinctions when the area of habitat is reduced. Such predictions are most needed for landscapes rather than for individual habitat fragments, but SAR-based predictions of extinctions for landscapes with highly fragmented habitat are likely to be biased because SAR assumes contiguous habitat. In reality, habitat loss is typically accompanied by habitat fragmentation. To quantify the effect of fragmentation in addition to the effect of habitat loss on the number of species, we extend the power-law SAR to the species–fragmented area relationship. This model unites the single-species metapopulation theory with the multispecies SAR for communities. We demonstrate with a realistic simulation model and with empirical data for forest-inhabiting subtropical birds that the species–fragmented area relationship gives a far superior prediction than SAR of the number of species in fragmented landscapes. The results demonstrate that for communities of species that are not well adapted to live in fragmented landscapes, the conventional SAR underestimates the number of extinctions for landscapes in which little habitat remains and it is highly fragmented. PMID:23858440

  1. Short-scale variations of the solar wind helium abundance

    SciTech Connect

    Šafránková, J.; Němeček, Z.; Cagaš, P.; Přech, L.; Pavlů, J.; Zastenker, G. N.; Riazantseva, M. O.; Koloskova, I. V.

    2013-11-20

    Abrupt changes of the relative He abundance in the solar wind are usually attributed to encounters with boundaries dividing solar wind streams from different sources in the solar corona. This paper presents a systematic study of fast variations of the He abundance that supports the idea that a majority of these variations on short timescales (3-30 s) are generated by in-transit turbulence that is probably driven by the speed difference between the ion species. This turbulence contributes to the solar wind heating and leads to a correlation of the temperature with He abundance.

  2. 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.

  3. 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).

  4. Ionized Gaseous Nebulae Abundance Determination from the Direct Method

    NASA Astrophysics Data System (ADS)

    Pérez-Montero, Enrique

    2017-04-01

    This tutorial explains the procedure used to analyze an optical emission-line spectrum produced by a nebula ionized by massive star formation. Particularly, the methodology used to derive physical properties, such as electron density and temperature, and the ionic abundances of the most representative elements whose emission lines are present in the optical spectrum is described. The main focus is on the direct method, which is based on the measurement of the electron temperature to derive the abundances, given that the ionization and thermal equilibrium of the ionized gas is dominated by the metallicity. The ionization correction factors used to obtain total abundances from the abundances of some of their ions are also given. Finally, some strong-line methods to derive abundances are described. Such methods are used when no estimation of the temperature can be derived, but which can be consistent with the direct method if they are empirically calibrated.

  5. 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

  6. 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

  7. Does tropical forest fragmentation increase long-term variability of butterfly communities?

    PubMed

    Leidner, Allison K; Haddad, Nick M; Lovejoy, Thomas E

    2010-03-10

    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.

  8. Collective phenomena in relativistic heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Wang, Shan

    1998-12-01

    Collective motion in the final state of relativistic nucleus-nucleus collisions, produced by the release of compressional energy built-up during the stage of maximum density, is widely accepted as a good observable to test models and a useful tool to probe the nuclear equation of state. This dissertation presents an experimental study of nuclear collisions at the Bevalac accelerator at Lawrence Berkeley National Laboratory, with special emphasis on collective phenomena. The main detector used is a time projection chamber with more than two million pixels. Using high statistics measurements of all charged final- state fragments in Au + Au reactions at 0.25, 0.4, 0.6, 0.8, 1.0, and 1.15A GeV, we present a new method to unify the description of light fragment spectra and the three main categories of collective motion: sideward flow, squeeze-out, and transverse expansion. In this alternative representation, the speed of collective expansion is shown to be slowest in the plane of the reaction, and is modulated sinusoidally according to fragment azimuth relative to this plane. This simple yet complete characterization of squeeze-out leads to its interpretation as an in-plane retardation of collective expansion. We test momentum space power law behavior by studying the momentum-space densities of fragments up to 4He. We conclude that the simple momentum-space power law consistently describes light participant fragment production at p⊥/A/ge0.2 GeV/c over a remarkably wide range of transverse momentum, azimuth relative to the reaction plane, rapidity, multiplicity and beam energy in intermediate-energy heavy-ion collisions and in particular, the increase in sideward flow with fragment mass is well described by a momentum- space power law under these conditions. This behavior is consistent with composite fragment formation through a statistical coalescence mechanism in momentum space. Our conclusion supports the use of models without composite formation to interpret flow

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. A metal-binding member of the late embryogenesis abundant protein family transports iron in the phloem of Ricinus communis L.

    PubMed

    Kruger, Claudia; Berkowitz, Oliver; Stephan, Udo W; Hell, Rudiger

    2002-07-12

    The transport of metal micronutrients to developing organs in a plant is mediated primarily by the sieve elements. Ligands are thought to form complexes with the free ions in order to prevent cellular damage, but no binding partners have been unequivocally identified from plants so far. This study has used the phloem-mediated transport of micronutrients during the germination of the castor bean seedling to identify an iron transport protein (ITP). It is demonstrated that essentially all (55)Fe fed to seedlings is associated with the protein fraction of phloem exudate. It is shown that ITP carries iron in vivo and binds additional iron in vitro. ITP was purified to homogeneity from minute amounts of phloem exudate using immobilized metal ion affinity chromatography. It preferentially binds to Fe(3+) but not to Fe(2+) and also complexes Cu(2+), Zn(2+), and Mn(2+) in vitro. The corresponding cDNA of ITP was cloned using internal peptide fragments. The deduced protein of 96 amino acids shows high similarity to the stress-related family of late embryogenesis abundant proteins. Its predicted characteristics and its RNA expression pattern are consistent with a function in metal ion binding. The ITP from Ricinus provides the first identified micronutrient binding partner for phloem-mediated long distance transport in plants and is the first member of the late embryogenesis abundant protein family shown to have such a function.

  14. Transport of Light Ions in Matter

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Cucinotta, F. A.; Tai, H.; Shinn, J. L.; Chun, S. Y.; Tripathi, R. K.; Sihver, L.

    1998-01-01

    A recent set of light ion experiments are analyzed using the Green's function method of solving the Boltzmann equation for ions of high charge and energy (the GRNTRN transport code) and the NUCFRG2 fragmentation database generator code. Although the NUCFRG2 code reasonably represents the fragmentation of heavy ions, the effects of light ion fragmentation requires a more detailed nuclear model including shell structure and short range correlations appearing as tightly bound clusters in the light ion nucleus. The most recent NTJCFRG2 code is augmented with a quasielastic alpha knockout model and semiempirical adjustments (up to 30 percent in charge removal) in the fragmentation process allowing reasonable agreement with the experiments to be obtained. A final resolution of the appropriate cross sections must await the full development of a coupled channel reaction model in which shell structure and clustering can be accurately evaluated.

  15. Measuring Solar Abundances with Seismology

    NASA Astrophysics Data System (ADS)

    Mussack, K.; Gough, D.

    2009-12-01

    The revision of the photospheric abundances proferred by Asplund et al. (2005) has rendered opacity theory inconsistent with the seismologically determined opacity through the Sun. This highlights the need for a direct seismological measurement of solar abundances. Here we describe the technique used to measure abundances with seismology, examine our ability to detect differences between solar models using this technique, and discuss its application in the Sun.

  16. Effects of pioneer tree species hyperabundance on forest fragments in northeastern Brazil.

    PubMed

    Tabarelli, Marcelo; Aguiar, Antonio V; Girão, Luciana C; Peres, Carlos A; Lopes, Ariadna V

    2010-12-01

    Despite many studies on fragmentation of tropical forests, the extent to which plant and animal communities are altered in small, isolated forest fragments remains obscure if not controversial. We examined the hypothesis that fragmentation alters the relative abundance of tree species with different vegetative and reproductive traits. In a fragmented landscape (670 km(2) ) of the Atlantic Forest of northeastern Brazil, we categorized 4056 trees of 182 species by leafing pattern, reproductive phenology, and morphology of seeds and fruit. We calculated relative abundance of traits in 50 1-ha plots in three types of forest configurations: forest edges, small forest fragments (3.4-83.6 ha), and interior of the largest forest fragment (3500 ha, old growth). Although evergreen species were the most abundant across all configurations, forest edges and small fragments had more deciduous and semideciduous species than interior forest. Edges lacked supra-annual flowering and fruiting species and had more species and stems with drupes and small seeds than small forest fragments and forest interior areas. In an ordination of species similarity and life-history traits, the three types of configurations formed clearly segregated clusters. Furthermore, the differences in the taxonomic and functional (i.e., trait-based) composition of tree assemblages we documented were driven primarily by the higher abundance of pioneer species in the forest edge and small forest fragments. Our work provides strong evidence that long-term transitions in phenology and seed and fruit morphology of tree functional groups are occurring in fragmented tropical forests. Our results also suggest that edge-induced shifts in tree assemblages of tropical forests can be larger than previously documented.

  17. Resonance methods in quadrupole ion traps

    NASA Astrophysics Data System (ADS)

    Snyder, Dalton T.; Peng, Wen-Ping; Cooks, R. Graham

    2017-01-01

    The quadrupole ion trap is widely used in the chemical physics community for making measurements on dynamical systems, both intramolecular (e.g. ion fragmentation reactions) and intermolecular (e.g. ion/molecule reactions). In this review, we discuss linear and nonlinear resonances in quadrupole ion traps, an understanding of which is critical for operation of these devices and interpretation of the data which they provide. The effect of quadrupole field nonlinearity is addressed, with important implications for promoting fragmentation and achieving unique methods of mass scanning. Methods that depend on ion resonances (i.e. matching an external perturbation with an ion's induced frequency of motion) are discussed, including ion isolation, ion activation, and ion ejection.

  18. Fragment screening and HIV therapeutics.

    PubMed

    Bauman, Joseph D; Patel, Disha; Arnold, Eddy

    2012-01-01

    Fragment screening has proven to be a powerful alternative to traditional methods for drug discovery. Biophysical methods, such as X-ray crystallography, NMR spectroscopy, and surface plasmon resonance, are used to screen a diverse library of small molecule compounds. Although compounds identified via this approach have relatively weak affinity, they provide a good platform for lead development and are highly efficient binders with respect to their size. Fragment screening has been utilized for a wide range of targets, including HIV-1 proteins. Here, we review the fragment screening studies targeting HIV-1 proteins using X-ray crystallography or surface plasmon resonance. These studies have successfully detected binding of novel fragments to either previously established or new sites on HIV-1 protease and reverse transcriptase. In addition, fragment screening against HIV-1 reverse transcriptase has been used as a tool to better understand the complex nature of ligand binding to a flexible target.

  19. Fragmentation functions in nuclear media

    NASA Astrophysics Data System (ADS)

    Sassot, Rodolfo; Stratmann, Marco; Zurita, Pia

    2010-03-01

    We perform a detailed phenomenological analysis of how well hadronization in nuclear environments can be described in terms of effective fragmentation functions. The medium modified fragmentation functions are assumed to factorize from the partonic scattering cross sections and evolve in the hard scale in the same way as the standard or vacuum fragmentation functions. Based on precise data on semi-inclusive deep-inelastic scattering off nuclei and hadron production in deuteron-gold collisions, we extract sets of effective fragmentation functions for pions and kaons at next-to-leading order accuracy. The obtained sets provide a rather accurate description of the kinematical dependence of the analyzed cross sections and are found to differ significantly from standard fragmentation functions both in shape and magnitude. Our results support the notion of factorization and universality in the studied nuclear environments, at least in an effective way and within the precision of the available data.

  20. Structure, fragmentation patterns, and magnetic properties of small nickel oxide clusters.

    PubMed

    Aguilera-Del-Toro, R H; Aguilera-Granja, F; Balbás, L C; Vega, A

    2017-01-25

    We report a comprehensive theoretical study of the structural and electronic properties of neutral and charged nickel oxide clusters, NinOm(0/±) (n = 3-8 and m = 1-10), in the context of recent experiments of photodissociation and Ion Mobility Mass Spectrometry. By means of density functional theory calculations in the generalized gradient approximation for exchange and correlation, we determined the putative ground states as well as the low-energy structural- and spin-isomers which were then used to explore the favorable fragmentation channels of the nickel oxide cationic clusters, and the resulting most abundant products, in good qualitative agreement with photodissociation measurements. Apart from stoichiometries different from those of their nickel oxide macroscopic counterparts, we found a tendency to form compact Ni subclusters, with reentrance of low-coordinated structures close to the equiatomic Ni-O concentration, taking the form of alternating Ni-O rings in the smaller sizes, in good qualitative agreement with Ion Mobility Mass Spectrometry measurements. This structural pattern is manifested in a drop of the total spin magnetic moment close to the equiatomic concentration due to the formation of antiparallel magnetic couplings. Although antiparallel couplings are found to a more or less extent in most clusters, especially in the oxygen rich phase, we identified certain clusters of special interest in the context of magnetic grains because of their large total magnetic moment and abundance. There are even some nickel oxide clusters with a higher total moment than their pure Ni counterparts, due to parallel magnetic couplings and the contribution of the oxygen atoms to the total moment.

  1. Flooding and fragment size interact to determine survival and regrowth after fragmentation in two stoloniferous Trifolium species

    PubMed Central

    Huber, Heidrun; Visser, Eric J. W.; Clements, Gijs; Peters, Janny L.

    2014-01-01

    Clonal plants, which reproduce by means of stolons and rhizomes, are common in frequently flooded habitats. Resilience to disturbance is an important trait enabling plants to survive in such highly disturbed habitats. Resource storage is thought to enable clonal plants to resume growth after clonal fragmentation caused by disturbance. Here we investigated if submergence prior to disturbance reduces survival and regrowth of clonal fragments and whether or not genotypes originating from highly disturbed riverine habitats are more resistant to mechanical disturbance than genotypes from less disturbed coastal dune slack habitats. We further tested if variation in survival and regrowth was affected by internode size. Clones from contrasting habitats of two closely related Trifolium species were first genotypically characterized by amplification fragment length polymorphism and then subjected to soil flooding and subsequent clonal fragmentation. These species differ with respect to their abundance in riverine and dune slack habitats, with Trifolium repens mainly occurring in riverine grasslands and Trifolium fragiferum in coastal dune slacks. Soil flooding decreased survival and regrowth by up to 80 %. Plants originating from riverine grasslands were less negatively affected by fragmentation than plants from dune slack habitats. Surprisingly, ramets did not always benefit from being attached to a larger internode, as internode size was often negatively correlated with survival after fragmentation. Regrowth, on the other hand, was generally positively correlated with internode size. These unexpected results indicate that there may be contrasting selection pressures on internode size in stoloniferous species growing in severely disturbed habitats. PMID:24887003

  2. Energetics and Dynamics of Fragmentation of Protonated Leucine Enkephalin from Time- and Energy-Resolved Surface-Induced Dissociation Studies

    SciTech Connect

    Laskin, Julia

    2006-07-01

    Dissociation of singly protonated leucine enkephalin (YGGFL) was studied using surface-induced dissociation in a Fourier transform ion cyclotron resonance mass spectrometer specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of seven primary dissociation channels were deduced from modeling the time- and energy-resolved fragmentation efficiency curves for different fragment ions using an RRKM-based approach developed at the Environmental Molecular Sciences Laboratory (EMSL).

  3. Doubly charged trimeric cluster ions: effective in mutual chiral recognition of tadalafil and three proton pump inhibitors.

    PubMed

    Wang, Lu; Chai, Yunfeng; Zhu, Wenquan; Pan, Yuanjiang; Sun, Cuirong; Zeng, Su

    2017-02-27

    Mutual chiral recognition of four stereoisomers of tadalafil and three pairs of enantiomers of proton pump inhibitors (PPIs) including pantoprazole, lansoprazole, and omeprazole, as well as quantitative analysis of enantiomeric excess is achieved on the basis of the competitive fragmentation of doubly charged trimeric Ni(II) cluster ions. Compared with a singly charged trimeric cluster ion, a doubly charged trimeric cluster ion was proved efficient in the recognition of chiral drugs with one or multiple chiral centers, due to its rich fragmentation ions. Upon collision-induced dissociation (CID), the cluster ion [Ni(II)(PPIs)(tadalafil)2](2+) yielded two diagnostic ions [tadalafil + H](+) and [tadalafil - benzo[d][1,3]dixoloe](+) through electrospray ionization quadrupole time-of-flight mass spectrometry. The abundance ratio of the two fragment ions relied mainly on the configuration of PPIs and tadalafil, and therefore the chiral selectivity (Rchiral) of one enantiomer relative to the others is different. The chiral recognition of all four stereoisomers of tadalafil was achieved by using S configuration PPIs as references, and S-omeprazole showed the best selectivity. The Rchiral values for R,R/S,S, R,S/S,R, R,R/R,S and R,R/S,R-tadalafils were 1.47, 1.17, 2.37, and 2.10, respectively. In a reciprocal process, the Rchiral was 1.36 and 1.31 for R/S-pantoprazole and R/S-lansoprazole, respectively, by using R,R-tadalafil as a reference. Although omeprazole is a racemic drug, it can also be discriminated with S-omeprazole. Calibration curves were constructed with favorable correlation coefficients (r(2) > 0.991) by relating the ln(Rchiral) values to the isomeric composition in a mixture. The sensitivity of the methodology allows mixtures to be analyzed for the enantiomeric excess (ee) by recording the ratios of fragment ion abundances in a mass spectrum. The sensitivity of the methodology allowed the determination of enantiomeric impurities of 5% molar composition in

  4. 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

  5. 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.

  6. Construction of confidence regions for isotopic abundance patterns in LC/MS data sets for rigorous determination of molecular formulas.

    PubMed

    Ipsen, Andreas; Want, Elizabeth J; Ebbels, Timothy M D

    2010-09-01

    It has long been recognized that estimates of isotopic abundance patterns may be instrumental in identifying the many unknown compounds encountered when conducting untargeted metabolic profiling using liquid chromatography/mass spectrometry. While numerous methods have been developed for assigning heuristic scores to rank the degree of fit of the observed abundance patterns with theoretical ones, little work has been done to quantify the errors that are associated with the measurements made. Thus, it is generally not possible to determine, in a statistically meaningful manner, whether a given chemical formula would likely be capable of producing the observed data. In this paper, we present a method for constructing confidence regions for the isotopic abundance patterns based on the fundamental distribution of the ion arrivals. Moreover, we develop a method for doing so that makes use of the information pooled together from the measurements obtained across an entire chromatographic peak, as well as from any adducts, dimers, and fragments observed in the mass spectra. This greatly increases the statistical power, thus enabling the analyst to rule out a potentially much larger number of candidate formulas while explicitly guarding against false positives. In practice, small departures from the model assumptions are possible due to detector saturation and interferences between adjacent isotopologues. While these factors form impediments to statistical rigor, they can to a large extent be overcome by restricting the analysis to moderate ion counts and by applying robust statistical methods. Using real metabolic data, we demonstrate that the method is capable of reducing the number of candidate formulas by a substantial amount, even when no bromine or chlorine atoms are present. We argue that further developments in our ability to characterize the data mathematically could enable much more powerful statistical analyses.

  7. Driven fragmentation of granular gases.

    PubMed

    Cruz Hidalgo, Raúl; Pagonabarraga, Ignacio

    2008-06-01

    The dynamics of homogeneously heated granular gases which fragment due to particle collisions is analyzed. We introduce a kinetic model which accounts for correlations induced at the grain collisions and analyze both the kinetics and relevant distribution functions these systems develop. The work combines analytical and numerical studies based on direct simulation Monte Carlo calculations. A broad family of fragmentation probabilities is considered, and its implications for the system kinetics are discussed. We show that generically these driven materials evolve asymptotically into a dynamical scaling regime. If the fragmentation probability tends to a constant, the grain number diverges at a finite time, leading to a shattering singularity. If the fragmentation probability vanishes, then the number of grains grows monotonously as a power law. We consider different homogeneous thermostats and show that the kinetics of these systems depends weakly on both the grain inelasticity and driving. We observe that fragmentation plays a relevant role in the shape of the velocity distribution of the particles. When the fragmentation is driven by local stochastic events, the long velocity tail is essentially exponential independently of the heating frequency and the breaking rule. However, for a Lowe-Andersen thermostat, numerical evidence strongly supports the conjecture that the scaled velocity distribution follows a generalized exponential behavior f(c) approximately exp(-cn) , with n approximately 1.2 , regarding less the fragmentation mechanisms.

  8. A fragmentation study of kaempferol using electrospray quadrupole time-of-flight mass spectrometry at high mass resolution

    NASA Astrophysics Data System (ADS)

    March, Raymond E.; Miao, Xiu-Sheng

    2004-02-01

    A mass spectrometric method based on the combined use of electrospray ionization, collision-induced dissociation and tandem mass spectrometry at high mass resolution has been applied to an investigation of the structural characterization of protonated and deprotonated kaempferol (3,5,7,4'-tetrahydroxyflavone). Low-energy product ion mass spectra of [M+H]+ ions showed simple fragmentations of the C ring that permitted characterization of the substituents in the A and B rings. In addition, four rearrangement reactions accompanied by losses of C2H2O, CHO[radical sign], CO, and H2O were observed. Low-energy product ion mass spectra of [M-H]- ions showed only four rearrangement reactions accompanied by losses of OH[radical sign], CO, CH2O, and C2H2O. The use of elevated cone voltages permitted observation of product ion mass spectra of selected primary and secondary fragment ions so that each fragment ion reported was observed as a direct product of its immediate precursor ion. Product ion mass spectra examined at high mass resolution allowed unambiguous determination of the elemental composition of fragment ions and resolution of two pairs of isobars. Fragmentation mechanisms and ion structures have been proposed.

  9. Theoretical model of HZE particle fragmentation by hydrogen targets

    NASA Technical Reports Server (NTRS)

    Townsend, L.W.; Cucinotta, F. A; Bagga, R.; Tripathi, R. K.

    1996-01-01

    The fragmenting of high energy, heavy ions (HZE particles) by hydrogen targets is an important, physical process in several areas of space radiation research. In this work quantum mechanical optical model methods for estimating cross sections for HZE particle fragmentation by hydrogen targets are presented. The cross sections are calculated using a modified abrasion-ablation collision formalism adapted from a nucleus-nucleus collision model. Elemental and isotopic production cross sections are estimated and compared with reported measurements for the breakup of neon, sulphur, and iron, nuclei at incident energies between 400 and 910 Mev/nucleon. Good agreement between theory and experiment is obtained.

  10. Fragmentation of light nuclei by intermediate energy photons

    NASA Astrophysics Data System (ADS)

    Turinge, A. A.; Lapik, A. M.; Mushkarenkov, A. N.; Nedorezov, V. G.; Rudnev, N. V.

    2017-01-01

    New data on the fragmentation of carbon nuclei by photons with energies from 800 to 1500 MeV, obtained in the collaboration GRAAL, are presented. These data include the yields of heavier fragments than nucleons. Comparison of new results with literature data, obtained with real and virtual photons in reactions with electrons and relativistic ions (Coulomb dissociation) is done using a general approach in frame of the Weizsäcker-Williams model. Possible reasons for the observed differences between them are discussed.

  11. Computational and Experimental Determination of Fragmentation for Naturally Fragmenting Warheads

    DTIC Science & Technology

    1981-05-01

    Table Page I Chemical analysis of Armco iron and HF-I steel ....................... 3 2 Summary of tensile-pull measurements for transverse-direction...ntered) REPORT DOCUMENTATION PAGE - E-EFORE COMTLETING FORM I REPORT NUMBER 2 GOVT ACCESSION NO. 3 RECIPIENT’S CATALOG NUMBERNSWC TR 80-238 4 TITLE (and...Sulbtitle) S TYPE OF REPORT & PERIOD COVERED COMPUTATIONAL AND EXPERIMENTAL 1 Final DETERMINATION OF FRAGMENTATION FOR NATURALLY FRAGMENTING WARHEADS

  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. Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization

    NASA Astrophysics Data System (ADS)

    Neustetter, M.; Jabbour Al Maalouf, E.; Limão-Vieira, P.; Denifl, S.

    2016-08-01

    Electron ionization of neat tungsten hexacarbonyl (W(CO)6) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO)6 clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO)n+ (0 ≤ n ≤ 6) and W2(CO)n+ (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO)n+ (0 ≤ n ≤ 3) and W2C(CO)n+ (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.

  14. Broad-Spectrum Drug Screening Using Liquid Chromatography-Hybrid Triple-Quadrupole Linear Ion Trap Mass Spectrometry.

    PubMed

    Stone, Judy

    2016-01-01

    Urine is processed with a simple C18 solid-phase extraction (SPE) and reconstituted in mobile phase. The liquid chromatography system (LC) injects 10 μL of extracted sample onto a reverse-phase LC column for gradient analysis with ammonium formate/acetonitrile mobile phases. Drugs in the column eluent become charged in the ion source using positive electrospray ionization (ESI). Pseudomolecular ions (M + H) are analyzed by a hybrid triple-quadrupole linear ion trap (QqQ and QqLIT) mass spectrometer using an SRM-IDA-EPI acquisition. An initial 125 compound selected ion monitoring (SRM) survey scan (triple quadrupole or QqQ mode) is processed by the information-dependent acquisition (IDA) algorithm. The IDA algorithm selects SRM signals from the survey scan with a peak height above the threshold (the three most abundant SRM signals above 1000 cps) to define precursor ions for subsequent dependent scanning. In the dependent QqLIT scan(s), selected precursor ion(s) are passed through the first quadrupole (Q1), fragmented with three different collision energies in the collision cell (Q2 or q), and product ions are collected in the third quadrupole (Q3), now operating as a linear ion trap (LIT). The ions are scanned out of the LIT in a mass dependent manner to produce a full-scan product ion spectrum (m/z 50-700) defined as an Enhanced (meaning acquired in LIT mode) Product Ion (EPI) spectrum (Mueller et al., Rapid Commun Mass Spectrom 19:1332-1338, 2005). Each EPI spectrum is linked to its precursor ion and to the associated SRM peak from the survey scan. EPI spectra are automatically searched against a 125 drug library of reference EPI spectra for identification. When the duty cycle is complete (one survey scan of 125 SRMs plus 0-3 dependent IDA-EPI scans) the mass spectrometer begins another survey scan of the 125 SRMs.

  15. Depleted Uranium Test Range Fragment Reclamation

    DTIC Science & Technology

    1982-07-01

    fragment drying was necessary in order to obtain adequate vacuum levels in the VIR furnaces . e. Vacuujm Induction Remelting Fragments and Casting...Acid Pickle and Water Rinse .... ........ 2 d. Drying the Fragments .... ............... 2 e. Vacuum Induction Remelting Fragments and Casting...feasibility of reclaiming test range fragments by vacuum induction remelting (VIR). The technical direction of Phase 11 was highly dependent upon the

  16. Fragmentation of drying paint layers

    NASA Astrophysics Data System (ADS)

    Bakos, Katinka; Dombi, András; Járai-Szabó, Ferenc; Néda, Zoltán

    2013-11-01

    Fragmentation of thin layers of drying granular materials on a frictional surface are studied both by experiments and computer simulations. Besides a qualitative description of the fragmentation phenomenon, the dependence of the average fragment size as a function of the layer thickness is thoroughly investigated. Experiments are done using a special nail polish, which forms characteristic crack structures during drying. In order to control the layer thickness, we diluted the nail polish in acetone and evaporated in a controlled manner different volumes of this solution on glass surfaces. During the evaporation process we managed to get an instable paint layer, which formed cracks as it dried out. In order to understand the obtained structures a previously developed spring-block model was implemented in a three-dimensional version. The experimental and simulation results proved to be in excellent qualitative and quantitative agreement. An earlier suggested scaling relation between the average fragment size and the layer thickness is reconfirmed.

  17. Gas-phase Structure and Fragmentation Pathways of Singly Protonated Peptides with N-terminal Arginine</